*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<< *>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<< *from *>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<< *>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<< *>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<< *>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<< *and * \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File /////// * \\\\\\\\\\\\\\\\\\ Developmental ///////////////////////// * Alexander D. MacKerell Jr. * August 1999 * All comments to ADM jr. email: alex,mmiris.ab.umd.edu * telephone: 410-706-7442 * 27 1 ! ! references ! !PROTEINS ! !MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; !Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; !Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, !C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, !W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; !Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom !empirical potential for molecular modeling and dynamics Studies of !proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. ! !PHOSPHOTYROSINE ! !Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C. !Structural Characterization of the Phosphotyrosine Binding Region of a !High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics !Simulation and Chemical Shift Calculations. Journal of the American !Chemical Society, 1996, 118: 11265-11277. ! !IONS (see lipid and nucleic acid topology and parameter files for !additional ions ! !ZINC ! !Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and !Solution: A Simple but Accurate Nonbonded Representation, PROTEINS: !Structure, Function, and Genetics 23:12-31 (1995) ! !references ! !LIPIDS ! !Feller, S. and MacKerell, Jr., A.D. manuscript in preparation ! !and ! !Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M. !Empirical Potential Energy Function for Phospholipids: Criteria for !Parameter Optimization and Applications, in "Biological Membranes: A !Molecular Perspective from Computation and Experiment," K.M. Merz and !B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81. ! !new ALKANES ! !Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach !for the Optimization of Lennard-Jones Parameters. Journal of !Computational Chemistry, 1998, 19: 334-338. ! !ALKENES ! !Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D., !Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: !Parameterization and Comparison with Diffraction Studies. Biophysical !Journal, 73:2269-2279, 1997. ! !new PHOSPHATE ! !MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics !of Dimethylphosphate and its Implications For DNA Structure, Journal !de Chimie Physique, 1997, 94: 1436-1447. ! !IONS ! !all ions from Roux and coworkers ! !Sodium ! !Beglov, D. and Roux, B., Finite Representation of an Infinite !Bulk System: Solvent Boundary Potential for Computer Simulations, !Journal of Chemical Physics, 1994, 100: 9050-9063 ! !NUCLEIC ACIDS ! !Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and !Condensed Phase Macromolecular Target Data. Journal of Computational !Chemistry, 2000, 21:86-104. ! !and ! !MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for !Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA !and RNA in Solution. Journal of Computational !Chemistry, 2000, 21:105-120. ! !NAD(P)+, NAD(P)H and PPI ! !Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A !Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate !Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: !221-239. ! MASS 1 H 1.00800 H ! polar H MASS 2 HC 1.00800 H ! N-ter H MASS 3 HA 1.00800 H ! nonpolar H MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN MASS 5 HP 1.00800 H ! aromatic H MASS 6 HB 1.00800 H ! backbone H MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2 MASS 8 HR2 1.00800 H ! (+) his HE1 MASS 9 HR3 1.00800 H ! neutral his HG, HD2 MASS 10 HS 1.00800 H ! thiol hydrogen MASS 11 HE1 1.00800 H ! for alkene; RHC=CR MASS 12 HE2 1.00800 H ! for alkene; H2C=CR MASS 20 C 12.01100 C ! carbonyl C, peptide backbone MASS 21 CA 12.01100 C ! aromatic C MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2 MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3 MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons MASS 26 CPH2 12.01100 C ! his CE1 carbon MASS 27 CPT 12.01100 C ! trp C between rings MASS 28 CY 12.01100 C ! TRP C in pyrrole ring MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA) MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG) MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD) MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2 MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1 MASS 34 CPA 12.01100 C ! heme alpha-C MASS 35 CPB 12.01100 C ! heme beta-C MASS 36 CPM 12.01100 C ! heme meso-C MASS 37 CM 12.01100 C ! heme CO carbon MASS 38 CS 12.01100 C ! thiolate carbon MASS 39 CE1 12.01100 C ! for alkene; RHC=CR MASS 40 CE2 12.01100 C ! for alkene; H2C=CR MASS 50 N 14.00700 N ! proline N MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen MASS 53 NR3 14.00700 N ! charged his ring nitrogen MASS 54 NH1 14.00700 N ! peptide nitrogen MASS 55 NH2 14.00700 N ! amide nitrogen MASS 56 NH3 14.00700 N ! ammonium nitrogen MASS 57 NC2 14.00700 N ! guanidinium nitroogen MASS 58 NY 14.00700 N ! TRP N in pyrrole ring MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal) MASS 60 NPH 14.00700 N ! heme pyrrole N MASS 70 O 15.99900 O ! carbonyl oxygen MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid MASS 72 OC 15.99900 O ! carboxylate oxygen MASS 73 OH1 15.99900 O ! hydroxyl oxygen MASS 74 OS 15.99940 O ! ester oxygen MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN MASS 76 OM 15.99900 O ! heme CO/O2 oxygen MASS 81 S 32.06000 S ! sulphur MASS 82 SM 32.06000 S ! sulfur C-S-S-C type MASS 83 SS 32.06000 S ! thiolate sulfur MASS 85 HE 4.00260 HE ! helium MASS 86 NE 20.17970 NE ! neon MASS 90 CAL 40.08000 CA ! calcium 2+ MASS 91 ZN 65.37000 ZN ! zinc (II) cation MASS 92 FE 55.84700 Fe ! heme iron 56 MASS 99 DUM 0.00000 H ! dummy atom !lipids section MASS 101 HL 1.008000 H ! polar H (equivalent to protein H) MASS 102 HCL 1.008000 H ! charged H for PE (equivalent to protein HC) !MASS 3 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 104 HOL 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 105 HAL1 1.008000 H ! alphatic proton MASS 106 HAL2 1.008000 H ! alphatic proton MASS 107 HAL3 1.008000 H ! alphatic proton MASS 108 HEL1 1.008000 H ! for alkene; RHC=CR MASS 109 HEL2 1.008000 H ! for alkene; H2C=CR MASS 120 CL 12.011000 C ! carbonyl C (acetic acid/methyl acetate) MASS 121 CTL1 12.011000 C ! sp3 carbon with 1 H (-CH1-) MASS 122 CTL2 12.011000 C ! carbon of methylene group (-CH2-) MASS 123 CTL3 12.011000 C ! carbon of methyl group (-CH3) MASS 124 CTL5 12.011000 C ! carbon of methyl group (-CH3) for tetramethylammonium MASS 125 CEL1 12.011000 C ! for alkene; RHC=CR MASS 126 CEL2 12.011000 C ! for alkene; H2C=CR MASS 140 NTL 14.007000 N ! ammonium nitrogen MASS 141 NH3L 14.007000 N ! nitrogen phosphatidylethanolamine MASS 160 OBL 15.999400 O ! acetic acid carboxyl oxygen (e. to protein OB) MASS 161 OCL 15.999400 O ! acetate oxygen !MASS 162 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 163 OSL 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 164 O2L 15.999400 O ! Nucleic acid =O in phosphate or sulfate MASS 165 OHL 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 180 PL 30.974000 P ! phosphorus MASS 185 SL 32.060000 S ! Sulfate sulfur MASS 190 CLA 35.450000 CL ! CHLORIDE Anion MASS 191 SOD 22.989770 NA ! Sodium Ion MASS 192 MG 24.305000 MG ! Magnesium Ion MASS 193 POT 39.102000 K ! Potassium Ion !MASS 199 DUM 0.000000 H ! dummy atom !nucleic acid section MASS 202 HN1 1.008000 H ! Nucleic acid amine proton MASS 203 HN2 1.008000 H ! Nucleic acid ring nitrogen proton MASS 204 HN3 1.008000 H ! Nucleic acid aromatic carbon proton MASS 205 HN3B 1.008000 H ! NAD+ aromatic hydrogen MASS 206 HN3C 1.008000 H ! Standard aromatic hydrogen (as in benzene) MASS 207 HNP 1.008000 H ! pure aromatic H MASS 208 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 209 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton MASS 210 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton MASS 211 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) MASS 212 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds MASS 213 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds MASS 214 HNE1 1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha) MASS 215 HNE2 1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha) MASS 220 CN1 12.011000 C ! Nucleic acid carbonyl carbon MASS 221 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon MASS 222 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2) MASS 223 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide MASS 224 CN3 12.011000 C ! Nucleic acid aromatic carbon MASS 225 CN3A 12.011000 C ! NAD+ aromatic carbon MASS 226 CN3B 12.011000 C ! NAD+ aromatic carbon MASS 227 CN3C 12.011000 C ! NADH aromatic carbon MASS 228 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC MASS 229 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5 MASS 230 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 MASS 231 CN5 12.011000 C ! Nucleic acid purine C4 and C5 MASS 232 CN5G 12.011000 C ! Nucleic acid guanine C5 MASS 233 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) MASS 234 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1' MASS 235 CN7C 12.011000 C ! C2' in arabinose MASS 236 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives MASS 237 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 238 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 239 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) MASS 240 CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha) MASS 241 CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha) MASS 242 CNA 12.011000 C ! pure aromatic carbon MASS 243 CNA2 12.011000 C ! pure aromatic carbon bound to F MASS 250 NN1 14.007000 N ! Nucleic acid amide nitrogen MASS 251 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha) MASS 252 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen MASS 253 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE MASS 254 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha) MASS 255 NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3 MASS 256 NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1 MASS 257 NN3 14.007000 N ! Nucleic acid unprotonated ring nitrogen MASS 258 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3 MASS 259 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 MASS 260 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3 MASS 261 NN4 14.007000 N ! Nucleic acid purine N7 MASS 262 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen MASS 263 NN6 14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3) !MASS 70 OT 15.999400 O ! TIPS3P WATER OXYGEN MASS 271 ON1 15.999400 O ! Nucleic acid carbonyl oxygen MASS 272 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 MASS 273 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 274 ON3 15.999400 O ! Nucleic acid =O in phosphate MASS 275 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 276 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen MASS 277 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen MASS 278 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen MASS 279 ON2b 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2) MASS 280 FN1 18.998400 F ! Fluorine for sugar derivatives (NF) MASS 281 FNA 18.998400 F ! Aromatic fluorine MASS 282 P 30.974000 P ! phosphorus MASS 283 P2 30.974000 P ! pyrophosphate phosphorus MASS 293 CES 132.900000 CS ! Cesium Ion !MASS 99 DUM 0.001 H ! dummy atom !MASS 102 CPH1 12.011000 C ! For imidazole model compound (NF) !MASS 103 CPH2 12.011000 C ! For imidazole model compound (NF) !MASS 104 HR3 1.008000 H ! For imidazole model compound (NF) !MASS 105 HR1 1.008000 H ! For imidazole model compound (NF) !MASS 106 NR1 14.007000 H ! For nitrogen in imidazol (NF) !MASS 107 NR2 14.007000 H ! For nitrogen in imidazol (NF) DECL -CA DECL -C DECL -O DECL +N DECL +HN DECL +CA DEFA FIRS NTER LAST CTER AUTO ANGLES DIHE RESI ALA 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB2 ATOM CB CT3 -0.27 ! | \ ATOM HB1 HA 0.09 ! | HB3 ATOM HB2 HA 0.09 ! O=C ATOM HB3 HA 0.09 ! | GROUP ! ATOM C C 0.51 ATOM O O -0.51 BOND CB CA N HN N CA BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996 IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390 IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558 IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297 IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613 IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461 IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840 IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109 IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119 IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114 RESI ARG 1.00 GROUP ATOM N NH1 -0.47 ! | HH11 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12 ATOM HA HB 0.09 ! | | | | | //(+) GROUP ! HA-CA--CB--CG--CD--NE--CZ ATOM CB CT2 -0.18 ! | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22 ATOM HB2 HA 0.09 ! O=C | GROUP ! | HH21 ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 0.20 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM NE NC2 -0.70 ATOM HE HC 0.44 ATOM CZ C 0.64 ATOM NH1 NC2 -0.80 ATOM HH11 HC 0.46 ATOM HH12 HC 0.46 ATOM NH2 NC2 -0.80 ATOM HH21 HC 0.46 ATOM HH22 HC 0.46 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE CD CZ NE BOND NH2 CZ N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2 BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22 DOUBLE O C CZ NH1 IMPR N -C CA HN C CA +N O IMPR CZ NH1 NH2 NE DONOR HN N DONOR HE NE DONOR HH11 NH1 DONOR HH12 NH1 DONOR HH21 NH2 DONOR HH22 NH2 ACCEPTOR O C IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973 IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227 IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511 IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271 IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565 IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552 IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836 IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475 IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163 IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124 IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384 IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121 IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143 IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034 IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143 IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150 IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401 IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065 IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311 IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903 IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023 IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292 IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899 IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914 RESI ASN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1) ATOM HA HB 0.09 ! | | || / GROUP ! HA-CA--CB--CG--ND2 ATOM CB CT2 -0.18 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CC 0.55 ATOM OD1 O -0.55 GROUP ATOM ND2 NH2 -0.62 ATOM HD21 H 0.32 ATOM HD22 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22 DOUBLE C O CG OD1 IMPR N -C CA HN C CA +N O IMPR CG ND2 CB OD1 CG CB ND2 OD1 IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21 DONOR HN N DONOR HD21 ND2 DONOR HD22 ND2 ACCEPTOR OD1 CG ACCEPTOR O C IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992 IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245 IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467 IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282 IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528 IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627 IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848 IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319 IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120 IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091 IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323 IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521 IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963 IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951 RESI ASP -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 OD1 ATOM HA HB 0.09 ! | | // GROUP ! HA-CA--CB--CG ATOM CB CT2 -0.28 ! | | \ ATOM HB1 HA 0.09 ! | HB2 OD2(-) ATOM HB2 HA 0.09 ! O=C ATOM CG CC 0.62 ! | ATOM OD1 OC -0.76 ATOM OD2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB OD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 DOUBLE O C CG OD1 IMPR N -C CA HN C CA +N O !IMPR OD1 CB OD2 CG IMPR CG CB OD2 OD1 DONOR HN N ACCEPTOR OD1 CG ACCEPTOR OD2 CG ACCEPTOR O C IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966 IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315 IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478 IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330 IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484 IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619 IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841 IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218 IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086 IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080 IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565 IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541 RESI CYS 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--SG ATOM CB CT2 -0.11 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM SG S -0.23 ! | ATOM HG1 HS 0.16 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA SG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 SG HG1 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N DONOR HG1 SG ACCEPTOR O C IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982 IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202 IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498 IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306 IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548 IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584 IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837 IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359 IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134 IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124 IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341 RESI GLN 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1) ATOM HA HB 0.09 ! | | | || / GROUP ! HA-CA--CB--CG--CD--NE2 ATOM CB CT2 -0.18 ! | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CC 0.55 ATOM OE1 O -0.55 GROUP ATOM NE2 NH2 -0.62 ATOM HE21 H 0.32 ATOM HE22 H 0.30 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG NE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 NE2 HE21 NE2 HE22 DOUBLE O C CD OE1 IMPR N -C CA HN C CA +N O IMPR CD NE2 CG OE1 CD CG NE2 OE1 IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21 DONOR HN N DONOR HE21 NE2 DONOR HE22 NE2 ACCEPTOR OE1 CD ACCEPTOR O C IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984 IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180 IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463 IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291 IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461 IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538 IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832 IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534 IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147 IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140 IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320 IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112 IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094 IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294 IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530 IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959 IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943 RESI GLU -1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 OE1 ATOM HA HB 0.09 ! | | | // GROUP ! HA-CA--CB--CG--CD ATOM CB CT2 -0.18 ! | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-) ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.28 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 ATOM CD CC 0.62 ATOM OE1 OC -0.76 ATOM OE2 OC -0.76 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG OE2 CD BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 DOUBLE O C CD OE1 IMPR N -C CA HN C CA +N O !IMPR OE1 CG OE2 CD IMPR CD CG OE2 OE1 DONOR HN N ACCEPTOR OE1 CD ACCEPTOR OE2 CD ACCEPTOR O C IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961 IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216 IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501 IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306 IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530 IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516 IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828 IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557 IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145 IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131 IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307 IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053 IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081 IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590 IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532 RESI GLY 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! N-H ATOM CA CT2 -0.02 ! | ATOM HA1 HB 0.09 ! | ATOM HA2 HB 0.09 ! HA1-CA-HA2 GROUP ! | ATOM C C 0.51 ! | ATOM O O -0.51 ! C=O ! | BOND N HN N CA C CA BOND C +N CA HA1 CA HA2 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992 IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971 IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479 IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289 IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560 IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814 IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817 PATCHING FIRS GLYP RESI HSD 0.00 ! neutral HIS, proton on ND1 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB CT2 -0.09 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | ATOM ND1 NR1 -0.36 ! | HD2 ATOM HD1 H 0.32 ATOM CG CPH1 -0.05 GROUP ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 ATOM NE2 NR2 -0.70 ATOM CD2 CPH1 0.22 ATOM HD2 HR3 0.10 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1 DOUBLE O C CG CD2 CE1 NE2 IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HD1 ND1 ACCEPTOR NE2 ACCEPTOR O C IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988 IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166 IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509 IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273 IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545 IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519 IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830 IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041 IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118 IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121 IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783 IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597 IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549 IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817 IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932 IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005 IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834 RESI HSE 0.00 ! neutral His, proton on NE2 GROUP ATOM N NH1 -0.47 ! | HE1 ATOM HN H 0.31 ! HN-N __ / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / | GROUP ! HA-CA--CB--CG | ATOM CB CT2 -0.08 ! | | \\ | ATOM HB1 HA 0.09 ! | HB2 CD2--NE2 ATOM HB2 HA 0.09 ! O=C | \ ATOM ND1 NR2 -0.70 ! | HD2 HE2 ATOM CG CPH1 0.22 ATOM CE1 CPH2 0.25 ATOM HE1 HR1 0.13 GROUP ATOM NE2 NR1 -0.36 ATOM HE2 H 0.32 ATOM CD2 CPH1 -0.05 ATOM HD2 HR3 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG BOND NE2 CD2 N HN N CA BOND C CA C +N NE2 CE1 CA HA CB HB1 BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1 DOUBLE O C CD2 CG CE1 ND1 IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1 IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HE2 NE2 ACCEPTOR ND1 ACCEPTOR O C IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991 IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166 IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446 IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290 IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505 IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578 IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833 IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109 IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114 IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101 IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859 IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596 IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170 IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782 IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929 IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996 IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809 RESI HSP 1.00 ! Protonated His GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 ND1--CE1 ATOM HA HB 0.09 ! | | / || GROUP ! HA-CA--CB--CG || ATOM CB CT2 -0.05 ! | | \\ || ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+) ATOM HB2 HA 0.09 ! O=C | \ ATOM CD2 CPH1 0.19 ! | HD2 HE2 ATOM HD2 HR1 0.13 ATOM CG CPH1 0.19 GROUP ATOM NE2 NR3 -0.51 ATOM HE2 H 0.44 ATOM ND1 NR3 -0.51 ATOM HD1 H 0.44 ATOM CE1 CPH2 0.32 ATOM HE1 HR2 0.18 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB ND1 CG CE1 ND1 BOND NE2 CD2 N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1 DOUBLE O C CD2 CG NE2 CE1 IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1 IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HD1 ND1 DONOR HE2 NE2 ACCEPTOR O C IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041 IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225 IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464 IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284 IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521 IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533 IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832 IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168 IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116 IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132 IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718 IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549 IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262 IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727 IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799 IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020 IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018 IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867 RESI ILE 0.00 GROUP ATOM N NH1 -0.47 ! | HG21 HG22 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | CG2--HG23 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB HD1 ATOM CB CT1 -0.09 ! | \ / ATOM HB HA 0.09 ! | CG1--CD--HD2 GROUP ! O=C / \ \ ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM CG1 CT2 -0.18 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 GROUP ATOM CD CT3 -0.27 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 ATOM HD3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB CD CG1 BOND N HN N CA C CA C +N BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21 BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978 IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190 IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465 IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300 IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467 IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681 IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826 IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498 IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195 IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452 IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100 IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102 IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105 IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381 IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130 IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141 IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115 IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113 IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103 RESI LEU 0.00 GROUP ATOM N NH1 -0.47 ! | HD11 HD12 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | HB1 CD1--HD13 ATOM HA HB 0.09 ! | | / GROUP ! HA-CA--CB--CG-HG ATOM CB CT2 -0.18 ! | | \ ATOM HB1 HA 0.09 ! | HB2 CD2--HD23 ATOM HB2 HA 0.09 ! O=C | \ GROUP ! | HD21 HD22 ATOM CG CT1 -0.09 ATOM HG HA 0.09 GROUP ATOM CD1 CT3 -0.27 ATOM HD11 HA 0.09 ATOM HD12 HA 0.09 ATOM HD13 HA 0.09 GROUP ATOM CD2 CT3 -0.27 ATOM HD21 HA 0.09 ATOM HD22 HA 0.09 ATOM HD23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD1 CG CD2 CG BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11 BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979 IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184 IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463 IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299 IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467 IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543 IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824 IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472 IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145 IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126 IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361 IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360 IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168 !IC CD1 CB *CG HG 1.5361 110.4800 116.6300 108.6800 1.1168 old IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111 IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112 IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108 IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116 IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086 IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115 RESI LYS 1.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1 ATOM HA HB 0.09 ! | | | | | / GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2 ATOM CB CT2 -0.18 ! | | | | | \ ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM CD CT2 -0.18 ATOM HD1 HA 0.09 ATOM HD2 HA 0.09 GROUP ATOM CE CT2 0.21 ATOM HE1 HA 0.05 ATOM HE2 HA 0.05 ATOM NZ NH3 -0.30 ATOM HZ1 HC 0.33 ATOM HZ2 HC 0.33 ATOM HZ3 HC 0.33 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD CG CE CD NZ CE BOND N HN N CA C CA BOND C +N CA HA CB HB1 CB HB2 CG HG1 BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2 DOUBLE O C BOND NZ HZ1 NZ HZ2 NZ HZ3 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HZ1 NZ DONOR HZ2 NZ DONOR HZ3 NZ ACCEPTOR O C IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988 IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187 IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478 IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277 IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487 IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568 IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833 IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435 IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146 IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131 IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397 IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138 IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143 IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350 IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141 IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146 IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604 IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128 IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123 IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404 IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402 IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401 RESI MET 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 HG1 HE1 ATOM HA HB 0.09 ! | | | | GROUP ! HA-CA--CB--CG--SD--CE--HE3 ATOM CB CT2 -0.18 ! | | | | ATOM HB1 HA 0.09 ! | HB2 HG2 HE2 ATOM HB2 HA 0.09 ! O=C GROUP ! | ATOM CG CT2 -0.14 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 ATOM SD S -0.09 ATOM CE CT3 -0.22 ATOM HE1 HA 0.09 ATOM HE2 HA 0.09 ATOM HE3 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB SD CG CE SD BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2 BOND CE HE1 CE HE2 CE HE3 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978 IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195 IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471 IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288 IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471 IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546 IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832 IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460 IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153 IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129 IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219 IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106 IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119 IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206 IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111 IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115 IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112 RESI PHE 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | | ATOM CA CT1 0.07 ! | HB1 CD1--CE1 ATOM HA HB 0.09 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--HZ ATOM CB CT2 -0.18 ! | | \ __ / ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA -0.115 ATOM HZ HP 0.115 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 N HN BOND N CA C CA C +N CA HA BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1 DOUBLE O C CD1 CG CZ CE1 CE2 CD2 BOND CE2 HE2 CZ HZ IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987 IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229 IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483 IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287 IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523 IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594 IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832 IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109 IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119 IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113 IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059 IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062 IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006 IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814 IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002 IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811 IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004 IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808 IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811 IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807 RESI PRO 0.00 GROUP ! HD1 HD2 ATOM N N -0.29 ! | \ / ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02 ATOM HD1 HA 0.09 ! | \ / ATOM HD2 HA 0.09 ! | CG ATOM CA CP1 0.02 ! | / \ ATOM HA HB 0.09 ! HA-CA--CB HG2 GROUP ! | / \ ATOM CB CP2 -0.18 ! | HB1 HB2 ATOM HB1 HA 0.09 ! O=C ATOM HB2 HA 0.09 ! | GROUP ATOM CG CP2 -0.18 ATOM HG1 HA 0.09 ATOM HG2 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND C CA C +N BOND N CA CA CB CB CG CG CD N CD BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB DOUBLE O C IMPR N -C CA CD IMPR C CA +N O ACCEPTOR O C IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624 IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399 IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569 IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316 IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517 IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399 IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837 IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322 IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317 IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131 IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088 IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077 IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143 IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137 IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144 PATCHING FIRS PROP RESI SER 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | HB1 ATOM HA HB 0.09 ! | | GROUP ! HA-CA--CB--OG ATOM CB CT2 0.05 ! | | \ ATOM HB1 HA 0.09 ! | HB2 HG1 ATOM HB2 HA 0.09 ! O=C ATOM OG OH1 -0.66 ! | ATOM HG1 H 0.43 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG CB N HN N CA BOND C CA C +N CA HA CB HB1 BOND CB HB2 OG HG1 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N DONOR HG1 OG ACCEPTOR OG ACCEPTOR O C IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999 IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166 IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448 IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290 IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529 IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585 IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821 IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341 IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140 IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136 IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655 RESI THR 0.00 GROUP ATOM N NH1 -0.47 ! | ATOM HN H 0.31 ! HN-N ATOM CA CT1 0.07 ! | OG1--HG1 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 0.14 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 ATOM OG1 OH1 -0.66 ! O=C / \ ATOM HG1 H 0.43 ! | HG21 HG22 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA OG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N DONOR HG1 OG1 ACCEPTOR OG1 ACCEPTOR O C IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995 IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162 IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449 IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294 IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525 IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693 IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817 IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252 IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174 IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324 IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633 IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104 IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109 IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113 RESI TRP 0.00 GROUP ATOM N NH1 -0.47 ! | HE3 ATOM HN H 0.31 ! HN-N | ATOM CA CT1 0.07 ! | HB1 CE3 ATOM HA HB 0.09 ! | | / \\ GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3 ATOM CB CT2 -0.18 ! | | || || | ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2 ATOM HB2 HA 0.09 ! O=C / \ / \ // GROUP ! | HD1 NE1 CZ2 ATOM CG CY -0.03 ! | | ATOM CD1 CA 0.035 ! HE1 HZ2 ATOM HD1 HP 0.115 ATOM NE1 NY -0.61 ATOM HE1 H 0.38 ATOM CE2 CPT 0.13 ATOM CD2 CPT -0.02 GROUP ATOM CE3 CA -0.115 ATOM HE3 HP 0.115 GROUP ATOM CZ3 CA -0.115 ATOM HZ3 HP 0.115 GROUP ATOM CZ2 CA -0.115 ATOM HZ2 HP 0.115 GROUP ATOM CH2 CA -0.115 ATOM HH2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG NE1 CD1 BOND CZ2 CE2 BOND N HN N CA C CA C +N BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1 BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2 BOND CZ3 HZ3 CH2 HH2 DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HE1 NE1 ACCEPTOR O C IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972 IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202 IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505 IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304 IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526 IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560 IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835 IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233 IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127 IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118 IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407 IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679 IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126 IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746 IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011 IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017 IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019 IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030 IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815 IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811 IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811 IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790 IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767 IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820 RESI TYR 0.00 GROUP ATOM N NH1 -0.47 ! | HD1 HE1 ATOM HN H 0.31 ! HN-N | | ATOM CA CT1 0.07 ! | HB1 CD1--CE1 ATOM HA HB 0.09 ! | | // \\ GROUP ! HA-CA--CB--CG CZ--OH ATOM CB CT2 -0.18 ! | | \ __ / \ ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH ATOM HB2 HA 0.09 ! O=C | | GROUP ! | HD2 HE2 ATOM CG CA 0.00 GROUP ATOM CD1 CA -0.115 ATOM HD1 HP 0.115 GROUP ATOM CE1 CA -0.115 ATOM HE1 HP 0.115 GROUP ATOM CZ CA 0.11 ATOM OH OH1 -0.54 ATOM HH H 0.43 GROUP ATOM CD2 CA -0.115 ATOM HD2 HP 0.115 GROUP ATOM CE2 CA -0.115 ATOM HE2 HP 0.115 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG CB CD2 CG CE1 CD1 BOND CZ CE2 OH CZ BOND N HN N CA C CA C +N BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2 BOND CE1 HE1 CE2 HE2 OH HH DOUBLE O C CD1 CG CE1 CZ CE2 CD2 IMPR N -C CA HN C CA +N O DONOR HN N DONOR HH OH ACCEPTOR OH ACCEPTOR O C IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986 IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232 IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484 IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287 IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513 IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606 IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833 IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113 IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119 IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115 IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064 IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068 IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026 IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814 IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022 IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813 IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978 IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799 IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798 IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063 IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594 RESI VAL 0.00 GROUP ATOM N NH1 -0.47 ! | HG11 HG12 ATOM HN H 0.31 ! HN-N | / ATOM CA CT1 0.07 ! | CG1--HG13 ATOM HA HB 0.09 ! | / GROUP ! HA-CA--CB-HB ATOM CB CT1 -0.09 ! | \ ATOM HB HA 0.09 ! | CG2--HG21 GROUP ! O=C / \ ATOM CG1 CT3 -0.27 ! | HG21 HG22 ATOM HG11 HA 0.09 ATOM HG12 HA 0.09 ATOM HG13 HA 0.09 GROUP ATOM CG2 CT3 -0.27 ATOM HG21 HA 0.09 ATOM HG22 HA 0.09 ATOM HG23 HA 0.09 GROUP ATOM C C 0.51 ATOM O O -0.51 BOND CB CA CG1 CB CG2 CB N HN BOND N CA C CA C +N CA HA BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21 BOND CG2 HG22 CG2 HG23 DOUBLE O C IMPR N -C CA HN C CA +N O DONOR HN N ACCEPTOR O C IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966 IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180 IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471 IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297 IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471 IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660 IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828 IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441 IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414 IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178 IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114 IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097 IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110 IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108 IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115 IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098 RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral GROUP ATOM OH2 OT -0.834 ATOM H1 HT 0.417 ATOM H2 HT 0.417 !BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake BOND OH2 H1 OH2 H2 ANGLE H1 OH2 H2 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p GROUP ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p ANGLE H1 OH2 H2 ! required ACCEPTOR OH2 PATCHING FIRS NONE LAST NONE RESI ZN2 2.00 ! Zinc ion GROUP ATOM ZN ZN 2.00 PATCHING FIRST NONE LAST NONE RESI HEME -2.00 ! 6-liganded planar heme GROUP ATOM FE FE 0.24 ! O2A O1A O2D O1D ATOM NA NPH -0.18 ! \\ // \\ // ATOM NB NPH -0.18 ! CGA CGD ATOM NC NPH -0.18 ! | | ATOM ND NPH -0.18 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2 ATOM C1A CPA 0.12 ! | | | ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2 ATOM C3A CPB -0.06 ! | / \ | ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D ATOM C1B CPA 0.12 ! | | | | ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1 ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2 ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3 ATOM C1C CPA 0.12 ! C4A \ / C1D ATOM C2C CPB -0.06 ! / \ / \ ATOM C3C CPB -0.06 ! HB--CHB FE CHD--HD ATOM C4C CPA 0.12 ! \ / \ / ATOM C1D CPA 0.12 ! C1B / \ C4C HAC ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ / ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1 GROUP ! | | | | CBC ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2 ATOM HA HA 0.10 ! | \_CHC_/ | GROUP ! CAB | CMC--HMC3 ATOM CHB CPM -0.10 ! // \ HC / | ATOM HB HA 0.10 ! CBB HAB HMC1 HMC2 GROUP ! / \ ATOM CHC CPM -0.10 ! HBB1 HBB2 ATOM HC HA 0.10 ! GROUP ATOM CHD CPM -0.10 ATOM HD HA 0.10 GROUP ATOM CMA CT3 -0.27 ATOM HMA1 HA 0.09 ATOM HMA2 HA 0.09 ATOM HMA3 HA 0.09 GROUP ATOM CAA CT2 -0.18 ATOM HAA1 HA 0.09 ATOM HAA2 HA 0.09 GROUP ATOM CBA CT2 -0.28 ATOM HBA1 HA 0.09 ATOM HBA2 HA 0.09 ATOM CGA CC 0.62 ATOM O1A OC -0.76 ATOM O2A OC -0.76 GROUP ATOM CMB CT3 -0.27 ATOM HMB1 HA 0.09 ATOM HMB2 HA 0.09 ATOM HMB3 HA 0.09 GROUP ATOM CAB C -0.20 ATOM HAB HA 0.20 GROUP ATOM CBB C -0.20 ATOM HBB1 HA 0.10 ATOM HBB2 HA 0.10 GROUP ATOM CMC CT3 -0.27 ATOM HMC1 HA 0.09 ATOM HMC2 HA 0.09 ATOM HMC3 HA 0.09 GROUP ATOM CAC C -0.20 ATOM HAC HA 0.20 GROUP ATOM CBC C -0.20 ATOM HBC1 HA 0.10 ATOM HBC2 HA 0.10 GROUP ATOM CMD CT3 -0.27 ATOM HMD1 HA 0.09 ATOM HMD2 HA 0.09 ATOM HMD3 HA 0.09 GROUP ATOM CAD CT2 -0.18 ATOM HAD1 HA 0.09 ATOM HAD2 HA 0.09 GROUP ATOM CBD CT2 -0.28 ATOM HBD1 HA 0.09 ATOM HBD2 HA 0.09 ATOM CGD CC 0.62 ATOM O1D OC -0.76 ATOM O2D OC -0.76 BOND FE NA FE NB FE NC FE ND NA C1A BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A BOND CHA HA CHB HB CHC HC CHD HD BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2 BOND CMA HMA1 CMA HMA2 CMA HMA3 BOND CMB HMB1 CMB HMB2 CMB HMB3 BOND CAB HAB CBB HBB1 CBB HBB2 BOND CMC HMC1 CMC HMC2 CMC HMC3 BOND CAC HAC CBC HBC1 CBC HBC2 BOND CMD HMD1 CMD HMD2 CMD HMD3 BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2 IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC IMPR C2D C1D C3D CMD C3D C2D C4D CAD IMPR CGA CBA O2A O1A CGD CBD O2D O1D IMPR C4A NA C1A C2A C1A NA C4A C3A IMPR C4B NB C1B C2B C1B NB C4B C3B IMPR C4C NC C1C C2C C1C NC C4C C3C IMPR C4D ND C1D C2D C1D ND C4D C3D IMPR NA C1A C2A C3A NA C4A C3A C2A IMPR NB C1B C2B C3B NB C4B C3B C2B IMPR NC C1C C2C C3C NC C4C C3C C2C IMPR ND C1D C2D C3D ND C4D C3D C2D IMPR NA C1A CHA C4D NA C4A CHB C1B IMPR NB C1B CHB C4A NB C4B CHC C1C IMPR NC C1C CHC C4B NC C4C CHD C1D IMPR ND C1D CHD C4C ND C4D CHA C1A IMPR CHA C1A C4D HA IMPR CHB C1B C4A HB IMPR CHC C1C C4B HC IMPR CHD C1D C4C HD IMPR C1A C2A CHA NA C4A C3A CHB NA IMPR C1B C2B CHB NB C4B C3B CHC NB IMPR C1C C2C CHC NC C4C C3C CHD NC IMPR C1D C2D CHD ND C4D C3D CHA ND IMPR NA C1A C4A FE IMPR NB C1B C4B FE IMPR NC C1C C4C FE IMPR ND C1D C4D FE IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1 IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1 ACCEPTOR NA ACCEPTOR O1A ! CGA ACCEPTOR O2A ! CGA ACCEPTOR NB ACCEPTOR NC ACCEPTOR ND ACCEPTOR O1D ! CGD ACCEPTOR O2D ! CGD IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000 IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000 IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000 IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000 IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000 IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000 IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000 IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000 IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000 PATCHING FIRS NONE LAST NONE PRES NTER 1.00 ! standard N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HT1 ATOM HT2 HC 0.33 ! (+)/ ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT1 0.21 ! | \ ATOM HA HB 0.10 ! HA HT3 DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES GLYP 1.00 ! Glycine N-terminus GROUP ! use in generate statement ATOM N NH3 -0.30 ! ATOM HT1 HC 0.33 ! HA1 HT1 ATOM HT2 HC 0.33 ! | (+)/ ATOM HT3 HC 0.33 ! --CA--N--HT2 ATOM CA CT2 0.13 ! | \ ATOM HA1 HB 0.09 ! HA2 HT3 ATOM HA2 HB 0.09 ! DELETE ATOM HN BOND HT1 N HT2 N HT3 N DONOR HT1 N DONOR HT2 N DONOR HT3 N IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000 IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000 PRES PROP 1.00 ! Proline N-Terminal GROUP ! use in generate statement ATOM N NP -0.07 ! HA ATOM HN1 HC 0.24 ! | ATOM HN2 HC 0.24 ! -CA HN1 ATOM CD CP3 0.16 ! / \ / ATOM HD1 HA 0.09 ! N(+) ATOM HD2 HA 0.09 ! / \ ATOM CA CP1 0.16 ! -CD HN2 ATOM HA HB 0.09 ! | \ BOND HN1 N HN2 N ! HD1 HD2 DONOR HN1 N DONOR HN2 N IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000 IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000 PRES ACE 0.00 ! acetylated N-terminus GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA HN ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ACP 0.00 ! acetylated N-terminus for proline GROUP ! use in generate statement ATOM CAY CT3 -0.27 ! ATOM HY1 HA 0.09 ! HY1 HY2 HY3 ATOM HY2 HA 0.09 ! \ | / ATOM HY3 HA 0.09 ! CAY GROUP ! | ATOM CY C 0.51 ! CY=OY ATOM OY O -0.51 ! | ! BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3 DOUBLE OY CY IMPR CY CAY N OY IMPR N CY CA CD ACCEPTOR OY CY IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000 IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000 IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000 IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000 IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES CTER -1.00 ! standard C-terminus GROUP ! use in generate statement ATOM C CC 0.34 ! OT2(-) ATOM OT1 OC -0.67 ! / ATOM OT2 OC -0.67 ! -C DELETE ATOM O ! \\ BOND C OT2 ! OT1 DOUBLE C OT1 !IMPR OT1 CA OT2 C IMPR C CA OT2 OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT1 0.00 ! methylated C-terminus from methyl acetate GROUP ! use in generate statement ATOM N NH1 -0.47 ! ATOM HN H 0.31 ! OT1 ATOM CA CT1 0.17 ! | // ATOM HA HB 0.09 ! -N--CA--C HT1 ATOM C CD 0.63 ! | | \ / ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2 ATOM OT2 OS -0.34 ! \ ATOM CT CT3 -0.14 ! HT3 ATOM HT1 HA 0.09 ! ATOM HT2 HA 0.09 ! ATOM HT3 HA 0.09 ! DELETE ATOM O BOND C OT2 OT2 CT BOND CT HT1 CT HT2 CT HT3 DOUBLE C OT1 IMPR C CA OT2 OT1 ACCEPTOR OT1 C ACCEPTOR OT2 C IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000 IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000 IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000 PRES CT2 0.00 ! amidated C-terminus GROUP ! use in generate statement ATOM C CC 0.55 ! ATOM O O -0.55 ! | GROUP ! O=C ATOM NT NH2 -0.62 ! | ATOM HT1 H 0.32 ! NT ATOM HT2 H 0.30 ! / \ BOND C NT ! HT1 HT2 BOND NT HT1 NT HT2 ! DIHE CA C NT HT2 ! (HT1 is cis to O) IMPR C NT CA O C CA NT O IMPR NT C HT1 HT2 NT C HT2 HT1 DONOR HT1 NT DONOR HT2 NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000 IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CT3 0.00 ! N-Methylamide C-terminus GROUP ! use in generate statement ATOM C C 0.51 ! ATOM O O -0.51 ! | GROUP ! C=O ATOM NT NH1 -0.47 ! | ATOM HNT H 0.31 ! NT-HNT ATOM CAT CT3 -0.11 ! | ATOM HT1 HA 0.09 ! HT1-CAT-HT3 ATOM HT2 HA 0.09 ! | ATOM HT3 HA 0.09 ! HT2 ! BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3 DIHE CA C NT CAT IMPR NT C CAT HNT C CA NT O DONOR HNT NT IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000 IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000 IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000 IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000 IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000 PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2 GROUP ! via acetic acid, use in a patch statement ATOM CB CT2 -0.21 ! ATOM HB1 HA 0.09 ! HB1 OD1 ATOM HB2 HA 0.09 ! | // ATOM CG CD 0.75 ! -CB--CG ATOM OD1 OB -0.55 ! | \ ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2 ATOM HD2 H 0.44 ! BOND OD2 HD2 ANGLE HD2 OD2 CG DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB DONOR HD2 OD2 IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2 GROUP ! via acetic acid, use in a patch statement ATOM CG CT2 -0.21 ! ATOM HG1 HA 0.09 ! HG1 OE1 ATOM HG2 HA 0.09 ! | // ATOM CD CD 0.75 ! -CG--CD ATOM OE1 OB -0.55 ! | \ ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2 ATOM HE2 H 0.44 ! BOND OE2 HE2 ANGLE HE2 OE2 CD DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG DONOR HE2 OE2 IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES LINK 0.00 ! linkage for IMAGES or for joining segments ! 1 refers to previous (N terminal) ! 2 refers to next (C terminal) ! use in a patch statement BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES CYSD -1.0 ! patch for deprotonated CYS GROUP ! The charges are invented!!! ATOM CB CT2 -0.30 ! ATOM SG SM -0.70 ! 2SG--2CB-- DELETE ATOM HG1 PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. GROUP ! use in a patch statement ATOM 1CB CT2 -0.10 ! ATOM 1SG SM -0.08 ! 2SG--2CB-- GROUP ! / ATOM 2SG SM -0.08 ! -1CB--1SG ATOM 2CB CT2 -0.10 ! DELETE ATOM 1HG1 DELETE ATOM 2HG1 BOND 1SG 2SG ANGLE 1CB 1SG 2SG 1SG 2SG 2CB DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA DIHE 1CB 1SG 2SG 2CB !DIHE 1CB 1SG 2SG 2CB IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000 IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2 GROUP ! use in a patch statement ATOM CE1 CPH2 0.25 ! HE1 ATOM HE1 HR1 0.13 ! / ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1 ATOM CG CPH1 0.22 ! | / | ATOM CB CT2 -0.08 ! -CB--CG | ATOM HB1 HA 0.09 ! | \ | ATOM HB2 HA 0.09 ! HB2 CD2--NE2 GROUP ! | \ ATOM NE2 NR1 -0.36 ! HD2 HE2 ATOM HE2 H 0.32 ATOM CD2 CPH1 -0.05 ATOM HD2 HR3 0.09 DELETE ATOM HD1 DELETE ACCE NE2 BOND NE2 HE2 ANGLE CD2 NE2 HE2 CE1 NE2 HE2 DIHE HE2 NE2 CE1 HE1 HE2 NE2 CE1 ND1 HE2 NE2 CD2 HD2 DIHE HE2 NE2 CD2 CG IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2 DONOR HE2 NE2 ACCEPTOR ND1 IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000 RESI O2 0.00 ! O2 ligand for heme GROUP ATOM O1 OM 0.021 ATOM O2 OM -0.021 BOND O1 O2 PATCHING FIRS NONE LAST NONE RESI CO 0.00 ! CO ligand for heme GROUP ATOM C CM 0.021 ATOM O OM -0.021 TRIPLE C O PATCHING FIRS NONE LAST NONE PRES FHEM 0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES ! unliganded heme patch DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND PRES PHEM 0.00 ! Patch for HEME to His link. ! Patch residues must be 1-HIS, and 2-HEME. DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND BOND 1NE2 2FE ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND IC 1CD2 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1CE1 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be ! 1-O2 , 2-HEME , and 3-HIS ! O1 of the oxygen is bonded to the iron. BOND 1O1 2FE ANGLE 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB ANGLE 1O1 2FE 2NC 1O1 2FE 2ND DIHE 1O2 1O1 2FE 2NA IC 1O2 1O1 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1O2 1O1 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be, ! 1-CO , 2-HEME , and 3-HIS BOND 1C 2FE ANGLE 1C 2FE 3NE2 ANGLE 1O 1C 2FE 1C 2FE 2NA 1C 2FE 2NB ANGLE 1C 2FE 2NC 1C 2FE 2ND IC 1O 1C 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000 IC 1O 1C 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000 ! patches for cyclic peptides PRES LIG1 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA DIHE 1CA 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG2 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus ! 2 refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA DIHE 1CA 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 PRES LIG3 0.00000 ! linkage for cyclic peptide ! 1 refers to the C terminus which is a glycine ! 2 refers to the N terminus which is a glycine ! use in a patch statement, perform initial ! generation using first NONE last NONE BOND 1C 2N ANGLE 1C 2N 2CA 1CA 1C 2N ANGLE 1O 1C 2N 1C 2N 2HN DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2 DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA DIHE 1CA 1C 2N 2CA IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000 IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000 IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000 RESI DUM 0.00 ! DUMMY ATOM GROUP ATOM DUM DUM 0.00 PATCHING FIRST NONE LAST NONE !END !phosphotyrosine information deleted ! !lipids section RESI MAS 0.00 ! methylacetate GROUP ! ATOM C1 CTL3 -0.17 ! H22 ATOM C CL 0.63 ! | ATOM OM OSL -0.34 ! H21-C2-H23 ATOM C2 CTL3 -0.14 ! \ ATOM O OBL -0.52 ! OM ATOM H11 HAL3 0.09 ! / ATOM H12 HAL3 0.09 ! O=C ATOM H13 HAL3 0.09 ! | ATOM H21 HAL3 0.09 ! H11-C1-H13 ATOM H22 HAL3 0.09 ! | ATOM H23 HAL3 0.09 ! H12 BOND C1 C C OM OM C2 DOUBLE C O BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 IMPR C OM C1 O ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 RESI ETAC 0.00 ! Ethylacetate ! H213 GROUP ! | ATOM C1 CTL3 -0.17 ! H211-C21-H212 ATOM C CL 0.63 ! / ATOM OM OSL -0.34 ! H22-C2-H23 ATOM C2 CTL2 -0.05 ! \ ATOM O OBL -0.52 ! OM ATOM H11 HAL3 0.09 ! / ATOM H12 HAL3 0.09 ! O=C ATOM H13 HAL3 0.09 ! \ ATOM H22 HAL2 0.09 ! H11-C1-H13 ATOM H23 HAL2 0.09 ! | GROUP ! H12 ATOM C21 CTL3 -0.27 ATOM H211 HAL3 0.09 ATOM H212 HAL3 0.09 ATOM H213 HAL3 0.09 BOND C1 C C OM OM C2 DOUBLE C O BOND C1 H11 C1 H12 C1 H13 BOND C2 C21 C2 H22 C2 H23 BOND C21 H211 C21 H212 C21 H213 IMPR C OM C1 O ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC C21 C2 OM C 1.520 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 IC H211 C21 C2 OM 1.1 108.90 180.0 116.7 1.437 IC H212 C21 C2 OM 1.1 108.90 60.0 116.7 1.437 IC H213 C21 C2 OM 1.1 108.90 -60.0 116.7 1.437 RESI MPRO 0.00 ! Methylpropionate GROUP ! ATOM C1 CTL2 -0.08 ! H22 ATOM C CL 0.63 ! | ATOM OM OSL -0.34 ! H21-C2-H23 ATOM C2 CTL3 -0.14 ! \ ATOM O OBL -0.52 ! OM ATOM H12 HAL2 0.09 ! / ATOM H13 HAL2 0.09 ! O=C ATOM H21 HAL3 0.09 ! \ ATOM H22 HAL3 0.09 ! H12-C1-H13 ATOM H23 HAL3 0.09 ! / GROUP ! H112-C11-H111 ATOM C11 CTL3 -0.27 ! | ATOM H111 HAL3 0.09 ! H113 ATOM H112 HAL3 0.09 ! ATOM H113 HAL3 0.09 ! BOND C1 C C OM C O OM C2 BOND C1 C11 C1 H12 C1 H13 BOND C11 H111 C11 H112 C11 H113 BOND C2 H21 C2 H22 C2 H23 IMPR C OM C1 O ! internal coordinates from experiment for heavy atoms IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437 IC O C OM C2 1.200 125.9 0.0 114.8 1.437 IC C11 C1 C OM 1.520 108.9 180.0 109.0 1.334 IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334 IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334 IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334 IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334 IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334 IC H111 C11 C1 C 1.1 109.75 180.0 109.0 1.520 IC H112 C11 C1 C 1.1 109.75 60.4 109.0 1.520 IC H113 C11 C1 C 1.1 109.75 -60.4 109.0 1.520 RESI ACEH 0.00 ! acetic acid ! atoms in proper order for molvib input GROUP ! ATOM C2 CTL3 -0.30 ! ATOM C1 CL 0.75 ! H21 O2 ATOM H21 HAL3 0.09 ! \ // ATOM H22 HAL3 0.09 ! H22-C2--C1 ATOM H23 HAL3 0.09 ! / \ ATOM O2 OBL -0.55 ! H23 O1-HO1 ATOM O1 OHL -0.61 ! ATOM HO1 HOL 0.44 ! BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23 DOUBLE C1 O2 IMPR C1 O1 C2 O2 IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000 IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000 IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000 IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000 RESI DMPA -1.00 ! Dimethylphosphate GROUP ! ATOM P1 PL 1.50 ! ATOM O3 O2L -0.78 ! ATOM O4 O2L -0.78 ! H11 ATOM O1 OSL -0.57 ! | ATOM O2 OSL -0.57 ! H13- C1-H12 ! \ ATOM C1 CTL3 -0.17 ! (-) O3 O1 ATOM H11 HAL3 0.09 ! \ / ATOM H12 HAL3 0.09 ! P1 (+) ATOM H13 HAL3 0.09 ! / \ ! (-) O4 O2 ATOM C2 CTL3 -0.17 ! / ATOM H21 HAL3 0.09 ! H23-C2-H22 ATOM H22 HAL3 0.09 ! | ATOM H23 HAL3 0.09 ! H21 ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2 BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23 ! IC FOR THE g,g conformation (3-21G* opt. structure) IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344 RESI MP_1 -1.00 ! Methylphosphate, anionic GROUP ! ! atom order for molvib ATOM C1 CTL3 -0.17 ! ATOM O1 OSL -0.62 ! H11 ATOM P1 PL 1.50 ! | ATOM O2 OHL -0.68 ! H13--C1--H12 ATOM O3 O2L -0.82 ! | ATOM O4 O2L -0.82 ! O1 ATOM H11 HAL3 0.09 ! | ATOM H12 HAL3 0.09 ! O4==P1==O3 (-) ATOM H13 HAL3 0.09 ! | ATOM H2 HOL 0.34 ! O2 ! \ ! H2 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 O2 H2 IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H2 O2 P1 O1 0.0000 000.00 000.0 000.00 0.0000 RESI MP_2 -2.00 ! Methylphosphate, dianionic GROUP ! ATOM P1 PL 1.10 ! ATOM O1 OSL -0.40 ! H11 ATOM O2 O2L -0.90 ! | ATOM O3 O2L -0.90 ! H13--C1--H12 ATOM O4 O2L -0.90 ! | GROUP ! O1 ATOM C1 CTL3 -0.27 ! | ATOM H11 HAL3 0.09 ! (-) O4--P1(+)--O3 (-) ATOM H12 HAL3 0.09 ! | ATOM H13 HAL3 0.09 ! O2 (-) ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 ! dummy to analyze cetain angles IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 RESI MSO4 -1.00 ! Methylsulfate GROUP ! ATOM S SL 1.33 ! OS2(-1) ATOM OS1 OSL -0.28 ! | ATOM OS2 O2L -0.65 ! (-1) OS2--S(+2)--OS4 (-1) ATOM OS3 O2L -0.65 ! | ATOM OS4 O2L -0.65 ! OS1 ATOM C1 CTL3 -0.37 ! \ ATOM H11 HAL3 0.09 ! H11-C1-H13 ATOM H12 HAL3 0.09 ! | ATOM H13 HAL3 0.09 ! H12 ! BOND S OS1 S OS2 S OS3 S OS4 OS1 C1 BOND C1 H11 C1 H12 C1 H13 ACCE OS1 ACCE OS2 ACCE OS3 ACCE OS4 IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS2 S OS2 OS3 0.0000 0.0000 -60.0000 0.0000 0.0000 IC OS3 S OS1 OS4 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS1 S OS3 OS2 0.0000 0.0000 60.0000 0.0000 0.0000 IC C1 OS1 S OS2 0.0000 0.0000 60.0000 0.0000 0.0000 IC S OS1 C1 OS3 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS1 S OS4 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OS1 S OS2 OS3 0.0000 0.0000 180.0000 0.0000 0.0000 IC OS1 S OS3 OS2 0.0000 0.0000 180.0000 0.0000 0.0000 IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS4 S OS3 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS3 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS4 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS2 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 IC OS3 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000 Resi BUTA 0.00 ! BUTANE Group Atom h11 HAL3 0.09 ! H2 Atom h12 HAL3 0.09 ! | Atom h13 HAL3 0.09 ! H1-C1-H3 Atom c1 CTL3 -0.27 ! | Group ! | Atom h21 HAL2 0.09 ! H4-C2-H5 Atom h22 HAL2 0.09 ! | Atom c2 CTL2 -0.18 ! | Group ! | Atom h31 HAL2 0.09 ! H6-C3-H7 Atom h32 HAL2 0.09 ! | atom c3 CTL2 -0.18 ! | Group ! | atom h41 HAL3 0.09 ! H8-C4-H10 atom h42 HAL3 0.09 ! | atom h43 HAL3 0.09 ! H9 atom c4 CTL3 -0.27 ! Bond h11 c1 h12 c1 h13 c1 c1 c2 Bond h21 c2 h22 c2 c2 c3 Bond h31 c3 h32 c3 c3 c4 Bond h41 c4 h42 c4 h43 c4 ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 ic c2 c3 c4 h41 0.00 0.00 180.0 0.00 0.00 ic c3 h41 *c4 h42 0.00 0.00 120.0 0.00 0.00 ic c3 h41 *c4 h43 0.00 0.00 -120.0 0.00 0.00 ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00 ic c2 h11 *c1 h12 0.00 0.00 120.0 0.00 0.00 ic c2 h11 *c1 h13 0.00 0.00 -120.0 0.00 0.00 ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00 ic c1 c3 *c2 h22 0.00 0.00 -120.0 0.00 0.00 ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00 ic c2 c4 *c3 h32 0.00 0.00 -120.0 0.00 0.00 Resi HEXA 0.00 ! hexane Group Atom h11 HAL3 0.09 ! H2 Atom h12 HAL3 0.09 ! | Atom h13 HAL3 0.09 ! H1-C1-H3 Atom c1 CTL3 -0.27 ! | Group ! | Atom h21 HAL2 0.09 ! H4-C2-H5 Atom h22 HAL2 0.09 ! | Atom c2 CTL2 -0.18 ! | Group ! | Atom h31 HAL2 0.09 ! H6-C3-H7 Atom h32 HAL2 0.09 ! | atom c3 CTL2 -0.18 ! | Group ! | atom h41 HAL2 0.09 ! H8-C4-H10 atom h42 HAL2 0.09 ! | atom c4 CTL2 -0.18 ! | Group ! | atom h51 HAL2 0.09 ! H51-C5-H152 atom h52 HAL2 0.09 ! | atom c5 CTL2 -0.18 ! | Group ! | atom h61 HAL2 0.09 ! H61-C4-H62 atom h62 HAL2 0.09 ! | atom h63 HAL2 0.09 ! H63 atom c6 CTL2 -0.27 ! Bond h11 c1 h12 c1 h13 c1 c1 c2 Bond h21 c2 h22 c2 c2 c3 Bond h31 c3 h32 c3 c3 c4 Bond h41 c4 h42 c4 c4 c5 Bond h51 c5 h52 c5 c5 c6 Bond h61 c6 h62 c6 c6 h63 ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00 ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00 ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00 ic h11 c2 *c1 h12 0.00 0.00 120.0 0.00 0.00 ic h11 c2 *c1 h13 0.00 0.00 240.0 0.00 0.00 ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00 ic c1 c3 *c2 h22 0.00 0.00 240.0 0.00 0.00 ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00 ic c2 c4 *c3 h32 0.00 0.00 240.0 0.00 0.00 ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00 ic c3 c5 *c4 h42 0.00 0.00 240.0 0.00 0.00 ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00 ic c4 c6 *c5 h52 0.00 0.00 240.0 0.00 0.00 ic c4 c5 c6 h61 0.00 0.00 180.0 0.00 0.00 ic h61 c5 *c6 h62 0.00 0.00 120.0 0.00 0.00 ic h61 c5 *c6 h63 0.00 0.00 240.0 0.00 0.00 Resi ETHE 0.00 ! ethylene, yin/adm jr. Group Atom c1 cel2 -0.42 ! Atom h11 hel2 0.21 ! H11 H21 Atom h12 hel2 0.21 ! \ / Group ! C1=C2 Atom c2 cel2 -0.42 ! / \ Atom h21 hel2 0.21 ! H12 H22 Atom h22 hel2 0.21 ! Bond c1 h11 c1 h12 Double c1 c2 Bond c2 h21 c2 h22 IMPR c1 c2 h12 h11 IMPR c1 c2 h11 h12 IMPR c2 c1 h22 h21 IMPR c2 c1 h21 h22 ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 ic h22 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 ic c1 c2 h21 h22 0.00 0.00 180.0 0.0 0.0 patc firs none last none Resi PRPE 0.00 ! propene, yin/adm jr. Group Atom c1 cel2 -0.42 ! Atom h11 hel2 0.21 ! H11 H21 Atom h12 hel2 0.21 ! \ / Group ! C1=C2 H31 Atom c2 cel1 -0.15 ! / \ / Atom h21 HEL1 0.15 ! H12 C3 Group ! / \ Atom c3 ctl3 -0.27 ! H33 H32 Atom h31 HAL3 0.09 ! Atom h32 HAL3 0.09 ! Atom h33 HAL3 0.09 ! Bond c1 h11 c1 h12 Double c1 c2 Bond c2 h21 Bond c2 c3 bond c3 h31 c3 h32 c3 h33 ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0 ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0 ic c3 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0 ic h31 c3 c2 c1 0.00 0.00 0.0 0.0 0.0 ic h32 c3 c2 c1 0.00 0.00 120.0 0.0 0.0 ic h33 c3 c2 c1 0.00 0.00 -120.0 0.0 0.0 patc firs none last none Resi BTE1 0.00 ! 1-Butene, yin/adm jr. Group Atom c1 cel2 -0.42 ! Atom h11 hel2 0.21 ! H11 H21 H41 Atom h12 hel2 0.21 ! \ / | Group ! C1=C2 C4-H42 Atom c2 cel1 -0.15 ! / \ / \ Atom h21 HEL1 0.15 ! H12 C3 H43 Group ! / \ Atom c3 ctl2 -0.18 ! H31 H32 Atom h31 HAL2 0.09 ! Atom h32 HAL2 0.09 ! Group Atom c4 ctl3 -0.27 Atom h41 HAL3 0.09 Atom h42 HAL3 0.09 Atom h43 HAL3 0.09 BOND c1 h11 c1 h12 Double c1 c2 BOND c2 h21 BOND c2 c3 BOND c3 h31 c3 h32 BOND c3 c4 BOND c4 h41 c4 h42 c4 h43 ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00 ic h11 c1 c2 c3 0.00 0.00 180.0 0.00 0.00 ic h12 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 ic h31 c2 *c3 c4 0.00 0.00 120.0 0.00 0.00 ic h32 c2 *c3 c4 0.00 0.00 -120.0 0.00 0.00 ic h41 c4 c3 c2 0.00 0.00 180.0 0.00 0.00 ic h42 c4 c3 c2 0.00 0.00 60.0 0.00 0.00 ic h43 c4 c3 c2 0.00 0.00 -60.0 0.00 0.00 patc firs none last none Resi BTE2 0.00 ! 2-Butene, yin/adm jr. Group Atom c1 ctl3 -0.27 ! H12 H13 Atom h11 HAL3 0.09 ! \ | Atom h12 HAL3 0.09 ! H13-C1 H31 Atom h13 HAL3 0.09 ! \ / Group ! C2=C3 Atom c2 cel1 -0.15 ! / \ Atom h21 HEL1 0.15 ! H21 C4-H41 Group ! | \ Atom c3 cel1 -0.15 ! H43 H42 Atom h31 HEL1 0.15 ! Group Atom c4 ctl3 -0.27 Atom h41 HAL3 0.09 Atom h42 HAL3 0.09 Atom h43 HAL3 0.09 BOND c1 h11 c1 h12 c1 h13 BOND c1 c2 BOND c2 h21 DOUBLE c2 c3 BOND c3 h31 BOND c3 c4 BOND c4 h41 c4 h42 c4 h43 ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00 ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 ic h31 c4 *c3 c2 0.00 0.00 120.0 0.00 0.00 ic h41 c4 c3 c2 0.00 0.00 0.0 0.00 0.00 ic h42 c4 c3 c2 0.00 0.00 120.0 0.00 0.00 ic h43 c4 c3 c2 0.00 0.00 -120.0 0.00 0.00 patc firs none last none Resi HXE2 0.00 ! 2-hexene, yin/adm jr. Group Atom c1 ctl3 -0.27 ! H12 H13 Atom h11 HAL3 0.09 ! \ | Atom h12 HAL3 0.09 ! H13-C1 H31 H51 H52 Atom h13 HAL3 0.09 ! \ / \ / Group ! C2=C3 C5 H61 Atom c2 cel1 -0.15 ! / \ / \ / Atom h21 HEL1 0.15 ! H21 C4 C6-H62 Group ! / \ \ Atom c3 cel1 -0.15 ! H41 H42 H63 Atom h31 HEL1 0.15 ! Group Atom c4 ctl2 -0.18 Atom h41 HAL2 0.09 Atom h42 HAL2 0.09 Group Atom c5 ctl2 -0.18 Atom h51 HAL2 0.09 Atom h52 HAL2 0.09 Group Atom c6 ctl3 -0.27 Atom h61 HAL3 0.09 Atom h62 HAL3 0.09 Atom h63 HAL3 0.09 BOND c1 h11 c1 h12 c1 h13 BOND c1 c2 BOND c2 h21 DOUBLE c2 c3 BOND c3 h31 BOND c3 c4 BOND c4 h41 c4 h42 BOND c4 c5 c5 h51 c5 h52 BOND c5 c6 c6 h61 c6 h62 c6 h63 ! all trans ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00 ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00 ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00 ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00 ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00 ic h31 c4 *c3 c2 0.00 0.00 120.0 0.00 0.00 ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00 ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00 ic c3 c5 *c4 h42 0.00 0.00 -120.0 0.00 0.00 ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00 ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00 ic c4 c6 *c5 h52 0.00 0.00 -120.0 0.00 0.00 ic h61 c6 c5 c4 0.00 0.00 180.0 0.00 0.00 ic h62 c6 c5 c4 0.00 0.00 60.0 0.00 0.00 ic h63 c6 c5 c4 0.00 0.00 300.0 0.00 0.00 patc firs none last none !RESI TIP3 0.00 ! TIPS3P WATER MODEL ! ! GENERATE USING NOANGLE NODIHEDRAL !GROUP ! !ATOM OH2 OT -0.834 !ATOM H1 HT 0.417 !ATOM H2 HT 0.417 !BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE !ANGLE H1 OH2 H2 ! REQUIRED !ACCEPTOR OH2 !PATCHING FIRS NONE LAST NONE !RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p !GROUP !ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup !ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup !ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup !BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p !ANGLE H1 OH2 H2 ! required !ACCEPTOR OH2 !PATCHING FIRS NONE LAST NONE RESI NC4 1.00 ! tetramethylammonium GROUP ! ATOM N NTL -0.60 ! H32 ATOM C1 CTL5 -0.35 ! | ATOM C2 CTL5 -0.35 ! H31-C3-H33 ATOM C3 CTL5 -0.35 ! H23 | H41 ATOM C4 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! H22-C2------N------C4-H42 (+) ATOM H12 HL 0.25 ! | | | ATOM H13 HL 0.25 ! H21 | H43 ATOM H21 HL 0.25 ! H11-C1-H13 ATOM H22 HL 0.25 ! | ATOM H23 HL 0.25 ! H12 ATOM H31 HL 0.25 ATOM H32 HL 0.25 ATOM H33 HL 0.25 ATOM H41 HL 0.25 ATOM H42 HL 0.25 ATOM H43 HL 0.25 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 H13 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 ! internal are wrong IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000 IC C2 N C1 H12 0.0000 0.0000 -60.0000 0.0000 0.0000 IC C2 N C1 H13 0.0000 0.0000 60.0000 0.0000 0.0000 IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000 IC C2 C1 *N C4 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3 N C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000 IC C3 N C2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C3 N C2 H23 0.0000 0.0000 120.0000 0.0000 0.0000 IC C4 N C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000 IC C4 N C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C4 N C3 H33 0.0000 0.0000 120.0000 0.0000 0.0000 IC C1 N C4 H41 0.0000 0.0000 0.0000 0.0000 0.0000 IC C1 N C4 H42 0.0000 0.0000 -120.0000 0.0000 0.0000 IC C1 N C4 H43 0.0000 0.0000 120.0000 0.0000 0.0000 RESI NC5 1.00 ! tetramethylammonium ethyl analog GROUP ATOM N NTL -0.60 ! ATOM C1 CTL2 -0.10 ! | ATOM C2 CTL5 -0.35 ! -C3- ATOM C3 CTL5 -0.35 ! | ATOM C4 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! -C2---N---C4- (+) ATOM H12 HL 0.25 ! | | | ATOM H21 HL 0.25 ! | ATOM H22 HL 0.25 ! -C1- ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! -C5- ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ATOM H42 HL 0.25 ATOM H43 HL 0.25 GROUP ATOM C5 CTL3 -0.27 ATOM H51 HAL3 0.09 ATOM H52 HAL3 0.09 ATOM H53 HAL3 0.09 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 C5 H53 ! ab-initio HF/6-31G* structure IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217 IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950 IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950 IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809 IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809 IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795 IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773 IC C1 N C2 H23 1.5176 111.12 -54.79 109.07 1.0797 IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795 IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773 IC C1 N C3 H33 1.5176 111.12 54.79 109.07 1.0797 IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793 IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793 IC C1 N C4 H43 1.5176 107.80 -60.03 109.12 1.0793 IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836 IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820 IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820 RESI CHOL 1.00 ! choline GROUP ! ATOM N NTL -0.60 ! ATOM C1 CTL2 -0.10 ! | ATOM C2 CTL5 -0.35 ! -C3- ATOM C3 CTL5 -0.35 ! | ATOM C4 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! -C2---N---C4- (+) ATOM H12 HL 0.25 ! | | | ATOM H21 HL 0.25 ! | ATOM H22 HL 0.25 ! -C1- ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! | ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ! | ATOM H42 HL 0.25 ! | ATOM H43 HL 0.25 ! | GROUP ! | ATOM C5 CTL2 0.05 ! | ATOM H51 HAL2 0.09 ! -C5- ATOM H52 HAL2 0.09 ! | ATOM OH1 OHL -0.66 ! OH1---HO1 ATOM HO1 HOL 0.43 ! BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND C5 OH1 OH1 HO1 ! ab-initio HF/6-31G* geometry of gauche conformer IC C4 N C1 C5 1.4964 107.76 161.60 116.58 1.5208 IC C5 C1 N C2 1.5208 116.58 -80.13 111.04 1.5031 IC C5 C1 N C3 1.5208 116.58 42.05 111.71 1.4945 IC N C1 C5 OH1 1.5158 116.58 56.02 109.57 1.3947 IC C1 C5 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491 IC C2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813 IC C3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802 IC C1 N C2 H21 1.5158 111.04 -179.38 108.21 1.0796 IC C3 N C2 H22 1.4945 109.20 -63.85 109.22 1.0746 IC C4 N C2 H23 1.4964 108.15 57.69 108.56 1.0794 IC C1 N C3 H31 1.5158 111.71 173.42 108.53 1.0794 IC C2 N C3 H32 1.5031 109.20 177.22 109.23 1.0800 IC C4 N C3 H33 1.4964 108.88 174.14 109.12 1.0773 IC C1 N C4 H41 1.5158 107.76 175.04 109.01 1.0793 IC C2 N C4 H42 1.5031 108.15 -64.86 109.05 1.0796 IC C3 N C4 H43 1.4945 108.88 56.40 109.30 1.0794 IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855 IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847 RESI ACHO 1.00 ! acetylcholine GROUP ! ATOM N NTL -0.60 ! ATOM C1 CTL2 -0.10 ! | ATOM C2 CTL5 -0.35 ! -C3- ATOM C3 CTL5 -0.35 ! | ATOM C4 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! -C2---N---C4- (+) ATOM H12 HL 0.25 ! | | | ATOM H21 HL 0.25 ! | ATOM H22 HL 0.25 ! -C1- ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! | ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ! | ATOM H42 HL 0.25 ! | ATOM H43 HL 0.25 ! | GROUP ! | ATOM C5 CTL2 -0.05 ! -C5- ATOM OM OSL -0.34 ! | ATOM C CL 0.63 ! OM ATOM C7 CTL3 -0.17 ! / ATOM O OBL -0.52 ! O==C ATOM H51 HAL2 0.09 ! | ATOM H52 HAL2 0.09 ! --C7-- ATOM H71 HAL3 0.09 ! | ATOM H72 HAL3 0.09 ! ATOM H73 HAL3 0.09 ! BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND C7 C C OM OM C5 DOUBLE C O BOND C7 H71 C7 H72 C7 H73 IMPR C OM C7 O IC C4 N C1 C5 0.0000 000.00 161.60 000.00 0.0000 IC C5 C1 N C2 0.0000 000.00 -80.13 000.00 0.0000 IC C5 C1 N C3 0.0000 000.00 42.05 000.00 0.0000 IC C2 N C1 H11 0.0000 000.00 158.76 000.00 0.0000 IC C3 N C1 H12 0.0000 000.00 165.25 000.00 0.0000 IC C1 N C2 H21 0.0000 000.00 -179.38 000.00 0.0000 IC C3 N C2 H22 0.0000 000.00 -63.85 000.00 0.0000 IC C4 N C2 H23 0.0000 000.00 57.69 000.00 0.0000 IC C1 N C3 H31 0.0000 000.00 173.42 000.00 0.0000 IC C2 N C3 H32 0.0000 000.00 177.22 000.00 0.0000 IC C4 N C3 H33 0.0000 000.00 174.14 000.00 0.0000 IC C1 N C4 H41 0.0000 000.00 175.04 000.00 0.0000 IC C2 N C4 H42 0.0000 000.00 -64.86 000.00 0.0000 IC C3 N C4 H43 0.0000 000.00 56.40 000.00 0.0000 IC N C1 C5 H51 0.0000 000.00 180.00 000.00 0.0000 IC N C1 C5 H52 0.0000 000.00 -60.0 000.00 0.0000 IC N C1 C5 OM 0.0000 000.00 72.0 000.00 0.0000 IC C1 C5 OM C 0.0000 000.00 166.9 000.00 0.0000 IC C7 C OM C5 0.0000 000.00 20.0 000.00 0.0000 IC O C OM C5 0.0000 000.00 -160.0 000.00 0.0000 IC H71 C7 C OM 0.0000 000.00 180.0 000.00 0.0000 IC H72 C7 C OM 0.0000 000.00 60.4 000.00 0.0000 IC H73 C7 C OM 0.0000 000.00 -60.4 000.00 0.0000 RESI PC 0.00 ! phosphatidylcholine GROUP ! ATOM N NTL -0.60 ! ATOM C1 CTL2 -0.10 ! | ATOM C2 CTL5 -0.35 ! -C3- ATOM C3 CTL5 -0.35 ! | ATOM C4 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! -C2---N---C4- (+) ATOM H12 HL 0.25 ! | | | ATOM H21 HL 0.25 ! | ATOM H22 HL 0.25 ! -C1- ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! | ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ! | ATOM H42 HL 0.25 ! | ATOM H43 HL 0.25 ! | GROUP ! | ATOM C5 CTL2 -0.08 ! | ATOM H51 HAL2 0.09 ! H52---C5---H51 ATOM H52 HAL2 0.09 ! | GROUP ! | ATOM P1 PL 1.50 ! (-) O3 O1 ATOM O3 O2L -0.78 ! \ / ATOM O4 O2L -0.78 ! P1 (+) ATOM O1 OSL -0.57 ! / \ ATOM O2 OSL -0.57 ! (-) O4 O2 GROUP ! | ATOM C6 CTL3 -0.17 ! | ATOM H61 HAL3 0.09 ! H63-C6-H62 ATOM H62 HAL3 0.09 ! | ATOM H63 HAL3 0.09 ! H61 ! BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6 BOND C6 H61 C6 H62 C6 H63 IC C4 N C1 C5 0.0000 000.00 112.00 000.00 0.0000 IC C5 C1 N C2 0.0000 000.00 -121.00 000.00 0.0000 IC C5 C1 N C3 0.0000 000.00 0.00 000.00 0.0000 IC C2 N C1 H11 0.0000 000.00 120.00 000.00 0.0000 IC C3 N C1 H12 0.0000 000.00 120.00 000.00 0.0000 IC C1 N C2 H21 0.0000 000.00 180.00 000.00 0.0000 IC C3 N C2 H22 0.0000 000.00 -60.00 000.00 0.0000 IC C4 N C2 H23 0.0000 000.00 60.00 000.00 0.0000 IC C1 N C3 H31 0.0000 000.00 180.00 000.00 0.0000 IC C2 N C3 H32 0.0000 000.00 180.00 000.00 0.0000 IC C4 N C3 H33 0.0000 000.00 180.00 000.00 0.0000 IC C1 N C4 H41 0.0000 000.00 180.00 000.00 0.0000 IC C2 N C4 H42 0.0000 000.00 -60.00 000.00 0.0000 IC C3 N C4 H43 0.0000 000.00 60.00 000.00 0.0000 IC N C1 C5 H51 0.0000 000.00 -150.00 000.00 0.0000 IC N C1 C5 H52 0.0000 000.00 100.00 000.00 0.0000 IC N C1 C5 O1 0.0000 000.00 -30.00 000.00 0.0000 IC C1 C5 O1 P1 0.0000 000.00 130.00 000.00 0.0000 IC C5 O1 P1 O2 0.0000 000.00 -160.0 000.00 0.0000 IC O3 P1 O1 C5 0.0000 000.00 80.00 000.00 0.0000 IC O4 P1 O1 C5 0.0000 000.00 -60.00 000.00 0.0000 IC O1 P1 O2 C6 0.0000 000.00 180.00 000.00 0.0000 IC H61 C6 O2 P1 0.0000 000.00 0.00 000.00 0.0000 IC H62 C6 O2 P1 0.0000 000.00 120.00 000.00 0.0000 IC H63 C6 O2 P1 0.0000 000.00 -120.00 000.00 0.0000 RESI GPC 0.00 ! glycerolphosphorylcholine GROUP ! ATOM N NTL -0.60 ! ATOM C1 CTL2 -0.10 ! | ATOM C2 CTL5 -0.35 ! -C3- ATOM C3 CTL5 -0.35 ! | ATOM C4 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! -C2---N---C4- (+) ATOM H12 HL 0.25 ! | | | ATOM H21 HL 0.25 ! | ATOM H22 HL 0.25 ! -C1- ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! | ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ! | ATOM H42 HL 0.25 ! | ATOM H43 HL 0.25 ! | GROUP ! | ATOM C5 CTL2 -0.08 ! | ATOM H51 HAL2 0.09 ! H51---C5---H52 ATOM H52 HAL2 0.09 ! | ATOM P PL 1.50 ! (-) O3 O1 ATOM O3 O2L -0.78 ! \ / ATOM O4 O2L -0.78 ! P (+) ATOM O1 OSL -0.57 ! / \ ATOM O2 OSL -0.57 ! (-) O4 O2 ATOM CG1 CTL2 -0.08 ! | ATOM HG11 HAL2 0.09 ! HG11-CG1-HG12 ATOM HG12 HAL2 0.09 ! | GROUP ! | ATOM CG2 CTL1 0.14 ! | ATOM HG21 HAL1 0.09 ! HG21-CG2-OG2-HO2 ATOM OG2 OHL -0.66 ! | ATOM HO2 HOL 0.43 ! | GROUP ! | ATOM CG3 CTL2 0.05 ! | ATOM HG31 HAL2 0.09 ! HG31-CG3-OG3-HO3 ATOM HG32 HAL2 0.09 ! | ATOM OG3 OHL -0.66 ! HG32 ATOM HO3 HOL 0.43 ! BOND CG1 O2 CG1 HG11 CG1 HG12 BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2 BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3 BOND N C1 N C2 N C3 N C4 BOND C1 H11 C1 H12 C1 C5 BOND C2 H21 C2 H22 C2 H23 BOND C3 H31 C3 H32 C3 H33 BOND C4 H41 C4 H42 C4 H43 BOND C5 H51 C5 H52 BOND P O1 P O2 P O3 P O4 O1 C5 ! internal coordinates for analysis ! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650, 21-51 (1981) ! glycerol backbone IC O2 CG1 CG2 CG3 0. 0. 0. 0. 0. ! t1 IC O2 CG1 CG2 OG2 0. 0. 0. 0. 0. ! t2 IC CG1 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 IC OG2 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3 ! ! zwitterionic headgroup IC P O2 CG1 CG2 0. 0. 0. 0. 0. ! a1 IC O1 P O2 CG1 0. 0. 0. 0. 0. ! a2 IC O2 P O1 C5 0. 0. 0. 0. 0. ! a3 IC C1 C5 O1 P 0. 0. 0. 0. 0. ! a4 IC N C1 C5 O1 0. 0. 0. 0. 0. ! a5 IC C2 N C1 C5 0. 0. 0. 0. 0. ! a6 IC C3 N C1 C5 0. 0. 0. 0. 0. ! a6 IC C4 N C1 C5 0. 0. 0. 0. 0. ! a6 IC O1 O2 *P O3 0. 0. 120. 0. 0. IC O1 O2 *P O4 0. 0. -120. 0. 0. RESI LPPC 0.00 ! deoxylysophosphatidylcholine ! Polar Head and glycerol backbone GROUP ! H15B ATOM N NTL -0.60 ! | ATOM C13 CTL5 -0.35 ! H15A-C15-H15C ATOM H13A HL 0.25 ! | ATOM H13B HL 0.25 ! H13B | H14A ATOM H13C HL 0.25 ! | | | ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) ATOM H14A HL 0.25 ! | | | ATOM H14B HL 0.25 ! H13C | H14C ATOM H14C HL 0.25 ! | ATOM C15 CTL5 -0.35 ! | ATOM H15A HL 0.25 ! | alpha6 ATOM H15B HL 0.25 ! | ATOM H15C HL 0.25 ! | ATOM C12 CTL2 -0.10 ! H12A--C12---H12B ATOM H12A HL 0.25 ! | ATOM H12B HL 0.25 ! | GROUP ! alpha5 ATOM C11 CTL2 -0.08 ! | ATOM H11A HAL2 0.09 ! H11A--C11---H11B ATOM H11B HAL2 0.09 ! | alpha4 ATOM P PL 1.50 ! (-) O13 O12 ATOM O13 O2L -0.78 ! \ / alpha3 ATOM O14 O2L -0.78 ! P (+) ATOM O11 OSL -0.57 ! / \ alpha2 ATOM O12 OSL -0.57 ! (-) O14 O11 ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! HA---C1---HB ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL2 -0.18 ! HR---C2----HS ATOM HS HAL2 0.09 ! | ATOM HR HAL2 0.09 ! | GROUP ! | ATOM C3 CTL2 -0.05 ! HX---C3---HY ATOM HX HAL2 0.09 ! | ATOM HY HAL2 0.09 ! | gamma1 ATOM O31 OSL -0.34 ! O32 O31 ATOM C31 CL 0.63 ! \\ / gamma2 ATOM O32 OBL -0.52 ! C31 ATOM C32 CTL2 -0.08 ! | gamma3 ATOM H2X HAL2 0.09 ! H2X---C32---H2Y ATOM H2Y HAL2 0.09 ! | GROUP ! ATOM C33 CTL2 -0.18 ! | ATOM H3X HAL2 0.09 ! H3X---C33---H3Y ATOM H3Y HAL2 0.09 ! | GROUP ! ATOM C34 CTL2 -0.18 ! | ATOM H4X HAL2 0.09 ! H4X---C34---H4Y ATOM H4Y HAL2 0.09 ! | GROUP ! ATOM C35 CTL2 -0.18 ! | ATOM H5X HAL2 0.09 ! H5X---C35---H5Y ATOM H5Y HAL2 0.09 ! | GROUP ! ATOM C36 CTL2 -0.18 ! | ATOM H6X HAL2 0.09 ! H6X---C36---H6Y ATOM H6Y HAL2 0.09 ! | GROUP ! ATOM C37 CTL2 -0.18 ! | ATOM H7X HAL2 0.09 ! H7X---C37---H7Y ATOM H7Y HAL2 0.09 ! | GROUP ! ATOM C38 CTL2 -0.18 ! | ATOM H8X HAL2 0.09 ! H8X---C38---H8Y ATOM H8Y HAL2 0.09 ! | GROUP ! ATOM C39 CTL2 -0.18 ! | ATOM H9X HAL2 0.09 ! H9X---C39---H9Y ATOM H9Y HAL2 0.09 ! | GROUP ! ATOM C310 CTL2 -0.18 ! | ATOM H10X HAL2 0.09 ! H10X---C310--H10Y ATOM H10Y HAL2 0.09 ! | GROUP ! ATOM C311 CTL2 -0.18 ! | ATOM H11X HAL2 0.09 ! H11X---C311--H11Y ATOM H11Y HAL2 0.09 ! | GROUP ! ATOM C312 CTL3 -0.27 ! | ATOM H12X HAL3 0.09 ! H12X---C312--H12Y ATOM H12Y HAL3 0.09 ! | ATOM H12Z HAL3 0.09 ! H12Z ! ! Polar Head BOND N C13 N C14 N C15 BOND C13 H13A C13 H13B C13 H13C BOND C14 H14A C14 H14B C14 H14C BOND C15 H15A C15 H15B C15 H15C BOND N C12 BOND C12 H12A C12 H12B C12 C11 BOND C11 H11A C11 H11B C11 O12 BOND O12 P P O11 P O13 P O14 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 C1 O11 BOND C2 HS C2 HR C2 C3 BOND C3 HX C3 HY C3 O31 ! Chain #3 BOND O31 C31 BOND C31 C32 DOUBLE C31 O32 BOND C32 H2X C32 H2Y C32 C33 BOND C33 H3X C33 H3Y C33 C34 BOND C34 H4X C34 H4Y C34 C35 BOND C35 H5X C35 H5Y C35 C36 BOND C36 H6X C36 H6Y C36 C37 BOND C37 H7X C37 H7Y C37 C38 BOND C38 H8X C38 H8Y C38 C39 BOND C39 H9X C39 H9Y C39 C310 BOND C310 H10X C310 H10Y C310 C311 BOND C311 H11X C311 H11Y C311 C312 BOND C312 H12X C312 H12Y C312 H12Z IMPR C31 O31 C32 O32 ! Polar head (angle names from Sundaralingam) IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3 IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0 IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0 IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4 IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0 IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0 IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5 IC C11 C12 N C13 0.0 0.0 180.0 0.0 0.0 !alpha6 IC C12 C13 *N C14 0.0 0.0 120.0 0.0 0.0 IC C12 C13 *N C15 0.0 0.0 240.0 0.0 0.0 ! Glycerol IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3 ! Chain 3 IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1 IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2 IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3 IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0 IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4 IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5 IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6 IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7 IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8 IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9 IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10 IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11 IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12 RESI ETAM 1.00 ! ethanolamine GROUP ! ATOM N NH3L -0.30 ! HN2 ATOM HN1 HCL 0.33 ! | ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 ATOM HN3 HCL 0.33 ! | ATOM C1 CTL2 0.13 ! | ATOM H11 HAL2 0.09 ! H12---C1---H11 ATOM H12 HAL2 0.09 ! | GROUP ! | ATOM C5 CTL2 0.05 ! | ATOM H51 HAL2 0.09 ! H52---C5---H51 ATOM H52 HAL2 0.09 ! | ATOM OH1 OHL -0.66 ! OH1---HO1 ATOM HO1 HOL 0.43 ! BOND N HN1 N HN2 N HN3 N C1 BOND C1 H11 C1 H12 C1 C5 BOND C5 H51 C5 H52 BOND C5 OH1 OH1 HO1 ! HF/6-31G* OPTIMIZED STRUCTURE: IC N C1 C5 OH1 1.5084 107.86 48.44 104.92 1.3987 IC C1 C5 OH1 HO1 1.5191 104.92 173.19 111.99 0.9495 IC HN1 N C1 C5 1.0145 108.35 -49.03 107.86 1.5191 IC HN2 N C1 C5 1.0107 112.05 69.23 107.86 1.5191 IC HN3 N C1 C5 1.0102 112.39 -169.37 107.86 1.5191 IC N C5 *C1 H11 0.0000 000.00 120.00 000.00 0.0000 IC N C5 *C1 H12 0.0000 000.00 -120.00 000.00 0.0000 IC OH1 C1 *C5 H51 0.0000 000.00 120.00 000.00 0.0000 IC OH1 C1 *C5 H52 0.0000 000.00 -120.00 000.00 0.0000 RESI GPE 0.00 ! L-alpha-glycerylphosphorylethanolamine ! GROUP ! ATOM N NH3L -0.30 ! HN2 ATOM HN1 HCL 0.33 ! | ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 ATOM HN3 HCL 0.33 ! | ATOM C12 CTL2 0.13 ! | ATOM H12A HAL2 0.09 ! H12A--C12---H12B ATOM H12B HAL2 0.09 ! | GROUP ! | alpha5 ATOM C11 CTL2 -0.08 ! | ATOM H11A HAL2 0.09 ! H11A--C11---H11B ATOM H11B HAL2 0.09 ! | alpha4 ATOM P PL 1.50 ! (-) O13 O12 ATOM O13 O2L -0.78 ! \ / alpha3 ATOM O14 O2L -0.78 ! P (+) ATOM O11 OSL -0.57 ! / \ alpha2 ATOM O12 OSL -0.57 ! (-) O14 O11 ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! HA---C1---HB ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL1 0.14 ! | ATOM HS HAL1 0.09 ! HS-C2-OH2-HO2 ATOM OH2 OHL -0.66 ! | ATOM HO2 HOL 0.43 ! | GROUP ! | ATOM C3 CTL2 0.05 ! | ATOM HX HAL2 0.09 ! HX-C3-OH3-HO3 ATOM HY HAL2 0.09 ! | ATOM OH3 OHL -0.66 ! HY ATOM HO3 HOL 0.43 ! ! Polar Head BOND N HN1 N HN2 N HN3 N C12 BOND C12 H12A C12 H12B C12 C11 BOND C11 H11A C11 H11B C11 O12 BOND O12 P P O11 P O13 P O14 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 C1 O11 BOND C2 HS C2 C3 C2 OH2 BOND C3 HX C3 HY C3 OH3 BOND OH2 HO2 BOND OH3 HO3 ! ! Polar head (angle names from Sundaralingam) IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3 IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0 IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0 IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4 IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0 IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0 IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5 IC C11 C12 N HN1 0.0 0.0 180.0 0.0 0.0 !alpha6 IC C12 HN1 *N HN2 0.0 0.0 120.0 0.0 0.0 IC C12 HN1 *N HN3 0.0 0.0 240.0 0.0 0.0 ! Glycerol IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 IC C1 C2 C3 OH3 0.0 0.0 180.0 0.0 0.0 !theta3 IC C1 C3 *C2 OH2 0.0 0.0 -120.0 0.0 0.0 ! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S) IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0 IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0 IC OH2 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0 IC OH3 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0 IC OH3 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0 IC C1 C2 OH2 HO2 0.0 0.0 180.0 0.0 0.0 !beta1 IC C2 C3 OH3 HO3 0.0 0.0 -120.0 0.0 0.0 !gamma1 RESI DLPE 0.00 ! 1,2 dilauroyl-DL-Phosphatidylethanolamine ! ! R1 - CH2 ! | (angles and atom names from Sundaralingam) ! R2 - CH ! | ! CH2 - PO4 - CH2 - CH2 - NH3 ! ! Polar Head and glycerol backbone GROUP ! ATOM N NH3L -0.30 ! HN2 ATOM HN1 HCL 0.33 ! | ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 ATOM HN3 HCL 0.33 ! | ATOM C12 CTL2 0.13 ! | ATOM H12A HAL2 0.09 ! H12A--C12---H12B ATOM H12B HAL2 0.09 ! | GROUP ! | alpha5 ATOM C11 CTL2 -0.08 ! | ATOM H11A HAL2 0.09 ! H11A--C11---H11B ATOM H11B HAL2 0.09 ! | alpha4 ATOM P PL 1.50 ! (-) O13 O12 ATOM O13 O2L -0.78 ! \ / alpha3 ATOM O14 O2L -0.78 ! P (+) ATOM O11 OSL -0.57 ! / \ alpha2 ATOM O12 OSL -0.57 ! (-) O14 O11 ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! H1A---C1---H1B ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL1 0.04 ! HS---C2- - - - - - - ATOM HS HAL1 0.09 ! | beta1 | ATOM O21 OSL -0.34 ! O22 O21 theta3 ATOM C21 CL 0.63 ! \\ / beta2 | ATOM O22 OBL -0.52 ! C21 ATOM C22 CTL2 -0.08 ! | beta3 | ATOM H2R HAL2 0.09 ! H2R---C22---H2S ATOM H2S HAL2 0.09 ! | | GROUP ! beta4 ATOM C3 CTL2 -0.05 ! | | ATOM HX HAL2 0.09 ! HX---C3---HY ATOM HY HAL2 0.09 ! | | gamma1 ATOM O31 OSL -0.34 ! O32 O31 ATOM C31 CL 0.63 ! | \\ / gamma2 ATOM O32 OBL -0.52 ! C31 ATOM C32 CTL2 -0.08 ! | | gamma3 ATOM H2X HAL2 0.09 ! H2X---C32---H2Y ATOM H2Y HAL2 0.09 ! | | GROUP ! gamma4 ATOM C23 CTL2 -0.18 ! | | ATOM H3R HAL2 0.09 ! H3R ---C23---H3S ATOM H3S HAL2 0.09 ! | | GROUP ! ATOM C24 CTL2 -0.18 ! | ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | ATOM H4S HAL2 0.09 ! | GROUP ! ATOM C25 CTL2 -0.18 ! | | ATOM H5R HAL2 0.09 ! H5R ---C25---H5S ATOM H5S HAL2 0.09 ! | | GROUP ! ATOM C26 CTL2 -0.18 ! | ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | ATOM H6S HAL2 0.09 ! | GROUP ! ATOM C27 CTL2 -0.18 ! | | ATOM H7R HAL2 0.09 ! H7R ---C27---H7S ATOM H7S HAL2 0.09 ! | | GROUP ! ATOM C28 CTL2 -0.18 ! | ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | ATOM H8S HAL2 0.09 ! | GROUP ! ATOM C29 CTL2 -0.18 ! | | ATOM H9R HAL2 0.09 ! H9R ---C29---H9S ATOM H9S HAL2 0.09 ! | | GROUP ! ATOM C210 CTL2 -0.18 ! | ATOM H10R HAL2 0.09 ! H10R---C210--H10S | ATOM H10S HAL2 0.09 ! | GROUP ! ATOM C211 CTL2 -0.18 ! | | ATOM H11R HAL2 0.09 ! H11R---C211--H11S ATOM H11S HAL2 0.09 ! | | GROUP ! ATOM C212 CTL3 -0.27 ! | ATOM H12R HAL3 0.09 ! H12R---C212--H12S | ATOM H12S HAL3 0.09 ! | ATOM H12T HAL3 0.09 ! H12T | GROUP ! ATOM C33 CTL2 -0.18 ! | ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y ATOM H3Y HAL2 0.09 ! | GROUP ! ATOM C34 CTL2 -0.18 ! | ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y ATOM H4Y HAL2 0.09 ! | GROUP ! ATOM C35 CTL2 -0.18 ! | ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y ATOM H5Y HAL2 0.09 ! | GROUP ! ATOM C36 CTL2 -0.18 ! | ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y ATOM H6Y HAL2 0.09 ! | GROUP ! ATOM C37 CTL2 -0.18 ! | ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y ATOM H7Y HAL2 0.09 ! | GROUP ! ATOM C38 CTL2 -0.18 ! | ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y ATOM H8Y HAL2 0.09 ! | GROUP ! ATOM C39 CTL2 -0.18 ! | ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y ATOM H9Y HAL2 0.09 ! | GROUP ! ATOM C310 CTL2 -0.18 ! | ATOM H10X HAL2 0.09 ! H10X---C310--H10Y ATOM H10Y HAL2 0.09 ! | GROUP ! ATOM C311 CTL2 -0.18 ! | ATOM H11X HAL2 0.09 ! H11X---C311--H11Y ATOM H11Y HAL2 0.09 ! | GROUP ! ATOM C312 CTL3 -0.27 ! | ATOM H12X HAL3 0.09 ! H12X---C312--H12Y ATOM H12Y HAL3 0.09 ! | ATOM H12Z HAL3 0.09 ! H12Z ! Polar Head BOND N HN1 N HN2 N HN3 N C12 BOND C12 H12A C12 H12B C12 C11 BOND C11 H11A C11 H11B C11 O12 BOND O12 P P O11 P O13 P O14 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 C1 O11 BOND C2 HS C2 C3 C2 O21 BOND C3 HX C3 HY C3 O31 ! Chain #2 BOND O21 C21 BOND C21 C22 DOUBLE C21 O22 BOND C22 H2R C22 H2S C22 C23 BOND C23 H3R C23 H3S C23 C24 BOND C24 H4R C24 H4S C24 C25 BOND C25 H5R C25 H5S C25 C26 BOND C26 H6R C26 H6S C26 C27 BOND C27 H7R C27 H7S C27 C28 BOND C28 H8R C28 H8S C28 C29 BOND C29 H9R C29 H9S C29 C210 BOND C210 H10R C210 H10S C210 C211 BOND C211 H11R C211 H11S C211 C212 BOND C212 H12R C212 H12S C212 H12T ! Chain #3 BOND O31 C31 BOND C31 C32 DOUBLE C31 O32 BOND C32 H2X C32 H2Y C32 C33 BOND C33 H3X C33 H3Y C33 C34 BOND C34 H4X C34 H4Y C34 C35 BOND C35 H5X C35 H5Y C35 C36 BOND C36 H6X C36 H6Y C36 C37 BOND C37 H7X C37 H7Y C37 C38 BOND C38 H8X C38 H8Y C38 C39 BOND C39 H9X C39 H9Y C39 C310 BOND C310 H10X C310 H10Y C310 C311 BOND C311 H11X C311 H11Y C311 C312 BOND C312 H12X C312 H12Y C312 H12Z IMPR C21 O21 C22 O22 C31 O31 C32 O32 ! Polar head (angle names from Sundaralingam) IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3 IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0 IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0 IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4 IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0 IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0 IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5 IC C11 C12 N HN1 0.0 0.0 180.0 0.0 0.0 !alpha6 IC C12 HN1 *N HN2 0.0 0.0 120.0 0.0 0.0 IC C12 HN1 *N HN3 0.0 0.0 240.0 0.0 0.0 ! Glycerol IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3 IC C1 C3 *C2 O21 0.0 0.0 -120.0 0.0 0.0 ! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S) IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0 IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0 IC O21 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0 IC O31 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0 IC O31 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0 ! Chain 1 IC C1 C2 O21 C21 0.0 0.0 180.0 0.0 0.0 !beta1 IC C2 O21 C21 C22 0.0 0.0 120.0 0.0 0.0 !beta2 IC O21 C21 C22 C23 0.0 0.0 180.0 0.0 0.0 !beta3 IC C22 O21 *C21 O22 0.0 0.0 180.0 0.0 0.0 IC C21 C22 C23 C24 0.0 0.0 180.0 0.0 0.0 !beta4 IC C22 C23 C24 C25 0.0 0.0 180.0 0.0 0.0 !beta5 IC C23 C24 C25 C26 0.0 0.0 180.0 0.0 0.0 !beta6 IC C24 C25 C26 C27 0.0 0.0 180.0 0.0 0.0 !beta7 IC C25 C26 C27 C28 0.0 0.0 180.0 0.0 0.0 !beta8 IC C26 C27 C28 C29 0.0 0.0 180.0 0.0 0.0 !beta9 IC C27 C28 C29 C210 0.0 0.0 180.0 0.0 0.0 !beta10 IC C28 C29 C210 C211 0.0 0.0 180.0 0.0 0.0 !beta11 IC C29 C210 C211 C212 0.0 0.0 180.0 0.0 0.0 !beta12 ! Chain 2 IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1 IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2 IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3 IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0 IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4 IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5 IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6 IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7 IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8 IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9 IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10 IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11 IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12 RESI DMPC 0.00 ! 1,2 dimiristoyl-SN-glycero-3-Phosphorylcholine ! ! R1 - CH2 ! | (angles and atom names from Sundaralingam) ! R2 - CH ! | ! CH2 - PO4 - CH2 - CH2 - N(CH3)3 ! ! Polar Head and glycerol backbone GROUP ! H15B ATOM N NTL -0.60 ! | ATOM C13 CTL5 -0.35 ! H15A-C15-H15C ATOM H13A HL 0.25 ! | ATOM H13B HL 0.25 ! H13B | H14A ATOM H13C HL 0.25 ! | | | ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+) ATOM H14A HL 0.25 ! | | | ATOM H14B HL 0.25 ! H13C | H14C ATOM H14C HL 0.25 ! | ATOM C15 CTL5 -0.35 ! | ATOM H15A HL 0.25 ! | alpha6 ATOM H15B HL 0.25 ! | ATOM H15C HL 0.25 ! | ATOM C12 CTL2 -0.10 ! H12A--C12---H12B ATOM H12A HL 0.25 ! | ATOM H12B HL 0.25 ! | GROUP ! alpha5 ATOM C11 CTL2 -0.08 ! | ATOM H11A HAL2 0.09 ! H11A--C11---H11B ATOM H11B HAL2 0.09 ! | alpha4 ATOM P PL 1.50 ! (-) O13 O12 ATOM O13 O2L -0.78 ! \ / alpha3 ATOM O14 O2L -0.78 ! P (+) ATOM O11 OSL -0.57 ! / \ alpha2 ATOM O12 OSL -0.57 ! (-) O14 O11 ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! HA---C1---HB ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL1 0.04 ! HS---C2- - - - - - - ATOM HS HAL1 0.09 ! | beta1 | ATOM O21 OSL -0.34 ! O22 O21 theta3 ATOM C21 CL 0.63 ! \\ / beta2 | ATOM O22 OBL -0.52 ! C21 ATOM C22 CTL2 -0.08 ! | beta3 | ATOM H2R HAL2 0.09 ! H2R---C22---H2S ATOM H2S HAL2 0.09 ! | | GROUP ! beta4 ATOM C3 CTL2 -0.05 ! | | ATOM HX HAL2 0.09 ! HX---C3---HY ATOM HY HAL2 0.09 ! | | gamma1 ATOM O31 OSL -0.34 ! O32 O31 ATOM C31 CL 0.63 ! | \\ / gamma2 ATOM O32 OBL -0.52 ! C31 ATOM C32 CTL2 -0.08 ! | | gamma3 ATOM H2X HAL2 0.09 ! H2X---C32---H2Y ATOM H2Y HAL2 0.09 ! | | GROUP ! gamma4 ATOM C23 CTL2 -0.18 ! | | ATOM H3R HAL2 0.09 ! H3R ---C23---H3S ATOM H3S HAL2 0.09 ! | | GROUP ! ATOM C24 CTL2 -0.18 ! | ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | ATOM H4S HAL2 0.09 ! | GROUP ! ATOM C25 CTL2 -0.18 ! | | ATOM H5R HAL2 0.09 ! H5R ---C25---H5S ATOM H5S HAL2 0.09 ! | | GROUP ! ATOM C26 CTL2 -0.18 ! | ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | ATOM H6S HAL2 0.09 ! | GROUP ! ATOM C27 CTL2 -0.18 ! | | ATOM H7R HAL2 0.09 ! H7R ---C27---H7S ATOM H7S HAL2 0.09 ! | | GROUP ! ATOM C28 CTL2 -0.18 ! | ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | ATOM H8S HAL2 0.09 ! | GROUP ! ATOM C29 CTL2 -0.18 ! | | ATOM H9R HAL2 0.09 ! H9R ---C29---H9S ATOM H9S HAL2 0.09 ! | | GROUP ! ATOM C210 CTL2 -0.18 ! | ATOM H10R HAL2 0.09 ! H10R---C210--H10S | ATOM H10S HAL2 0.09 ! | GROUP ! ATOM C211 CTL2 -0.18 ! | | ATOM H11R HAL2 0.09 ! H11R---C211--H11S ATOM H11S HAL2 0.09 ! | | GROUP ! ATOM C212 CTL2 -0.18 ! | ATOM H12R HAL2 0.09 ! H12R---C212--H12S | ATOM H12S HAL2 0.09 ! | GROUP ! ATOM C213 CTL2 -0.18 ! | | ATOM H13R HAL2 0.09 ! H13R---C213--H13S ATOM H13S HAL2 0.09 ! | | GROUP ! ATOM C214 CTL3 -0.27 ! | ATOM H14R HAL3 0.09 ! H14R---C214--H14S | ATOM H14S HAL3 0.09 ! | ATOM H14T HAL3 0.09 ! H14T | GROUP ! ATOM C33 CTL2 -0.18 ! | ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y ATOM H3Y HAL2 0.09 ! | GROUP ! ATOM C34 CTL2 -0.18 ! | ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y ATOM H4Y HAL2 0.09 ! | GROUP ! ATOM C35 CTL2 -0.18 ! | ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y ATOM H5Y HAL2 0.09 ! | GROUP ! ATOM C36 CTL2 -0.18 ! | ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y ATOM H6Y HAL2 0.09 ! | GROUP ! ATOM C37 CTL2 -0.18 ! | ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y ATOM H7Y HAL2 0.09 ! | GROUP ! ATOM C38 CTL2 -0.18 ! | ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y ATOM H8Y HAL2 0.09 ! | GROUP ! ATOM C39 CTL2 -0.18 ! | ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y ATOM H9Y HAL2 0.09 ! | GROUP ! ATOM C310 CTL2 -0.18 ! | ATOM H10X HAL2 0.09 ! H10X---C310--H10Y ATOM H10Y HAL2 0.09 ! | GROUP ! ATOM C311 CTL2 -0.18 ! | ATOM H11X HAL2 0.09 ! H11X---C311--H11Y ATOM H11Y HAL2 0.09 ! | GROUP ! ATOM C312 CTL2 -0.18 ! | ATOM H12X HAL2 0.09 ! H12X---C312--H12Y ATOM H12Y HAL2 0.09 ! | GROUP ! ATOM C313 CTL2 -0.18 ! | ATOM H13X HAL2 0.09 ! H13X---C313--H13Y ATOM H13Y HAL2 0.09 ! | GROUP ! ATOM C314 CTL3 -0.27 ! | ATOM H14X HAL3 0.09 ! H14X---C314--H14Y ATOM H14Y HAL3 0.09 ! | ATOM H14Z HAL3 0.09 ! H14Z ! Polar Head BOND N C13 N C14 N C15 BOND C13 H13A C13 H13B C13 H13C BOND C14 H14A C14 H14B C14 H14C BOND C15 H15A C15 H15B C15 H15C BOND N C12 BOND C12 H12A C12 H12B C12 C11 BOND C11 H11A C11 H11B C11 O12 BOND O12 P P O11 P O13 P O14 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 C1 O11 BOND C2 HS C2 C3 C2 O21 BOND C3 HX C3 HY C3 O31 ! Chain #2 BOND O21 C21 BOND C21 C22 DOUBLE C21 O22 BOND C22 H2R C22 H2S C22 C23 BOND C23 H3R C23 H3S C23 C24 BOND C24 H4R C24 H4S C24 C25 BOND C25 H5R C25 H5S C25 C26 BOND C26 H6R C26 H6S C26 C27 BOND C27 H7R C27 H7S C27 C28 BOND C28 H8R C28 H8S C28 C29 BOND C29 H9R C29 H9S C29 C210 BOND C210 H10R C210 H10S C210 C211 BOND C211 H11R C211 H11S C211 C212 BOND C212 H12R C212 H12S C212 C213 BOND C213 H13R C213 H13S C213 C214 BOND C214 H14R C214 H14S C214 H14T ! Chain #3 BOND O31 C31 BOND C31 C32 DOUBLE C31 O32 BOND C32 H2X C32 H2Y C32 C33 BOND C33 H3X C33 H3Y C33 C34 BOND C34 H4X C34 H4Y C34 C35 BOND C35 H5X C35 H5Y C35 C36 BOND C36 H6X C36 H6Y C36 C37 BOND C37 H7X C37 H7Y C37 C38 BOND C38 H8X C38 H8Y C38 C39 BOND C39 H9X C39 H9Y C39 C310 BOND C310 H10X C310 H10Y C310 C311 BOND C311 H11X C311 H11Y C311 C312 BOND C312 H12X C312 H12Y C312 C313 BOND C313 H13X C313 H13Y C313 C314 BOND C314 H14X C314 H14Y C314 H14Z IMPR C21 O21 C22 O22 C31 O31 C32 O32 ! Polar head (angle names from Sundaralingam) IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1 IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2 IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0 IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0 IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3 IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0 IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0 IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4 IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0 IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0 IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5 IC C11 C12 N C13 0.0 0.0 180.0 0.0 0.0 !alpha6 IC C12 C13 *N C14 0.0 0.0 120.0 0.0 0.0 IC C12 C13 *N C15 0.0 0.0 240.0 0.0 0.0 ! Glycerol IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1 IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3 IC C1 C3 *C2 O21 0.0 0.0 -120.0 0.0 0.0 ! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S) IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0 IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0 IC O21 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0 IC O31 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0 IC O31 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0 ! Chain 1 IC C1 C2 O21 C21 0.0 0.0 180.0 0.0 0.0 !beta1 IC C2 O21 C21 C22 0.0 0.0 120.0 0.0 0.0 !beta2 IC O21 C21 C22 C23 0.0 0.0 180.0 0.0 0.0 !beta3 IC C22 O21 *C21 O22 0.0 0.0 180.0 0.0 0.0 IC C21 C22 C23 C24 0.0 0.0 180.0 0.0 0.0 !beta4 IC C22 C23 C24 C25 0.0 0.0 180.0 0.0 0.0 !beta5 IC C23 C24 C25 C26 0.0 0.0 180.0 0.0 0.0 !beta6 IC C24 C25 C26 C27 0.0 0.0 180.0 0.0 0.0 !beta7 IC C25 C26 C27 C28 0.0 0.0 180.0 0.0 0.0 !beta8 IC C26 C27 C28 C29 0.0 0.0 180.0 0.0 0.0 !beta9 IC C27 C28 C29 C210 0.0 0.0 180.0 0.0 0.0 !beta10 IC C28 C29 C210 C211 0.0 0.0 180.0 0.0 0.0 !beta11 IC C29 C210 C211 C212 0.0 0.0 180.0 0.0 0.0 !beta12 IC C210 C211 C212 C213 0.0 0.0 180.0 0.0 0.0 !beta13 IC C211 C212 C213 C214 0.0 0.0 180.0 0.0 0.0 !beta14 ! Chain 2 IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1 IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2 IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3 IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0 IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4 IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5 IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6 IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7 IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8 IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9 IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10 IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11 IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12 IC C310 C311 C312 C313 0.0 0.0 180.0 0.0 0.0 !gamma13 IC C311 C312 C313 C314 0.0 0.0 180.0 0.0 0.0 !gamma14 RESI SDS -1.00 ! Dodecylsulphate ! based on methylsulfate GROUP ATOM S SL 1.33 ! OS2(-1) ATOM OS1 OSL -0.28 ! | ATOM OS2 O2L -0.65 ! (-) OS2--S(+2)--OS4 (-) ATOM OS3 O2L -0.65 ! | ATOM OS4 O2L -0.65 ! OS1 ATOM C1 CTL2 -0.28 ! \ ATOM H11 HAL2 0.09 ! H11-C1-H12 ATOM H12 HAL2 0.09 ! | GROUP ! | ATOM C2 CTL2 -0.18 ! H21-C2-H22 ATOM H21 HAL2 0.09 ! | ATOM H22 HAL2 0.09 ! | GROUP ! | ATOM C3 CTL2 -0.18 ! H31-C3-H32 ATOM H31 HAL2 0.09 ! | ATOM H32 HAL2 0.09 ! | GROUP ! | ATOM C4 CTL2 -0.18 ! H41-C4-H42 ATOM H41 HAL2 0.09 ! | ATOM H42 HAL2 0.09 ! | GROUP ! | ATOM C5 CTL2 -0.18 ! H51-C5-H52 ATOM H51 HAL2 0.09 ! | ATOM H52 HAL2 0.09 ! | GROUP ! | ATOM C6 CTL2 -0.18 ! H61-C6-H62 ATOM H61 HAL2 0.09 ! | ATOM H62 HAL2 0.09 ! | GROUP ! | ATOM C7 CTL2 -0.18 ! H71-C7-H72 ATOM H71 HAL2 0.09 ! | ATOM H72 HAL2 0.09 ! | GROUP ! | ATOM C8 CTL2 -0.18 ! H81-C8-H82 ATOM H81 HAL2 0.09 ! | ATOM H82 HAL2 0.09 ! | GROUP ! | ATOM C9 CTL2 -0.18 ! H91-C9-H92 ATOM H91 HAL2 0.09 ! | ATOM H92 HAL2 0.09 ! | GROUP ! | ATOM C10 CTL2 -0.18 ! H101-C10-H102 ATOM H101 HAL2 0.09 ! | ATOM H102 HAL2 0.09 ! | GROUP ! | ATOM C11 CTL2 -0.18 ! H111-C11-H112 ATOM H111 HAL2 0.09 ! | ATOM H112 HAL2 0.09 ! | GROUP ! | ATOM C12 CTL3 -0.27 ! H121-C12-H123 ATOM H121 HAL3 0.09 ! | ATOM H122 HAL3 0.09 ! H122 ATOM H123 HAL3 0.09 ! BOND S OS1 S OS2 S OS3 S OS4 BOND OS1 C1 C1 H11 C1 H12 BOND C1 C2 C2 H21 C2 H22 BOND C2 C3 C3 H31 C3 H32 BOND C3 C4 C4 H41 C4 H42 BOND C4 C5 C5 H51 C5 H52 BOND C5 C6 C6 H61 C6 H62 BOND C6 C7 C7 H71 C7 H72 BOND C7 C8 C8 H81 C8 H82 BOND C8 C9 C9 H91 C9 H92 BOND C9 C10 C10 H101 C10 H102 BOND C10 C11 C11 H111 C11 H112 BOND C11 C12 C12 H121 C12 H122 C12 H123 ACCE OS1 ACCE OS2 ACCE OS3 ACCE OS4 IC C2 OS1 OS2 S 2.56 179.99 0.0 40.1 0.00 IC OS1 OS2 *S OS3 2.37 40.1 120.0 0.00 0.00 IC OS1 OS2 *S OS4 2.37 40.1 -120.0 0.00 0.00 IC OS2 S OS1 C1 0.00 0.00 180.0 0.00 0.00 IC OS4 S OS2 OS1 1.4530 113.50 -113.75 40.11 2.3733 IC OS2 S OS2 OS3 1.4522 0.00 0.00 33.26 2.4296 IC OS3 S OS1 OS4 1.4530 105.51 121.17 35.54 2.4088 IC OS1 S OS3 OS2 1.5716 105.51 112.45 33.24 2.4296 IC C1 OS1 S OS2 1.4263 114.59 -180.00 103.34 1.4522 IC S OS1 C1 OS3 1.5716 114.59 -30.52 56.05 2.8947 IC OS1 S OS4 OS2 1.5716 105.51 -112.45 33.24 2.4296 IC OS1 S OS2 OS3 1.5716 103.34 -113.75 33.26 2.4296 IC OS1 S OS3 OS2 1.5716 105.51 112.45 33.24 2.4296 IC OS4 S OS2 OS1 1.4530 113.50 -113.75 40.11 2.3733 IC OS4 S OS3 OS1 1.4530 114.15 115.37 38.95 2.4088 IC OS3 S OS2 OS1 1.4530 113.50 113.75 40.11 2.3733 IC OS4 S OS1 C1 1.4530 105.51 -60.58 114.59 1.4263 IC OS2 S OS1 C1 1.4522 103.34 -180.00 114.59 1.4263 IC OS3 S OS1 C1 1.4530 105.51 60.58 114.59 1.4263 ! REMAINDER IS ALL TRANS IC S OS1 C1 C2 0.0 0.00 180.00 0.0 0.0 IC OS1 C1 C2 C3 0.0 0.00 180.00 0.0 0.0 IC C1 C2 C3 C4 0.0 0.00 180.00 0.0 0.0 IC C2 C3 C4 C5 0.0 0.00 180.00 0.0 0.0 IC C3 C4 C5 C6 0.0 0.00 180.00 0.0 0.0 IC C4 C5 C6 C7 0.0 0.00 180.00 0.0 0.0 IC C5 C6 C7 C8 0.0 0.00 180.00 0.0 0.0 IC C6 C7 C8 C9 0.0 0.00 180.00 0.0 0.0 IC C7 C8 C9 C10 0.0 0.00 180.00 0.0 0.0 IC C8 C9 C10 C11 0.0 0.00 180.00 0.0 0.0 IC C9 C10 C11 C12 0.0 0.00 180.00 0.0 0.0 IC OS1 C2 *C1 H11 0.0 0.00 120.00 0.0 0.0 IC OS1 C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0 IC C1 C3 *C2 H21 0.0 0.00 120.00 0.0 0.0 IC C1 C3 *C2 H22 0.0 0.00 -120.00 0.0 0.0 IC C2 C4 *C3 H31 0.0 0.00 120.00 0.0 0.0 IC C2 C4 *C3 H32 0.0 0.00 -120.00 0.0 0.0 IC C3 C5 *C4 H41 0.0 0.00 120.00 0.0 0.0 IC C3 C5 *C4 H42 0.0 0.00 -120.00 0.0 0.0 IC C4 C6 *C5 H51 0.0 0.00 120.00 0.0 0.0 IC C4 C6 *C5 H52 0.0 0.00 -120.00 0.0 0.0 IC C5 C7 *C6 H61 0.0 0.00 120.00 0.0 0.0 IC C5 C7 *C6 H62 0.0 0.00 -120.00 0.0 0.0 IC C6 C8 *C7 H71 0.0 0.00 120.00 0.0 0.0 IC C6 C8 *C7 H72 0.0 0.00 -120.00 0.0 0.0 IC C7 C9 *C8 H81 0.0 0.00 120.00 0.0 0.0 IC C7 C9 *C8 H82 0.0 0.00 -120.00 0.0 0.0 IC C8 C10 *C9 H91 0.0 0.00 120.00 0.0 0.0 IC C8 C10 *C9 H92 0.0 0.00 -120.00 0.0 0.0 IC C9 C11 *C10 H101 0.0 0.00 120.00 0.0 0.0 IC C9 C11 *C10 H102 0.0 0.00 -120.00 0.0 0.0 IC C10 C12 *C11 H111 0.0 0.00 120.00 0.0 0.0 IC C10 C12 *C11 H112 0.0 0.00 -120.00 0.0 0.0 IC C10 C11 C12 H121 0.0 0.00 180.00 0.0 0.0 IC C11 H121 *C12 H122 0.0 0.00 120.00 0.0 0.0 IC C11 H121 *C12 H123 0.0 0.00 -120.00 0.0 0.0 RESI POPC 0.00 ! 1-palmytoil-2-oleoyl-sn-glycero- ! 3-Phosphatidylcholine ! ! (May 14, 1999 Carlos F. Lopez) ! No IC's (read in coordinates from file) ! ! Palmytoil - CH2 ! | ! Oleyl - CH ! | (-) (+) ! CH2 - PO4 - CH2 - CH2 - N-(CH3)3 ! ! Polar Head and glycerol backbone GROUP ! H31 ATOM N NTL -0.60 ! | ATOM C11 CTL2 -0.10 ! H33-C13-H32 ATOM C12 CTL5 -0.35 ! | ATOM C13 CTL5 -0.35 ! H21 | H43 ATOM C14 CTL5 -0.35 ! | | | ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+) ATOM H12 HL 0.25 ! | | | ATOM H21 HL 0.25 ! H23 | H41 ATOM H22 HL 0.25 ! | ATOM H23 HL 0.25 ! | ATOM H31 HL 0.25 ! | ATOM H32 HL 0.25 ! H11-C11-H12 ATOM H33 HL 0.25 ! | ATOM H41 HL 0.25 ! | ATOM H42 HL 0.25 ! | ATOM H43 HL 0.25 ! | GROUP ! | ATOM C15 CTL2 -0.08 ! | ATOM H51 HAL2 0.09 ! H51---C15---H52 ATOM H52 HAL2 0.09 ! | GROUP ! | ATOM P1 PL 1.50 ! (-) O3 O1 ATOM O3 O2L -0.78 ! \ / ATOM O4 O2L -0.78 ! P1 (+) ATOM O1 OSL -0.57 ! / \ ATOM O2 OSL -0.57 ! (-) O4 O2 GROUP ! | ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! HA---C1---HB ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL1 0.04 ! HS---C2-------------- ATOM HS HAL1 0.09 ! | beta1 | ATOM O21 OSL -0.34 ! O22 O21 theta3 ATOM C21 CL 0.63 ! \\ / beta2 | ATOM O22 OBL -0.52 ! C21 | ATOM C22 CTL2 -0.08 ! | beta3 | ATOM H2R HAL2 0.09 ! H2R---C22---H2S | ATOM H2S HAL2 0.09 ! | | GROUP ! | beta4 | ATOM C3 CTL2 -0.05 ! | | ATOM HX HAL2 0.09 ! | HX---C3---HY ATOM HY HAL2 0.09 ! | | gamma1 ATOM O31 OSL -0.34 ! | O32 O31 ATOM C31 CL 0.63 ! | \\ / gamma2 ATOM O32 OBL -0.52 ! | C31 ATOM C32 CTL2 -0.08 ! | | gamma3 ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y ATOM H2Y HAL2 0.09 ! | | GROUP ! | | gamma4 ATOM C23 CTL2 -0.18 ! | | ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | ATOM H3S HAL2 0.09 ! | | GROUP ! | | ATOM C24 CTL2 -0.18 ! | | ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | ATOM H4S HAL2 0.09 ! | | GROUP ! | | ATOM C25 CTL2 -0.18 ! | | ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | ATOM H5S HAL2 0.09 ! | | GROUP ! | | ATOM C26 CTL2 -0.18 ! | | ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | ATOM H6S HAL2 0.09 ! | | GROUP ! | | ATOM C27 CTL2 -0.18 ! | | ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | ATOM H7S HAL2 0.09 ! | | GROUP ! | | ATOM C28 CTL2 -0.18 ! | | ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | ATOM H8S HAL2 0.09 ! | | GROUP ! | | ATOM C29 CEL1 -0.15 ! | | ATOM H91 HEL1 0.15 ! H91 ---C29 | GROUP ! || (CIS) | ATOM C210 CEL1 -0.15 ! || | ATOM H101 HEL1 0.15 ! H101---C210 | GROUP ! | | ATOM C211 CTL2 -0.18 ! | | ATOM H11R HAL2 0.09 ! H11R---C211--H11S | ATOM H11S HAL2 0.09 ! | | GROUP ! | | ATOM C212 CTL2 -0.18 ! | | ATOM H12R HAL2 0.09 ! H12R---C212--H12S | ATOM H12S HAL2 0.09 ! | | GROUP ! | | ATOM C213 CTL2 -0.18 ! | | ATOM H13R HAL2 0.09 ! H13R---C213--H13S | ATOM H13S HAL2 0.09 ! | | GROUP ! | | ATOM C214 CTL2 -0.18 ! | | ATOM H14R HAL2 0.09 ! H14R---C214--H14S | ATOM H14S HAL2 0.09 ! | | GROUP ! | | ATOM C215 CTL2 -0.18 ! | | ATOM H15R HAL2 0.09 ! H15R---C215--H15S | ATOM H15S HAL2 0.09 ! | | GROUP ! | | ATOM C216 CTL2 -0.18 ! | | ATOM H16R HAL2 0.09 ! H16R---C216--H16S | ATOM H16S HAL2 0.09 ! | | GROUP ! | | ATOM C217 CTL2 -0.18 ! | | ATOM H17R HAL2 0.09 ! H17R---C217--H17S | ATOM H17S HAL2 0.09 ! | | GROUP ! | | ATOM C218 CTL3 -0.27 ! | | ATOM H18R HAL3 0.09 ! H18R---C218--H18S | ATOM H18S HAL3 0.09 ! | | ATOM H18T HAL3 0.09 ! H18T | GROUP ! | ATOM C33 CTL2 -0.18 ! | ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y ATOM H3Y HAL2 0.09 ! | GROUP ! | ATOM C34 CTL2 -0.18 ! | ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y ATOM H4Y HAL2 0.09 ! | GROUP ! | ATOM C35 CTL2 -0.18 ! | ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y ATOM H5Y HAL2 0.09 ! | GROUP ! | ATOM C36 CTL2 -0.18 ! | ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y ATOM H6Y HAL2 0.09 ! | GROUP ! | ATOM C37 CTL2 -0.18 ! | ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y ATOM H7Y HAL2 0.09 ! | GROUP ! | ATOM C38 CTL2 -0.18 ! | ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y ATOM H8Y HAL2 0.09 ! | GROUP ! | ATOM C39 CTL2 -0.18 ! | ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y ATOM H9Y HAL2 0.09 ! | GROUP ! | ATOM C310 CTL2 -0.18 ! | ATOM H10X HAL2 0.09 ! H10X---C310--H10Y ATOM H10Y HAL2 0.09 ! | GROUP ! | ATOM C311 CTL2 -0.18 ! | ATOM H11X HAL2 0.09 ! H11X---C311--H11Y ATOM H11Y HAL2 0.09 ! | GROUP ! | ATOM C312 CTL2 -0.18 ! | ATOM H12X HAL2 0.09 ! H12X---C312--H12Y ATOM H12Y HAL2 0.09 ! | GROUP ! | ATOM C313 CTL2 -0.18 ! | ATOM H13X HAL2 0.09 ! H13X---C313--H13Y ATOM H13Y HAL2 0.09 ! | GROUP ! | ATOM C314 CTL2 -0.18 ! | ATOM H14X HAL2 0.09 ! H14X---C314--H14Y ATOM H14Y HAL2 0.09 ! | GROUP ! | ATOM C315 CTL2 -0.18 ! | ATOM H15X HAL2 0.09 ! H15X---C315--H15Y ATOM H15Y HAL2 0.09 ! | GROUP ! | ATOM C316 CTL3 -0.27 ! | ATOM H16X HAL3 0.09 ! H16X---C316--H16Y ATOM H16Y HAL3 0.09 ! | ATOM H16Z HAL3 0.09 ! H16Z !BONDING FROM PC BOND N C11 N C12 N C13 N C14 BOND C11 H11 C11 H12 C11 C15 BOND C12 H21 C12 H22 C12 H23 BOND C13 H31 C13 H32 C13 H33 BOND C14 H41 C14 H42 C14 H43 BOND C15 H51 C15 H52 BOND P1 O1 P1 O2 P1 O3 P1 O4 BOND O1 C15 O2 C1 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 BOND C2 HS C2 C3 C2 O21 BOND C3 HX C3 HY C3 O31 ! Chain from C2 BOND O21 C21 BOND C21 C22 DOUBLE C21 O22 BOND C22 H2R C22 H2S C22 C23 BOND C23 H3R C23 H3S C23 C24 BOND C24 H4R C24 H4S C24 C25 BOND C25 H5R C25 H5S C25 C26 BOND C26 H6R C26 H6S C26 C27 BOND C27 H7R C27 H7S C27 C28 BOND C28 H8R C28 H8S C28 C29 BOND C29 H91 DOUBLE C29 C210 BOND C210 H101 C210 C211 BOND C211 H11R C211 H11S C211 C212 BOND C212 H12R C212 H12S C212 C213 BOND C213 H13R C213 H13S C213 C214 BOND C214 H14R C214 H14S C214 C215 BOND C215 H15R C215 H15S C215 C216 BOND C216 H16R C216 H16S C216 C217 BOND C217 H17R C217 H17S C217 C218 BOND C218 H18R C218 H18S C218 H18T ! Chain From C3 BOND O31 C31 BOND C31 C32 DOUBLE C31 O32 BOND C32 H2X C32 H2Y C32 C33 BOND C33 H3X C33 H3Y C33 C34 BOND C34 H4X C34 H4Y C34 C35 BOND C35 H5X C35 H5Y C35 C36 BOND C36 H6X C36 H6Y C36 C37 BOND C37 H7X C37 H7Y C37 C38 BOND C38 H8X C38 H8Y C38 C39 BOND C39 H9X C39 H9Y C39 C310 BOND C310 H10X C310 H10Y C310 C311 BOND C311 H11X C311 H11Y C311 C312 BOND C312 H12X C312 H12Y C312 C313 BOND C313 H13X C313 H13Y C313 C314 BOND C314 H14X C314 H14Y C314 C315 BOND C315 H15X C315 H15Y C315 C316 BOND C316 H16X C316 H16Y C316 H16Z IMPR C21 O21 C22 O22 C31 O31 C32 O32 !IC table from IC generate, geometry is guessed IC C12 C11 *N C13 1.4999 109.15 122.15 111.71 1.4949 IC C12 C11 *N C14 1.4999 109.15 -116.51 109.19 1.5011 IC C12 N C11 C15 1.4999 109.15 43.57 118.04 1.5524 IC C15 N *C11 H11 1.5524 118.04 -121.93 109.13 1.0811 IC H11 N *C11 H12 1.0811 109.13 -117.56 108.83 1.0835 IC C11 N C12 H21 1.5284 109.15 -59.57 108.41 1.0953 IC H21 N *C12 H22 1.0953 108.41 -116.60 113.14 1.0854 IC H21 N *C12 H23 1.0953 108.41 118.64 112.84 1.0777 IC C11 N C13 H31 1.5284 111.71 -61.34 110.98 1.0826 IC H31 N *C13 H32 1.0826 110.98 121.24 110.98 1.0826 IC H31 N *C13 H33 1.0826 110.98 -119.19 110.09 1.0845 IC C11 N C14 H41 1.5284 109.19 173.62 112.23 1.0785 IC H41 N *C14 H42 1.0785 112.23 125.69 112.79 1.0778 IC H41 N *C14 H43 1.0785 112.23 -117.12 108.08 1.0983 IC N C11 C15 O1 1.5284 118.04 63.61 111.07 1.4249 IC O1 C11 *C15 H51 1.4249 111.07 -126.47 109.40 1.1165 IC H51 C11 *C15 H52 1.1165 109.40 -115.09 108.53 1.1137 IC C11 C15 O1 P1 1.5524 111.07 -132.50 121.66 1.5873 IC C15 O1 P1 O2 1.4249 121.66 95.32 99.37 1.5870 IC O2 O1 *P1 O3 1.5870 99.37 -113.40 108.96 1.4773 IC O2 O1 *P1 O4 1.5870 99.37 114.27 109.52 1.4735 IC O1 P1 O2 C1 1.5873 99.37 -136.11 119.34 1.4276 IC P1 O2 C1 C2 1.5870 119.34 -174.88 109.28 1.5468 IC C2 O2 *C1 HA 1.5468 109.28 119.70 111.34 1.1169 IC HA O2 *C1 HB 1.1169 111.34 119.72 110.33 1.1141 IC O2 C1 C2 O21 1.4276 109.28 -167.70 109.50 1.4378 IC O21 C1 *C2 C3 1.4378 109.50 -121.42 111.45 1.5543 IC C3 C1 *C2 HS 1.5543 111.45 -117.17 108.32 1.1156 IC C1 C2 O21 C21 1.5468 109.50 90.28 116.64 1.3217 IC C2 O21 C21 C22 1.4378 116.64 174.47 109.18 1.5303 IC C22 O21 *C21 O22 1.5303 109.18 -178.13 126.27 1.2213 IC O21 C21 C22 C23 1.3217 109.18 -78.33 110.83 1.5447 IC C23 C21 *C22 H2R 1.5447 110.83 121.63 109.32 1.1103 IC H2R C21 *C22 H2S 1.1103 109.32 117.81 107.94 1.1092 IC C1 C2 C3 O31 1.5468 111.45 -172.66 111.94 1.4454 IC O31 C2 *C3 HX 1.4454 111.94 -126.15 109.39 1.1150 IC HX C2 *C3 HY 1.1150 109.39 -114.93 107.39 1.1133 IC C2 C3 O31 C31 1.5543 111.94 -96.66 116.55 1.3325 IC C3 O31 C31 C32 1.4454 116.55 177.97 109.29 1.5306 IC C32 O31 *C31 O32 1.5306 109.29 -179.43 126.40 1.2162 IC O31 C31 C32 C33 1.3325 109.29 -177.61 111.07 1.5445 IC C33 C31 *C32 H2X 1.5445 111.07 120.97 108.77 1.1094 IC H2X C31 *C32 H2Y 1.1094 108.77 118.39 108.38 1.1099 IC C21 C22 C23 C24 1.5303 110.83 177.84 113.15 1.5345 IC C24 C22 *C23 H3R 1.5345 113.15 -120.52 109.51 1.1149 IC H3R C22 *C23 H3S 1.1149 109.51 -117.98 109.32 1.1137 IC C22 C23 C24 C25 1.5447 113.15 174.44 112.06 1.5345 IC C25 C23 *C24 H4R 1.5345 112.06 121.05 109.09 1.1140 IC H4R C23 *C24 H4S 1.1140 109.09 117.86 109.72 1.1131 IC C23 C24 C25 C26 1.5345 112.06 175.38 112.95 1.5340 IC C26 C24 *C25 H5R 1.5340 112.95 -121.08 109.34 1.1131 IC H5R C24 *C25 H5S 1.1131 109.34 -117.43 108.99 1.1132 IC C24 C25 C26 C27 1.5345 112.95 174.94 112.21 1.5351 IC C27 C25 *C26 H6R 1.5351 112.21 121.27 109.00 1.1134 IC H6R C25 *C26 H6S 1.1134 109.00 117.60 109.50 1.1130 IC C25 C26 C27 C28 1.5340 112.21 175.67 112.60 1.5394 IC C28 C26 *C27 H7R 1.5394 112.60 -121.40 108.58 1.1142 IC H7R C26 *C27 H7S 1.1142 108.58 -116.93 108.44 1.1140 IC C26 C27 C28 C29 1.5351 112.60 178.25 111.01 1.5083 IC C29 C27 *C28 H8R 1.5083 111.01 119.62 107.18 1.1139 IC H8R C27 *C28 H8S 1.1139 107.18 115.86 109.35 1.1118 IC C27 C28 C29 C210 1.5391 111.34 -141.40 127.31 1.3462 IC C210 C28 *C29 H91 1.3462 127.31 -176.71 114.35 1.1001 IC C28 C29 C210 C211 1.5073 127.31 1.24 127.43 1.5089 IC C211 C29 *C21 H101 1.5089 127.43 179.21 118.33 1.1011 IC C29 C210 C211 C212 1.3462 127.43 -120.91 110.88 1.5393 IC C212 C210 *C21 H11R 1.5393 110.88 121.06 112.51 1.1124 IC H11R C210 *C21 H11S 1.1124 112.51 119.00 109.81 1.1127 IC C210 C211 C212 C213 1.5089 110.88 -176.36 112.76 1.5347 IC C213 C211 *C21 H12R 1.5347 112.76 -120.93 109.33 1.1142 IC H12R C211 *C21 H12S 1.1142 109.33 -118.17 109.94 1.1138 IC C211 C212 C213 C214 1.5393 112.76 -179.47 112.21 1.5338 IC C214 C212 *C21 H13R 1.5338 112.21 121.29 109.31 1.1130 IC H13R C212 *C21 H13S 1.1130 109.31 117.74 109.05 1.1131 IC C212 C213 C214 C215 1.5347 112.21 -178.99 112.92 1.5339 IC C215 C213 *C21 H14R 1.5339 112.92 -121.37 109.00 1.1134 IC H14R C213 *C21 H14S 1.1134 109.00 -117.34 109.08 1.1132 IC C213 C214 C215 C216 1.5338 112.92 179.95 112.20 1.5339 IC C216 C214 *C21 H15R 1.5339 112.20 121.17 109.14 1.1131 IC H15R C214 *C21 H15S 1.1131 109.14 117.63 109.22 1.1132 IC C214 C215 C216 C217 1.5339 112.20 179.53 112.96 1.5328 IC C217 C215 *C21 H16R 1.5328 112.96 -121.41 109.07 1.1135 IC H16R C215 *C21 H16S 1.1135 109.07 -117.43 109.05 1.1130 IC C215 C216 C217 C218 1.5339 112.96 -179.21 113.03 1.5305 IC C218 C216 *C21 H17R 1.5305 113.03 121.55 108.80 1.1140 IC H17R C216 *C21 H17S 1.1140 108.80 116.88 108.83 1.1142 IC C216 C217 C218 H18R 1.5328 113.03 60.41 110.37 1.1113 IC H18R C217 *C21 H18S 1.1113 110.37 -119.78 110.49 1.1115 IC H18R C217 *C21 H18T 1.1113 110.37 120.07 110.59 1.1111 IC C31 C32 C33 C34 1.5333 111.40 179.66 112.54 1.5345 IC C34 C32 *C33 H3X 1.5345 112.54 -121.73 109.66 1.1133 IC H3X C32 *C33 H3Y 1.1133 109.66 -117.45 109.37 1.1151 IC C32 C33 C34 C35 1.5440 112.54 178.40 112.54 1.5346 IC C35 C33 *C34 H4X 1.5346 112.54 121.75 110.03 1.1131 IC H4X C33 *C34 H4Y 1.1131 110.03 117.75 108.84 1.1139 IC C33 C34 C35 C36 1.5345 112.54 -175.14 112.09 1.5349 IC C36 C34 *C35 H5X 1.5349 112.09 -122.26 109.27 1.1127 IC H5X C34 *C35 H5Y 1.1127 109.27 -117.42 109.08 1.1138 IC C34 C35 C36 C37 1.5346 112.09 174.19 113.84 1.5368 IC C37 C35 *C36 H6X 1.5368 113.84 122.38 109.13 1.1124 IC H6X C35 *C36 H6Y 1.1124 109.13 117.02 108.50 1.1143 IC C35 C36 C37 C38 1.5349 113.84 65.26 113.87 1.5343 IC C38 C36 *C37 H7X 1.5343 113.87 120.83 108.55 1.1137 IC H7X C36 *C37 H7Y 1.1137 108.55 116.91 109.10 1.1132 IC C36 C37 C38 C39 1.5368 113.87 178.14 112.45 1.5354 IC C39 C37 *C38 H8X 1.5354 112.45 121.43 109.97 1.1123 IC H8X C37 *C38 H8Y 1.1123 109.97 117.71 108.91 1.1127 IC C37 C38 C39 C310 1.5343 112.45 -176.66 111.96 1.5320 IC C310 C38 *C39 H9X 1.5320 111.96 120.68 109.20 1.1133 IC H9X C38 *C39 H9Y 1.1133 109.20 117.81 109.34 1.1127 IC C38 C39 C310 C311 1.5354 111.96 178.35 113.81 1.5336 IC C311 C39 *C31 H10X 1.5336 113.81 -120.14 108.22 1.1126 IC H10X C39 *C31 H10Y 1.1126 108.22 -117.07 109.45 1.1132 IC C39 C310 C311 C312 1.5320 113.81 -175.46 111.16 1.5334 IC C312 C310 *C31 H11X 1.5334 111.16 120.27 109.12 1.1138 IC H11X C310 *C31 H11Y 1.1138 109.12 118.20 110.02 1.1119 IC C310 C311 C312 C313 1.5336 111.16 173.60 113.47 1.5330 IC C313 C311 *C31 H12X 1.5330 113.47 -120.74 108.01 1.1140 IC H12X C311 *C31 H12Y 1.1140 108.01 -116.85 109.45 1.1130 IC C311 C312 C313 C314 1.5334 113.47 -174.75 111.86 1.5335 IC C314 C312 *C31 H13X 1.5335 111.86 120.28 108.66 1.1135 IC H13X C312 *C31 H13Y 1.1135 108.66 118.03 110.08 1.1125 IC C312 C313 C314 C315 1.5330 111.86 175.21 113.05 1.5325 IC C315 C313 *C31 H14X 1.5325 113.05 -120.81 108.37 1.1133 IC H14X C313 *C31 H14Y 1.1133 108.37 -117.18 109.40 1.1131 IC C313 C314 C315 C316 1.5335 113.05 -177.76 112.89 1.5300 IC C316 C314 *C31 H15X 1.5300 112.89 121.41 108.55 1.1149 IC H15X C314 *C31 H15Y 1.1149 108.55 117.05 109.21 1.1136 IC C314 C315 C316 H16X 1.5325 112.89 57.15 110.07 1.1113 IC H16X C315 *C31 H16Y 1.1113 110.07 -119.27 110.55 1.1106 IC H16X C315 *C31 H16Z 1.1113 110.07 120.81 110.70 1.1116 RESI POPE 0.00 ! 1-palmytoil-2-oleoyl-sn-glycero- ! 3-Phosphatidylethanolamine ! ! (May 14, 1999 Carlos F. Lopez) ! ! Palmytoil - CH2 ! | ! Oleyl - CH ! | ! CH2 - PO4 - CH2 - CH2 - NH3 ! ! Polar Head and glycerol backbone GROUP ! ATOM N NH3L -0.30 ! HN2 ATOM HN1 HCL 0.33 ! | ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3 ATOM HN3 HCL 0.33 ! | ATOM C12 CTL2 0.13 ! | ATOM H12A HAL2 0.09 ! H12A--C12---H12B ATOM H12B HAL2 0.09 ! | GROUP ! | alpha5 ATOM C11 CTL2 -0.08 ! | ATOM H11A HAL2 0.09 ! H11A--C11---H11B ATOM H11B HAL2 0.09 ! | alpha4 ATOM P PL 1.50 ! (-) O13 O12 ATOM O13 O2L -0.78 ! \ / alpha3 ATOM O14 O2L -0.78 ! P (+) ATOM O11 OSL -0.57 ! / \ alpha2 ATOM O12 OSL -0.57 ! (-) O14 O11 ATOM C1 CTL2 -0.08 ! | alpha1 ATOM HA HAL2 0.09 ! HA---C1---HB ATOM HB HAL2 0.09 ! | theta1 GROUP ! | ATOM C2 CTL1 0.04 ! HS---C2-------------- ATOM HS HAL1 0.09 ! | beta1 | ATOM O21 OSL -0.34 ! O22 O21 theta3 ATOM C21 CL 0.63 ! \\ / beta2 | ATOM O22 OBL -0.52 ! C21 | ATOM C22 CTL2 -0.08 ! | beta3 | ATOM H2R HAL2 0.09 ! H2R---C22---H2S | ATOM H2S HAL2 0.09 ! | | GROUP ! | beta4 | ATOM C3 CTL2 -0.05 ! | | ATOM HX HAL2 0.09 ! | HX---C3---HY ATOM HY HAL2 0.09 ! | | gamma1 ATOM O31 OSL -0.34 ! | O32 O31 ATOM C31 CL 0.63 ! | \\ / gamma2 ATOM O32 OBL -0.52 ! | C31 ATOM C32 CTL2 -0.08 ! | | gamma3 ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y ATOM H2Y HAL2 0.09 ! | | GROUP ! | | gamma4 ATOM C23 CTL2 -0.18 ! | | ATOM H3R HAL2 0.09 ! H3R ---C23---H3S | ATOM H3S HAL2 0.09 ! | | GROUP ! | | ATOM C24 CTL2 -0.18 ! | | ATOM H4R HAL2 0.09 ! H4R ---C24---H4S | ATOM H4S HAL2 0.09 ! | | GROUP ! | | ATOM C25 CTL2 -0.18 ! | | ATOM H5R HAL2 0.09 ! H5R ---C25---H5S | ATOM H5S HAL2 0.09 ! | | GROUP ! | | ATOM C26 CTL2 -0.18 ! | | ATOM H6R HAL2 0.09 ! H6R ---C26---H6S | ATOM H6S HAL2 0.09 ! | | GROUP ! | | ATOM C27 CTL2 -0.18 ! | | ATOM H7R HAL2 0.09 ! H7R ---C27---H7S | ATOM H7S HAL2 0.09 ! | | GROUP ! | | ATOM C28 CTL2 -0.18 ! | | ATOM H8R HAL2 0.09 ! H8R ---C28---H8S | ATOM H8S HAL2 0.09 ! | | GROUP ! | | ATOM C29 CEL1 -0.15 ! | | ATOM H91 HEL1 0.15 ! H91 ---C29 | GROUP ! || (CIS) | ATOM C210 CEL1 -0.15 ! || | ATOM H101 HEL1 0.15 ! H101---C210 | GROUP ! | | ATOM C211 CTL2 -0.18 ! | | ATOM H11R HAL2 0.09 ! H11R---C211--H11S | ATOM H11S HAL2 0.09 ! | | GROUP ! | | ATOM C212 CTL2 -0.18 ! | | ATOM H12R HAL2 0.09 ! H12R---C212--H12S | ATOM H12S HAL2 0.09 ! | | GROUP ! | | ATOM C213 CTL2 -0.18 ! | | ATOM H13R HAL2 0.09 ! H13R---C213--H13S | ATOM H13S HAL2 0.09 ! | | GROUP ! | | ATOM C214 CTL2 -0.18 ! | | ATOM H14R HAL2 0.09 ! H14R---C214--H14S | ATOM H14S HAL2 0.09 ! | | GROUP ! | | ATOM C215 CTL2 -0.18 ! | | ATOM H15R HAL2 0.09 ! H15R---C215--H15S | ATOM H15S HAL2 0.09 ! | | GROUP ! | | ATOM C216 CTL2 -0.18 ! | | ATOM H16R HAL2 0.09 ! H16R---C216--H16S | ATOM H16S HAL2 0.09 ! | | GROUP ! | | ATOM C217 CTL2 -0.18 ! | | ATOM H17R HAL2 0.09 ! H17R---C217--H17S | ATOM H17S HAL2 0.09 ! | | GROUP ! | | ATOM C218 CTL3 -0.27 ! | | ATOM H18R HAL3 0.09 ! H18R---C218--H18S | ATOM H18S HAL3 0.09 ! | | ATOM H18T HAL3 0.09 ! H18T | GROUP ! | ATOM C33 CTL2 -0.18 ! | ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y ATOM H3Y HAL2 0.09 ! | GROUP ! | ATOM C34 CTL2 -0.18 ! | ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y ATOM H4Y HAL2 0.09 ! | GROUP ! | ATOM C35 CTL2 -0.18 ! | ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y ATOM H5Y HAL2 0.09 ! | GROUP ! | ATOM C36 CTL2 -0.18 ! | ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y ATOM H6Y HAL2 0.09 ! | GROUP ! | ATOM C37 CTL2 -0.18 ! | ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y ATOM H7Y HAL2 0.09 ! | GROUP ! | ATOM C38 CTL2 -0.18 ! | ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y ATOM H8Y HAL2 0.09 ! | GROUP ! | ATOM C39 CTL2 -0.18 ! | ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y ATOM H9Y HAL2 0.09 ! | GROUP ! | ATOM C310 CTL2 -0.18 ! | ATOM H10X HAL2 0.09 ! H10X---C310--H10Y ATOM H10Y HAL2 0.09 ! | GROUP ! | ATOM C311 CTL2 -0.18 ! | ATOM H11X HAL2 0.09 ! H11X---C311--H11Y ATOM H11Y HAL2 0.09 ! | GROUP ! | ATOM C312 CTL2 -0.18 ! | ATOM H12X HAL2 0.09 ! H12X---C312--H12Y ATOM H12Y HAL2 0.09 ! | GROUP ! | ATOM C313 CTL2 -0.18 ! | ATOM H13X HAL2 0.09 ! H13X---C313--H13Y ATOM H13Y HAL2 0.09 ! | GROUP ! | ATOM C314 CTL2 -0.18 ! | ATOM H14X HAL2 0.09 ! H14X---C314--H14Y ATOM H14Y HAL2 0.09 ! | GROUP ! | ATOM C315 CTL2 -0.18 ! | ATOM H15X HAL2 0.09 ! H15X---C315--H15Y ATOM H15Y HAL2 0.09 ! | GROUP ! | ATOM C316 CTL3 -0.27 ! | ATOM H16X HAL3 0.09 ! H16X---C316--H16Y ATOM H16Y HAL3 0.09 ! | ATOM H16Z HAL3 0.09 ! H16Z ! Polar Head BOND N HN1 N HN2 N HN3 N C12 BOND C12 H12A C12 H12B C12 C11 BOND C11 H11A C11 H11B C11 O12 BOND O12 P P O11 P O13 P O14 ! Glycerol Backbone BOND C1 HA C1 HB C1 C2 C1 O11 BOND C2 HS C2 C3 C2 O21 BOND C3 HX C3 HY C3 O31 ! Chain from C2 BOND O21 C21 BOND C21 C22 DOUBLE C21 O22 BOND C22 H2R C22 H2S C22 C23 BOND C23 H3R C23 H3S C23 C24 BOND C24 H4R C24 H4S C24 C25 BOND C25 H5R C25 H5S C25 C26 BOND C26 H6R C26 H6S C26 C27 BOND C27 H7R C27 H7S C27 C28 BOND C28 H8R C28 H8S C28 C29 BOND C29 H91 DOUBLE C29 C210 BOND C210 H101 C210 C211 BOND C211 H11R C211 H11S C211 C212 BOND C212 H12R C212 H12S C212 C213 BOND C213 H13R C213 H13S C213 C214 BOND C214 H14R C214 H14S C214 C215 BOND C215 H15R C215 H15S C215 C216 BOND C216 H16R C216 H16S C216 C217 BOND C217 H17R C217 H17S C217 C218 BOND C218 H18R C218 H18S C218 H18T ! Chain From C3 BOND O31 C31 BOND C31 C32 DOUBLE C31 O32 BOND C32 H2X C32 H2Y C32 C33 BOND C33 H3X C33 H3Y C33 C34 BOND C34 H4X C34 H4Y C34 C35 BOND C35 H5X C35 H5Y C35 C36 BOND C36 H6X C36 H6Y C36 C37 BOND C37 H7X C37 H7Y C37 C38 BOND C38 H8X C38 H8Y C38 C39 BOND C39 H9X C39 H9Y C39 C310 BOND C310 H10X C310 H10Y C310 C311 BOND C311 H11X C311 H11Y C311 C312 BOND C312 H12X C312 H12Y C312 C313 BOND C313 H13X C313 H13Y C313 C314 BOND C314 H14X C314 H14Y C314 C315 BOND C315 H15X C315 H15Y C315 C316 BOND C316 H16X C316 H16Y C316 H16Z IMPR C21 O21 C22 O22 C31 O31 C32 O32 !IC table from IC generate, geometry is guessed IC HN1 C12 *N HN2 1.0524 110.54 127.93 115.12 1.0338 IC HN1 C12 *N HN3 1.0524 110.54 -112.33 100.76 1.0488 IC HN1 N C12 C11 1.0524 110.54 70.07 107.99 1.5341 IC C11 N *C12 H12A 1.5341 107.99 -122.80 109.40 1.1069 IC H12A N *C12 H12B 1.1069 109.40 -119.69 107.75 1.1114 IC N C12 C11 O12 1.5038 107.99 46.85 109.27 1.4315 IC O12 C12 *C11 H11A 1.4315 109.27 -121.18 109.30 1.1164 IC H11A C12 *C11 H11B 1.1164 109.30 -117.51 109.07 1.1179 IC C12 C11 O12 P 1.5341 109.27 178.59 119.49 1.5904 IC C11 O12 P O11 1.4315 119.49 104.93 100.57 1.5835 IC O11 O12 *P O13 1.5835 100.57 -114.66 107.37 1.4782 IC O11 O12 *P O14 1.5835 100.57 115.52 107.48 1.4694 IC O12 P O11 C1 1.5904 100.57 -68.41 122.45 1.4279 IC P O11 C1 C2 1.5835 122.45 113.33 109.83 1.5458 IC C2 O11 *C1 HA 1.5458 109.83 118.28 108.95 1.1134 IC HA O11 *C1 HB 1.1134 108.95 118.31 112.84 1.1153 IC O11 C1 C2 O21 1.4279 109.83 -169.38 109.43 1.4399 IC O21 C1 *C2 C3 1.4399 109.43 -120.76 111.51 1.5508 IC C3 C1 *C2 HS 1.5508 111.51 -116.85 107.06 1.1136 IC C1 C2 O21 C21 1.5458 109.43 123.06 117.42 1.3213 IC C2 O21 C21 C22 1.4399 117.42 163.64 109.74 1.5303 IC C22 O21 *C21 O22 1.5303 109.74 -176.86 126.01 1.2239 IC O21 C21 C22 C23 1.3213 109.74 -113.72 109.53 1.5428 IC C23 C21 *C22 H2R 1.5428 109.53 120.69 110.65 1.1107 IC H2R C21 *C22 H2S 1.1107 110.65 118.78 108.83 1.1092 IC C1 C2 C3 O31 1.5458 111.51 -171.21 111.32 1.4465 IC O31 C2 *C3 HX 1.4465 111.32 -126.25 108.41 1.1159 IC HX C2 *C3 HY 1.1159 108.41 -114.81 107.61 1.1132 IC C2 C3 O31 C31 1.5508 111.32 -117.52 117.59 1.3317 IC C3 O31 C31 C32 1.4465 117.59 -177.93 109.00 1.5333 IC C32 O31 *C31 O32 1.5333 109.00 -179.19 126.42 1.2107 IC O31 C31 C32 C33 1.3317 109.00 -176.00 111.40 1.5440 IC C33 C31 *C32 H2X 1.5440 111.40 120.79 108.80 1.1093 IC H2X C31 *C32 H2Y 1.1093 108.80 118.57 108.70 1.1101 IC C21 C22 C23 C24 1.5303 109.53 168.08 112.83 1.5322 IC C24 C22 *C23 H3R 1.5322 112.83 -119.08 109.34 1.1146 IC H3R C22 *C23 H3S 1.1146 109.34 -118.17 109.92 1.1133 IC C22 C23 C24 C25 1.5428 112.83 179.85 112.06 1.5333 IC C25 C23 *C24 H4R 1.5333 112.06 120.31 108.77 1.1150 IC H4R C23 *C24 H4S 1.1150 108.77 117.76 110.16 1.1129 IC C23 C24 C25 C26 1.5322 112.06 172.89 112.33 1.5326 IC C26 C24 *C25 H5R 1.5326 112.33 -120.75 109.47 1.1135 IC H5R C24 *C25 H5S 1.1135 109.47 -117.79 109.27 1.1131 IC C24 C25 C26 C27 1.5333 112.33 175.30 112.46 1.5342 IC C27 C25 *C26 H6R 1.5342 112.46 121.40 108.94 1.1138 IC H6R C25 *C26 H6S 1.1138 108.94 117.47 109.32 1.1131 IC C25 C26 C27 C28 1.5326 112.46 176.92 112.22 1.5391 IC C28 C26 *C27 H7R 1.5391 112.22 -121.53 108.81 1.1141 IC H7R C26 *C27 H7S 1.1141 108.81 -117.10 108.50 1.1141 IC C26 C27 C28 C29 1.5342 112.22 177.27 111.34 1.5073 IC C29 C27 *C28 H8R 1.5073 111.34 119.85 107.24 1.1140 IC H8R C27 *C28 H8S 1.1140 107.24 115.81 109.06 1.1117 IC C27 C28 C29 C210 1.5391 111.34 -141.40 127.31 1.3462 IC C210 C28 *C29 H91 1.3462 127.31 -176.71 114.35 1.1001 IC C28 C29 C210 C211 1.5073 127.31 1.24 127.43 1.5089 IC C211 C29 *C21 H101 1.5089 127.43 179.21 118.33 1.1011 IC C29 C210 C211 C212 1.3462 127.43 -120.91 110.88 1.5393 IC C212 C210 *C21 H11R 1.5393 110.88 121.06 112.51 1.1124 IC H11R C210 *C21 H11S 1.1124 112.51 119.00 109.81 1.1127 IC C210 C211 C212 C213 1.5089 110.88 -176.36 112.76 1.5347 IC C213 C211 *C21 H12R 1.5347 112.76 -120.93 109.33 1.1142 IC H12R C211 *C21 H12S 1.1142 109.33 -118.17 109.94 1.1138 IC C211 C212 C213 C214 1.5393 112.76 -179.47 112.21 1.5338 IC C214 C212 *C21 H13R 1.5338 112.21 121.29 109.31 1.1130 IC H13R C212 *C21 H13S 1.1130 109.31 117.74 109.05 1.1131 IC C212 C213 C214 C215 1.5347 112.21 -178.99 112.92 1.5339 IC C215 C213 *C21 H14R 1.5339 112.92 -121.37 109.00 1.1134 IC H14R C213 *C21 H14S 1.1134 109.00 -117.34 109.08 1.1132 IC C213 C214 C215 C216 1.5338 112.92 179.95 112.20 1.5339 IC C216 C214 *C21 H15R 1.5339 112.20 121.17 109.14 1.1131 IC H15R C214 *C21 H15S 1.1131 109.14 117.63 109.22 1.1132 IC C214 C215 C216 C217 1.5339 112.20 179.53 112.96 1.5328 IC C217 C215 *C21 H16R 1.5328 112.96 -121.41 109.07 1.1135 IC H16R C215 *C21 H16S 1.1135 109.07 -117.43 109.05 1.1130 IC C215 C216 C217 C218 1.5339 112.96 -179.21 113.03 1.5305 IC C218 C216 *C21 H17R 1.5305 113.03 121.55 108.80 1.1140 IC H17R C216 *C21 H17S 1.1140 108.80 116.88 108.83 1.1142 IC C216 C217 C218 H18R 1.5328 113.03 60.41 110.37 1.1113 IC H18R C217 *C21 H18S 1.1113 110.37 -119.78 110.49 1.1115 IC H18R C217 *C21 H18T 1.1113 110.37 120.07 110.59 1.1111 IC C31 C32 C33 C34 1.5333 111.40 179.66 112.54 1.5345 IC C34 C32 *C33 H3X 1.5345 112.54 -121.73 109.66 1.1133 IC H3X C32 *C33 H3Y 1.1133 109.66 -117.45 109.37 1.1151 IC C32 C33 C34 C35 1.5440 112.54 178.40 112.54 1.5346 IC C35 C33 *C34 H4X 1.5346 112.54 121.75 110.03 1.1131 IC H4X C33 *C34 H4Y 1.1131 110.03 117.75 108.84 1.1139 IC C33 C34 C35 C36 1.5345 112.54 -175.14 112.09 1.5349 IC C36 C34 *C35 H5X 1.5349 112.09 -122.26 109.27 1.1127 IC H5X C34 *C35 H5Y 1.1127 109.27 -117.42 109.08 1.1138 IC C34 C35 C36 C37 1.5346 112.09 174.19 113.84 1.5368 IC C37 C35 *C36 H6X 1.5368 113.84 122.38 109.13 1.1124 IC H6X C35 *C36 H6Y 1.1124 109.13 117.02 108.50 1.1143 IC C35 C36 C37 C38 1.5349 113.84 65.26 113.87 1.5343 IC C38 C36 *C37 H7X 1.5343 113.87 120.83 108.55 1.1137 IC H7X C36 *C37 H7Y 1.1137 108.55 116.91 109.10 1.1132 IC C36 C37 C38 C39 1.5368 113.87 178.14 112.45 1.5354 IC C39 C37 *C38 H8X 1.5354 112.45 121.43 109.97 1.1123 IC H8X C37 *C38 H8Y 1.1123 109.97 117.71 108.91 1.1127 IC C37 C38 C39 C310 1.5343 112.45 -176.66 111.96 1.5320 IC C310 C38 *C39 H9X 1.5320 111.96 120.68 109.20 1.1133 IC H9X C38 *C39 H9Y 1.1133 109.20 117.81 109.34 1.1127 IC C38 C39 C310 C311 1.5354 111.96 178.35 113.81 1.5336 IC C311 C39 *C31 H10X 1.5336 113.81 -120.14 108.22 1.1126 IC H10X C39 *C31 H10Y 1.1126 108.22 -117.07 109.45 1.1132 IC C39 C310 C311 C312 1.5320 113.81 -175.46 111.16 1.5334 IC C312 C310 *C31 H11X 1.5334 111.16 120.27 109.12 1.1138 IC H11X C310 *C31 H11Y 1.1138 109.12 118.20 110.02 1.1119 IC C310 C311 C312 C313 1.5336 111.16 173.60 113.47 1.5330 IC C313 C311 *C31 H12X 1.5330 113.47 -120.74 108.01 1.1140 IC H12X C311 *C31 H12Y 1.1140 108.01 -116.85 109.45 1.1130 IC C311 C312 C313 C314 1.5334 113.47 -174.75 111.86 1.5335 IC C314 C312 *C31 H13X 1.5335 111.86 120.28 108.66 1.1135 IC H13X C312 *C31 H13Y 1.1135 108.66 118.03 110.08 1.1125 IC C312 C313 C314 C315 1.5330 111.86 175.21 113.05 1.5325 IC C315 C313 *C31 H14X 1.5325 113.05 -120.81 108.37 1.1133 IC H14X C313 *C31 H14Y 1.1133 108.37 -117.18 109.40 1.1131 IC C313 C314 C315 C316 1.5335 113.05 -177.76 112.89 1.5300 IC C316 C314 *C31 H15X 1.5300 112.89 121.41 108.55 1.1149 IC H15X C314 *C31 H15Y 1.1149 108.55 117.05 109.21 1.1136 IC C314 C315 C316 H16X 1.5325 112.89 57.15 110.07 1.1113 IC H16X C315 *C31 H16Y 1.1113 110.07 -119.27 110.55 1.1106 IC H16X C315 *C31 H16Z 1.1113 110.07 120.81 110.70 1.1116 !The following two residues (PALM and PCGL) and the two subsequent !patches (EST1 and EST2) are a modular way to create DPPC. !See the comments with EST1 and EST2 for more details. adm jr., Jul 99 RESI PALM -1.00 ! Palmitate ! based on methylsulfate GROUP O1 O2 (-) ATOM C1 CL 0.62 ! \\ / ATOM O1 OCL -0.76 ! C1 ATOM O2 OCL -0.76 ! | ! | ATOM C2 CTL2 -0.28 ! H2A-C2-H2B ATOM H2A HAL2 0.09 ! | ATOM H2B HAL2 0.09 ! | GROUP ! | ATOM C3 CTL2 -0.18 ! H3A-C3-H3B ATOM H3A HAL2 0.09 ! | ATOM H3B HAL2 0.09 ! | GROUP ! | ATOM C4 CTL2 -0.18 ! H4A-C4-H4B ATOM H4A HAL2 0.09 ! | ATOM H4B HAL2 0.09 ! | GROUP ! | ATOM C5 CTL2 -0.18 ! H5A-C5-H5B ATOM H5A HAL2 0.09 ! | ATOM H5B HAL2 0.09 ! | GROUP ! | ATOM C6 CTL2 -0.18 ! H6A-C6-H6B ATOM H6A HAL2 0.09 ! | ATOM H6B HAL2 0.09 ! | GROUP ! | ATOM C7 CTL2 -0.18 ! H7A-C7-H7B ATOM H7A HAL2 0.09 ! | ATOM H7B HAL2 0.09 ! | GROUP ! | ATOM C8 CTL2 -0.18 ! H8A-C8-H8B ATOM H8A HAL2 0.09 ! | ATOM H8B HAL2 0.09 ! | GROUP ! | ATOM C9 CTL2 -0.18 ! H9A-C9-H9B ATOM H9A HAL2 0.09 ! | ATOM H9B HAL2 0.09 ! | GROUP ! | ATOM C10 CTL2 -0.18 ! H10A-C10-H10B ATOM H10A HAL2 0.09 ! | ATOM H10B HAL2 0.09 ! | GROUP ! | ATOM C11 CTL2 -0.18 ! H11A-C11-H11B ATOM H11A HAL2 0.09 ! | ATOM H11B HAL2 0.09 ! | GROUP ! | ATOM C12 CTL2 -0.18 ! H12A-C12-H12B ATOM H12A HAL2 0.09 ! | ATOM H12B HAL2 0.09 ! | GROUP ! | ATOM C13 CTL2 -0.18 ! H13A-C13-H13B ATOM H13A HAL2 0.09 ! | ATOM H13B HAL2 0.09 ! | GROUP ! | ATOM C14 CTL2 -0.18 ! H14A-C14-H14B ATOM H14A HAL2 0.09 ! | ATOM H14B HAL2 0.09 ! | GROUP ! | ATOM C15 CTL2 -0.18 ! H15A-C15-H15B ATOM H15A HAL2 0.09 ! | ATOM H15B HAL2 0.09 ! | GROUP ! | ATOM C16 CTL3 -0.27 ! H16A-C16-H16B ATOM H16A HAL3 0.09 ! | ATOM H16B HAL3 0.09 ! H16C ATOM H16C HAL3 0.09 ! BOND C1 O1 C1 O2 BOND C1 C2 C2 H2A C2 H2B BOND C2 C3 C3 H3A C3 H3B BOND C3 C4 C4 H4A C4 H4B BOND C4 C5 C5 H5A C5 H5B BOND C5 C6 C6 H6A C6 H6B BOND C6 C7 C7 H7A C7 H7B BOND C7 C8 C8 H8A C8 H8B BOND C8 C9 C9 H9A C9 H9B BOND C9 C10 C10 H10A C10 H10B BOND C10 C11 C11 H11A C11 H11B BOND C11 C12 C12 H12A C12 H12B BOND C12 C13 C13 H13A C13 H13B BOND C13 C14 C14 H14A C14 H14B BOND C14 C15 C15 H15A C15 H15B BOND C15 C16 C16 H16A C16 H16B C16 H16C IMPR C1 O1 C2 O2 ACCE O1 ACCE O2 !IC table insufficent to create cartesian coordinates IC O1 C2 *C1 O2 0.0000 0.00 180.00 0.00 0.0000 IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000 IC C3 C1 *C2 H2A 0.0000 0.00 120.00 0.00 0.0000 IC H2A C1 *C2 H2B 0.0000 0.00 -120.00 0.00 0.0000 IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000 IC C4 C2 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000 IC H3A C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000 IC C5 C3 *C4 H4A 0.0000 0.00 120.00 0.00 0.0000 IC H4A C3 *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000 IC C6 C4 *C5 H5A 0.0000 0.00 120.00 0.00 0.0000 IC H5A C4 *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000 IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000 IC C7 C5 *C6 H6A 0.0000 0.00 120.00 0.00 0.0000 IC H6A C5 *C6 H6B 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000 IC C8 C6 *C7 H7A 0.0000 0.00 120.00 0.00 0.0000 IC H7A C6 *C7 H7B 0.0000 0.00 -120.00 0.00 0.0000 IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000 IC C9 C7 *C8 H8A 0.0000 0.00 120.00 0.00 0.0000 IC H8A C7 *C8 H8B 0.0000 0.00 -120.00 0.00 0.0000 IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC C10 C8 *C9 H9A 0.0000 0.00 120.00 0.00 0.0000 IC H9A C8 *C9 H9B 0.0000 0.00 -120.00 0.00 0.0000 IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000 IC C11 C9 *C10 H10A 0.0000 0.00 120.00 0.00 0.0000 IC H10A C9 *C10 H10B 0.0000 0.00 -120.00 0.00 0.0000 IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000 IC C12 C10 *C11 H11A 0.0000 0.00 120.00 0.00 0.0000 IC H11A C10 *C11 H11B 0.0000 0.00 -120.00 0.00 0.0000 IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000 IC C13 C11 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000 IC H12A C11 *C12 H12B 0.0000 0.00 -120.00 0.00 0.0000 IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000 IC C14 C12 *C13 H13A 0.0000 0.00 120.00 0.00 0.0000 IC H13A C12 *C13 H13B 0.0000 0.00 -120.00 0.00 0.0000 IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000 IC C15 C13 *C14 H14A 0.0000 0.00 120.00 0.00 0.0000 IC H14A C13 *C14 H14B 0.0000 0.00 -120.00 0.00 0.0000 IC C13 C14 C15 C16 0.0000 0.00 180.00 0.00 0.0000 IC C16 C14 *C15 H15A 0.0000 0.00 120.00 0.00 0.0000 IC H15A C14 *C15 H15B 0.0000 0.00 -120.00 0.00 0.0000 IC C14 C15 C16 H16A 0.0000 0.00 180.00 0.00 0.0000 IC H16A C15 *C16 H16B 0.0000 0.00 120.00 0.00 0.0000 IC H16A C15 *C16 H16C 0.0000 0.00 -120.00 0.00 0.0000 RESI PCGL 0.00 ! glycerolphosphorylcholine ! nomenclature for creation of DPPC GROUP ! from PALM and PCGL via patches EST1 and EST2 ATOM N NTL -0.60 ! ATOM C5 CTL2 -0.10 ! | ATOM C6 CTL5 -0.35 ! -C7- ATOM C7 CTL5 -0.35 ! | ATOM C8 CTL5 -0.35 ! | | | ATOM H5A HL 0.25 ! -C6---N---C8- (+) ATOM H5B HL 0.25 ! | | | ATOM H6A HL 0.25 ! | ATOM H6B HL 0.25 ! -C5- ATOM H6C HL 0.25 ! | ATOM H7A HL 0.25 ! | ATOM H7B HL 0.25 ! | ATOM H7C HL 0.25 ! | ATOM H8A HL 0.25 ! | ATOM H8B HL 0.25 ! | ATOM H8C HL 0.25 ! | GROUP ! | ATOM C4 CTL2 -0.08 ! | ATOM H4A HAL2 0.09 ! H4A---C4---H4B ATOM H4B HAL2 0.09 ! | ATOM P PL 1.50 ! (-) OP3 OP2 ATOM OP3 O2L -0.78 ! \ / ATOM OP4 O2L -0.78 ! P (+) ATOM OP1 OSL -0.57 ! / \ ATOM OP2 OSL -0.57 ! (-) OP4 OP1 ATOM C3 CTL2 -0.08 ! | ATOM H3A HAL2 0.09 ! H3A-C3-H3B ATOM H3B HAL2 0.09 ! | GROUP ! | ATOM C2 CTL1 0.14 ! | ATOM H2A HAL1 0.09 ! H2A-C2-O2-H2 ATOM O2 OHL -0.66 ! | ATOM H2 HOL 0.43 ! | GROUP ! | ATOM C1 CTL2 0.05 ! | ATOM H1A HAL2 0.09 ! H1A-C1-O1-H1 ATOM H1B HAL2 0.09 ! | ATOM O1 OHL -0.66 ! H1B ATOM H1 HOL 0.43 ! BOND N C5 N C6 N C7 N C8 BOND C5 C4 C4 OP2 OP2 P P OP1 BOND P OP3 P OP4 BOND OP1 C3 C3 C2 C2 C1 BOND C2 O2 C1 O1 BOND O1 H1 O2 H2 BOND C1 H1A C1 H1B BOND C2 H2A BOND C3 H3A C3 H3B BOND C4 H4A C4 H4B BOND C5 H5A C5 H5B BOND C6 H6A C6 H6B C6 H6C BOND C7 H7A C7 H7B C7 H7C BOND C8 H8A C8 H8B C8 H8C !IC table insufficent to create cartesian coordinates IC C6 C5 *N C7 0.0000 0.00 120.00 0.00 0.0000 IC C6 C5 *N C8 0.0000 0.00 -120.00 0.00 0.0000 IC C6 N C5 C4 0.0000 0.00 180.00 0.00 0.0000 IC C4 N *C5 H5A 0.0000 0.00 120.00 0.00 0.0000 IC C4 N *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000 IC C5 N C6 H6A 0.0000 0.00 180.00 0.00 0.0000 IC H6A N *C6 H6B 0.0000 0.00 120.00 0.00 0.0000 IC H6A N *C6 H6C 0.0000 0.00 -120.00 0.00 0.0000 IC C5 N C7 H7A 0.0000 0.00 180.00 0.00 0.0000 IC H7A N *C7 H7B 0.0000 0.00 120.00 0.00 0.0000 IC H7A N *C7 H7C 0.0000 0.00 -120.00 0.00 0.0000 IC C5 N C8 H8A 0.0000 0.00 180.00 0.00 0.0000 IC H8A N *C8 H8B 0.0000 0.00 120.00 0.00 0.0000 IC H8A N *C8 H8C 0.0000 0.00 -120.00 0.00 0.0000 IC N C5 C4 OP2 0.0000 0.00 180.00 0.00 0.0000 IC OP2 C5 *C4 H4A 0.0000 0.00 120.00 0.00 0.0000 IC OP2 C5 *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000 IC C5 C4 OP2 P 0.0000 0.00 180.00 0.00 0.0000 IC C4 OP2 P OP1 0.0000 0.00 180.00 0.00 0.0000 IC OP1 OP2 *P OP3 0.0000 0.00 120.00 0.00 0.0000 IC OP1 OP2 *P OP4 0.0000 0.00 -120.00 0.00 0.0000 IC OP2 P OP1 C3 0.0000 0.00 180.00 0.00 0.0000 IC P OP1 C3 C2 0.0000 0.00 180.00 0.00 0.0000 IC C2 OP1 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000 IC C2 OP1 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000 IC OP1 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000 IC C1 C3 *C2 O2 0.0000 0.00 120.00 0.00 0.0000 IC C1 C3 *C2 H2A 0.0000 0.00 -120.00 0.00 0.0000 IC C3 C2 O2 H2 0.0000 0.00 180.00 0.00 0.0000 IC C3 C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000 IC O1 C2 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000 IC O1 C2 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000 IC C2 C1 O1 H1 0.0000 0.00 180.00 0.00 0.0000 PRES EST1 0.00 !patch to link O1 of PCGL to C1 of PALM ! residue 1 is PCGL, residue 2 is PALM DELETE ATOM 1H1 DELETE ATOM 2O2 ATOM 1C1 CTL2 -0.05 ! 1H1A--1C1--1H1B ATOM 1H1A HAL2 0.09 ! | ATOM 1H1B HAL2 0.09 ! | ATOM 1O1 OSL -0.34 ! 2O1 1O1 ATOM 2C1 CL 0.63 ! \\ / ATOM 2O1 OBL -0.52 ! 2C1 ATOM 2C2 CTL2 -0.08 ! | ATOM 2H2A HAL2 0.09 ! 2H2A--2C2--2H2B ATOM 2H2B HAL2 0.09 ! | BOND 1O1 2C1 PRES EST2 0.00 !patch to link O2 of PCGL to C1 of PALM ! residue 1 is PCGL, residue 2 is PALM DELETE ATOM 1H2 DELETE ATOM 2O2 GROUP ATOM 1C2 CTL1 0.04 ! 1H2A--1C2-- ATOM 1H2A HAL1 0.09 ! | ATOM 1O2 OSL -0.34 ! 2O1 1O2 ATOM 2C1 CL 0.63 ! \\ / ATOM 2O1 OBL -0.52 ! 2C1 ATOM 2C2 CTL2 -0.08 ! | ATOM 2H2A HAL2 0.09 ! 2H2A--2C2--2H2B ATOM 2H2B HAL2 0.09 ! | BOND 1O2 2C1 ! Nucleic acids section ! ----------------------- ! The following patches for phosphotyrosine must be used with a ! parameter file containing both the protein and nucleic acid parameters. ! In addition, the commented parameters listed below must be included ! in the combined parameter file ! ! ! patch to convert tyrosine to phenolphosphate !PATCH TP1 TYR 1 SETUP WARN ! ! this patch requires that the use of the following ! !1) protein topology file that contains mass list of atoms in both ! the protein and nucleic acid topology files and ! ! add to the topology file !MASS 179 ON2b 15.999400 ! Nucleic acid phosphate ester oxygen (pres tp1/tp2) ! !2) parameter file that contains both the protein and nucleic acid ! parameters plus the parameters listed below ! ! parameters to be added to the protein/nucleic acid parameter file ! !bonds !CA ON2b 340.0 1.38 !phenol phosphate, 6/94, adm jr. !ON2b P 270.0 1.61 !phenol phosphate, 6/94, adm jr. !angles !CA CA ON2b 75.0 120.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P 90.0 120.0 20. 2.30 !phenol phosphate, 6/94, adm jr. !ON4 P ON2b 48.1 108.0 !phenol phosphate, 6/94, adm jr. !ON3 P ON2b 98.9 103.0 !phenol phosphate, 6/94, adm jr. !dihedrals !CA CA CA ON2b 3.10 2 180.0 !phenol phosphate, 6/94, adm jr. !HP CA CA ON2b 4.20 2 180.0 !phenol phosphate, 6/94, adm jr. !CA CA ON2b P 1.40 2 180.0 !phenol phosphate, 6/94, adm jr. !CA CA ON2b P 0.20 3 180.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON4 0.95 2 0.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON4 0.50 3 0.0 !phenol phosphate, 6/94, adm jr. !CA ON2b P ON3 0.10 3 0.0 !phenol phosphate, 6/94, adm jr. !nonbonded !ON2b 0.0 -0.1521 1.77 ! ! end of parameters to be added !nucleic acid section RESI GUA -1.00 ! O6 ATOM P P 1.50 ! || ATOM O1P ON3 -0.78 ! C6 ATOM O2P ON3 -0.78 ! / \ ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\ ATOM C5' CN8B -0.08 ! | || C8-H8 ATOM H5' HN8 0.09 ! C2 C4--N9/ ATOM H5'' HN8 0.09 ! / \\ / \ GROUP ! H21-N2 N3 \ ATOM C4' CN7 0.16 ! | \ ATOM H4' HN7 0.09 ! H22 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N9 NN2B -0.02 ! | | \ / \ ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1' ATOM N2 NN1 -0.68 ! / \ / \ ATOM H21 HN1 0.32 ! O3' H3' O2' H2'' ATOM H22 HN1 0.35 ! | | ATOM N3 NN3G -0.74 ! H2' ATOM C2 CN2 0.75 ATOM N1 NN2G -0.34 ATOM H1 HN2 0.26 ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 DONO H21 N2 DONO H22 N2 DONO H1 N1 DONO H2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' ! Chi and sugar-phosphate backbone in B-DNA like conformation BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI ADE -1.00 ! H61 H62! ATOM P P 1.50 ! \ / ATOM O1P ON3 -0.78 ! N6 ATOM O2P ON3 -0.78 ! | ATOM O5' ON2 -0.57 ! C6 ATOM C5' CN8B -0.08 ! // \ ATOM H5' HN8 0.09 ! N1 C5--N7\\ ATOM H5'' HN8 0.09 ! | || C8-H8 GROUP ! C2 C4--N9/ ATOM C4' CN7 0.16 ! / \\ / \ ATOM H4' HN7 0.09 ! H2 N3 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! \ ATOM H1' HN7 0.09 ! \ GROUP ! O1P H5' H4' O4' \ ATOM N9 NN2 -0.05 ! | | \ / \ \ ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1' ATOM N7 NN4 -0.71 ! | | \ / \ ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1' ATOM H8 HN3 0.12 ! / \ / \ ATOM N1 NN3A -0.74 ! O3' H3' O2' H2'' ATOM C2 CN4 0.50 ! | | ATOM H2 HN3 0.13 ! H2' ATOM N3 NN3A -0.75 ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI CYT -1.00 ATOM P P 1.50 ! ATOM O1P ON3 -0.78 ! H42 H41 ATOM O2P ON3 -0.78 ! \ / ATOM O5' ON2 -0.57 ! N4 ATOM C5' CN8B -0.08 ! | ATOM H5' HN8 0.09 ! C4 ATOM H5'' HN8 0.09 ! / \\ GROUP ! H5-C5 N3 ATOM C4' CN7 0.16 ! || | ATOM H4' HN7 0.09 ! H6-C6 C2 ATOM O4' ON6B -0.50 ! \ / \\ ATOM C1' CN7B 0.16 ! N1 O2 ATOM H1' HN7 0.09 ! \ GROUP ! \ ATOM N1 NN2 -0.13 ! \ ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ ATOM H6 HN3 0.17 ! | | \ / \ \ ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1' ATOM H5 HN3 0.07 ! | | \ / \ ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1' ATOM O2 ON1C -0.49 ! / \ / \ ATOM N3 NN3 -0.66 ! O3' H3' O2' H2'' ATOM C4 CN2 0.65 ! | | ATOM N4 NN1 -0.75 ! H2' ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 C4 N4 N4 H41 N4 H42 BOND C4 C5 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C2 N1 N3 O2 C4 N3 C5 N4 IMPR N4 C4 H41 H42 DONO H42 N4 DONO H2' O2' DONO H41 N4 ACCE O2 C2 ACCE N3 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI THY -1.00 ! H51 O4 ATOM P P 1.50 ! | || ATOM O1P ON3 -0.78 ! H52-C5M C4 H3 ATOM O2P ON3 -0.78 ! | \ / \ / ATOM O5' ON2 -0.57 ! H53 C5 N3 ATOM C5' CN8B -0.08 ! || | ATOM H5' HN8 0.09 ! H6-C6 C2 ATOM H5'' HN8 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN7 0.16 ! \ ATOM H4' HN7 0.09 ! \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.34 ! | | \ / \ ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.17 ! / \ / \ ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.41 ! | | ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 ! ATOM C4 CN1 0.50 ! ATOM O4 ON1 -0.45 ! ATOM C5 CN3T -0.15 ATOM C5M CN9 -0.11 ATOM H51 HN9 0.07 ATOM H52 HN9 0.07 ATOM H53 HN9 0.07 GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M DONO H3 N3 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 RESI URA -1.00 ! O4 ATOM P P 1.50 ! || ATOM O1P ON3 -0.78 ! C4 H3 ATOM O2P ON3 -0.78 ! / \ / ATOM O5' ON2 -0.57 ! H5-C5 N3 ATOM C5' CN8B -0.08 ! || | ATOM H5' HN8 0.09 ! H6-C6 C2 ATOM H5'' HN8 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN7 0.16 ! \ ATOM H4' HN7 0.09 ! \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.34 ! | | \ / \ ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.14 ! / \ / \ ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.45 ! | | ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 ! ATOM C4 CN1 0.53 ! ATOM O4 ON1 -0.48 ! ATOM C5 CN3 -0.15 ! ATOM H5 HN3 0.10 ! GROUP ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57 BOND P O1P P O2P P O5' BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 DONO H3 N3 DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5' BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI MP_0 0.00 ! Methylphosphate, neutral GROUP ! ! atom order for molvib ATOM C1 CN9 -0.17 ! ATOM O1 ON2 -0.56 ! H11 ATOM P1 P 1.50 ! | ATOM O2 ON4 -0.63 ! H13--C1--H12 ATOM O3 ON4 -0.63 ! | ATOM O4 ON3 -0.64 ! O1 ATOM H11 HN9 0.09 ! | ATOM H12 HN9 0.09 ! O4==P1--O3 ATOM H13 HN9 0.09 ! | \ ATOM H2 HN4 0.43 ! O2 H3 ATOM H3 HN4 0.43 ! \ ! H2 ! BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 BOND C1 H11 C1 H12 C1 H13 O2 H2 O3 H3 IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000 IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000 IC H2 O2 P1 O1 0.0000 000.00 180.0 000.00 0.0000 IC H3 O3 P1 O1 0.0000 000.00 180.0 000.00 0.0000 ! dummies to analyze cetain angles IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0 ! Ion parameters from Benoit Roux and Coworkers ! As of 8/98 no NBFIX terms required ! RESI SOD 1.00 ! Sodium Ion GROUP ATOM SOD SOD 1.00 PATCHING FIRST NONE LAST NONE RESI MG 2.00 ! Magnesium Ion GROUP ATOM MG MG 2.00 PATCHING FIRST NONE LAST NONE RESI POT 1.00 ! Potassium Ion GROUP ATOM POT POT 1.00 PATCHING FIRST NONE LAST NONE RESI CES 1.00 ! Cesium Ion GROUP ATOM CES CES 1.00 PATCHING FIRST NONE LAST NONE RESI CAL 2.00 ! Calcium Ion GROUP ATOM CAL CAL 2.00 PATCHING FIRST NONE LAST NONE RESI CLA -1.00 ! Chloride Ion GROUP ATOM CLA CLA -1.00 PATCHING FIRST NONE LAST NONE ! NOTE the option to regenerate all angles and dihedrals allows ! the explicit inclusion of the THET and DIHE terms to be omitted ! even if the PRES is used in a PATCH statement. It is important to ! inspect the patches prior to use to determine if they should be used ! in a GENErate or PATCh statement and/or if the AUTOgeneration of ! angles and dihedrals is required. ! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the ! documentation RESI NIC 1.00 ! oxidized nicotinamide, jjp1/adm jr. ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! ! H15 GROUP ! \ ATOM H1 HN2 0.45 ! H16-N14 H8 ATOM N2 NN2 -0.52 ! \ | ATOM C3 CN3B 0.16 ! C12 C7 ATOM H4 HN3B 0.19 ! // \ / \\ ATOM C5 CN3 -0.10 ! O13 C9 C5-H6 ATOM H6 HN3B 0.16 ! || | ATOM C7 CN3A -0.05 ! H11-C10 C3-H4 ATOM H8 HN3B 0.16 ! \+ // ATOM C9 CN3 0.05 ! N2 ATOM C10 CN3B 0.18 ! | ATOM H11 HN3B 0.16 ! H1 ATOM C12 CN1A 0.68 ! ATOM O13 ON1 -0.40 ! ATOM N14 NN1 -0.82 ! ATOM H15 HN1 0.34 ! trans to O13 ATOM H16 HN1 0.36 ! cis to O13 BOND N2 H1 C3 H4 C3 C5 C5 H6 BOND C7 H8 C7 C9 N2 C10 BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 DOUBLE C12 O13 C9 C10 C5 C7 N2 C3 ! amide impropers IMPR C12 N14 C9 O13 C12 C9 N14 O13 IMPR N14 C12 H16 H15 N14 C12 H15 H16 ! ring hydrogen impropers IMPR N2 C10 C3 H1 C3 N2 C5 H4 C5 C3 C7 H6 IMPR C7 C5 C9 H8 C10 C9 N2 H11 ! ic table for analysis IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 patch first none last none RESI NICH 0.00 ! reduced nicotinamide, jjp1/adm jr. ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! HN3 to HN6 atom type switch to maintain proper vdw params, 9/98 ! ! H15 GROUP ! \ ATOM H1 HN2 0.42 ! H16-N14 H8 H17 ATOM N2 NN2 -0.69 ! \ \ / ATOM C3 CN3C -0.06 ! C12 C7 ATOM H4 HN6 0.17 ! / \ / \ ATOM C5 CN3 -0.18 ! O13 C9 C5-H6 ATOM H6 HN6 0.14 ! || || ATOM C7 CN8 -0.28 ! H11-C10 C3-H4 ATOM H8 HN8 0.09 ! \ / ATOM H17 HN8 0.09 ! N2 ATOM C10 CN3C -0.10 ! | ATOM H11 HN6 0.14 ! H1 ATOM C9 CN3 0.36 ! ATOM C12 CN1A 0.55 ! ATOM O13 ON1 -0.51 ! ATOM N14 NN1 -0.72 ! ATOM H15 HN1 0.26 ! trans to O13 ATOM H16 HN1 0.32 ! cis to O13 BOND N2 H1 N2 C3 C3 H4 C5 H6 BOND C5 C7 C7 H8 C7 H17 C7 C9 N2 C10 BOND C10 H11 C9 C12 C12 N14 N14 H15 N14 H16 DOUBLE C12 O13 C9 C10 C3 C5 ! amide impropers IMPR C12 N14 C9 O13 C12 C9 N14 O13 IMPR N14 C12 H16 H15 N14 C12 H15 H16 ! ring hydrogen impropers IMPR N2 C10 C3 H1 C3 N2 C5 H4 C5 C3 C7 H6 IMPR C10 C9 N2 H11 ! ic table for analysis IC N2 C3 C5 C7 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 C9 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C10 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C10 N2 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 C3 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 C5 0.0000 000.00 000.00 000.00 0.000 IC C9 C10 N2 H1 0.0000 000.00 000.00 000.00 0.000 IC C10 N2 C3 H4 0.0000 000.00 000.00 000.00 0.000 IC N2 C3 C5 H6 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 H8 0.0000 000.00 000.00 000.00 0.000 IC C3 C5 C7 H17 0.0000 000.00 000.00 000.00 0.000 IC C5 C7 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC N2 C10 C9 C12 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 O13 0.0000 000.00 000.00 000.00 0.000 IC C7 C9 C12 N14 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H15 0.0000 000.00 000.00 000.00 0.000 IC O13 C12 N14 H16 0.0000 000.00 000.00 000.00 0.000 patch first none last none RESI PPI1 -3.00 ! Inorganic phosphate, jjp1/adm jr. GROUP ! ATOM C1 CN9 -0.17 ! ATOM O11 ON2 -0.62 ! ATOM P1 P 1.50 ! H11 ATOM O12 ON2 -0.74 ! | ATOM O13 ON3 -0.82 ! H13--C1--H12 ATOM O14 ON3 -0.82 ! | ! O11 ATOM P2 P2 1.10 ! | ATOM O22 ON3 -0.90 ! O14==P1==O13 (-) ATOM O23 ON3 -0.90 ! | ATOM O24 ON3 -0.90 ! O12 ! | ATOM H11 HN9 0.09 ! (-) O24==P2==O23 (-) ATOM H12 HN9 0.09 ! || ATOM H13 HN9 0.09 ! O22 BOND P1 O11 P1 O12 P1 O13 P1 O14 O11 C1 BOND C1 H11 C1 H12 C1 H13 BOND O12 P2 P2 O22 P2 O23 P2 O24 ! IC Table IC C1 O11 P1 O12 0.0000 000.00 180.0 000.00 0.0000 IC O11 P1 O12 P2 0.0000 000.00 180.0 000.00 0.0000 IC P1 O12 P2 O22 0.0000 000.00 180.0 000.00 0.0000 IC C1 O11 P1 O13 0.0000 000.00 60.0 000.00 0.0000 IC C1 O11 P1 O14 0.0000 000.00 -60.0 000.00 0.0000 IC P1 O12 P2 O23 0.0000 000.00 60.0 000.00 0.0000 IC P1 O12 P2 O24 0.0000 000.00 -60.0 000.00 0.0000 IC P1 O11 C1 H11 0.0000 000.00 180.0 000.00 0.0000 IC P1 O11 C1 H12 0.0000 000.00 60.0 000.00 0.0000 IC P1 O11 C1 H13 0.0000 000.00 -60.0 000.00 0.0000 PATC FIRS NONE LAST NONE RESI ADP -3.00 ! adenosine diphosphate, jjp1/adm jr. ! atom names correspond to pdb nomenclature GROUP ATOM C4' CN7 0.16 ! H61 H62 ATOM H4' HN7 0.09 ! \ / ATOM O4' ON6B -0.50 ! N6 ATOM C1' CN7B 0.16 ! | ATOM H1' HN7 0.09 ! C6 GROUP ! // \ ATOM C5 CN5 0.28 ! N1 C5--N7\\ ATOM N7 NN4 -0.71 ! | || C8-H8 ATOM C8 CN4 0.34 ! C2 C4--N9/ ATOM H8 HN3 0.12 ! / \\ / \ ATOM N9 NN2 -0.05 ! H2 N3 \ ! \ ATOM N1 NN3A -0.74 ! \ ATOM C2 CN4 0.50 ! \ ATOM H2 HN3 0.13 ! O3B O1A H5' H4' O4' \ ATOM N3 NN3A -0.75 ! | | | \ / \ \ ATOM C4 CN5 0.43 ! O1B=PB-O3A--PA-O5'-C5'---C4' C1' ATOM C6 CN2 0.46 ! | | | \ / \ ! O2B O2A H5'' C3'--C2' H1' ATOM N6 NN1 -0.77 ! / \ / \ ATOM H61 HN1 0.38 ! O3' H3' O2' H2'' ATOM H62 HN1 0.38 ! | | GROUP ! H3T H2' ATOM C2' CN7 0.14 ! ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.14 ATOM H3' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H3T HN5 0.43 GROUP ATOM C5' CN8 -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM O5' ON2 -0.62 ATOM PA P 1.50 ATOM O1A ON3 -0.82 ATOM O2A ON3 -0.82 ATOM O3A ON2 -0.74 ATOM PB P2 1.10 ATOM O1B ON3 -0.90 ATOM O2B ON3 -0.90 ATOM O3B ON3 -0.90 BOND PB O3A PB O1B PB O2B PB O3B O3A PA BOND PA O1A PA O2A PA O5' O3' H3T BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' ACCE O3A ACCE O3B ACCE O2B ACCE O1B IC PA O3A PB O1B 0.0000 000.00 180.0 000.00 0.0000 IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 IC PA O3A PB O2B 0.0000 000.00 60.0 000.00 0.0000 IC PA O3A PB O3B 0.0000 000.00 -60.0 000.00 0.0000 IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI ATP -4.00 !adenosine triphosphate , jjp1/adm jr. !atom names correspond to pdb nomenclature ! GROUP ATOM C4' CN7 0.16 ! H61 H62 ATOM H4' HN7 0.09 ! \ / ATOM O4' ON6B -0.50 ! N6 ATOM C1' CN7B 0.16 ! | ATOM H1' HN7 0.09 ! C6 GROUP ! // \ ATOM C5 CN5 0.28 ! N1 C5--N7\\ ATOM N7 NN4 -0.71 ! | || C8-H8 ATOM C8 CN4 0.34 ! C2 C4--N9/ ATOM H8 HN3 0.12 ! / \\ / \ ATOM N9 NN2 -0.05 ! H2 N3 \ ! \ ATOM N1 NN3A -0.74 ! \ ATOM C2 CN4 0.50 ! \ ATOM H2 HN3 0.13 ! (-)O3G O2B O1A H5' H4' O4' \ ATOM N3 NN3A -0.75 ! | | | | \ / \ \ ATOM C4 CN5 0.43 !O1G=PG-O3B-PB-O3A-PA-O5'-C5'---C4' C1' ATOM C6 CN2 0.46 ! | | | | \ / \ ! (-)O2G (-)O1B (-)O2A H5'' C3'--C2' H1' ATOM N6 NN1 -0.77 ! / \ / \ ATOM H61 HN1 0.38 ! O3' H3' O2' H2'' ATOM H62 HN1 0.38 ! | | GROUP ! H3T H2' ATOM C2' CN7 0.14 ! ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP ATOM C3' CN7 0.14 ATOM H3' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H3T HN5 0.43 GROUP ATOM C5' CN8 -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM O5' ON2 -0.62 ATOM PA P 1.50 ATOM O1A ON3 -0.82 ATOM O2A ON3 -0.82 ATOM O3A ON2 -0.74 ATOM PB P2 1.50 ATOM O1B ON3 -0.82 ATOM O2B ON3 -0.82 ATOM O3B ON2 -0.86 ! charge adjusted to yield total triP of -4.0 ATOM PG P2 1.10 ATOM O1G ON3 -0.90 ATOM O2G ON3 -0.90 ATOM O3G ON3 -0.90 BOND O5' C5' O5' PA PA O1A PA O2A PA O3A BOND O3A PB PB O1B PB O2B PB O3B O3B PG BOND PG O1G PG O2G PG O3G BOND C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' H3T BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2 DOUBLE N1 C6 N3 C2 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3 ACCE N7 ACCE N1 ACCE O1A PA ACCE O2A PA ACCE O2' ACCE O3' ACCE O4' ACCE O5' ACCE O3A ACCE O2B ACCE O1B ACCE O3B ACCE O3G ACCE O2G ACCE O2G IC PA O3A PB O3B 0.0000 000.00 180.0 000.00 0.0000 IC O3A PB O3B PG 0.0000 000.00 180.0 000.00 0.0000 IC PB O3B PG O1G 0.0000 000.00 180.0 000.00 0.0000 IC C5' O5' PA O1A 0.0000 000.00 60.0 000.00 0.0000 IC C5' O5' PA O2A 0.0000 000.00 -60.0 000.00 0.0000 IC PA O3A PB O1B 0.0000 000.00 60.0 000.00 0.0000 IC PA O3A PB O2B 0.0000 000.00 -60.0 000.00 0.0000 IC PB O3B PG O2G 0.0000 000.00 60.0 000.00 0.0000 IC PB O3B PG O3G 0.0000 000.00 -60.0 000.00 0.0000 IC PA O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 IC H3T O3' C3' C4' 0.9650 105.47 38.18 111.98 1.5386 IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 IC C3' C2' C1' N9 1.5284 101.97 144.39 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703 IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NAD -1.00 ! oxidized nicotinamide adenine dinucleotide, jjp1/adm jr. ! atom names correspond to pdb nomenclature ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params GROUP ! ATOM AC4' CN7 0.16 ! AH61 AH62 ATOM AH4' HN7 0.09 ! \ / ATOM AO4' ON6B -0.50 ! AN6 ATOM AC1' CN7B 0.16 ! | ATOM AH1' HN7 0.09 ! AC6 GROUP ! // \ ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NN4 -0.71 ! | || AC8-AH8 ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ ATOM AH8 HN3 0.12 ! / \\ / \ ATOM AN9 NN2 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NN3A -0.74 ! \ ATOM AC2 CN4 0.50 ! \ ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NN3A -0.75 ! | | | \ / \ \ ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CN2 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NN1 -0.77 ! \ / \ / \ ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HN1 0.38 ! \ | | GROUP ! \ AH3T AH2T ATOM AC2' CN7B 0.14 ! \ NH71 ATOM AH2' HN7 0.09 ! \ \ ATOM AO2' ON5 -0.66 ! \ NH72-NN7 NH4 ATOM AH2T HN5 0.43 ! \ \ | GROUP ! \ NC7 NC4 ATOM AC3' CN7 0.14 ! \ / \ / \ ATOM AH3' HN7 0.09 ! \ NO7 NC3 NC5-NH5 ATOM AO3' ON5 -0.66 ! \ | | ATOM AH3T HN5 0.43 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 GROUP ! \ | \ / \ \+ / ATOM AC5' CN8B -0.08 ! NC5'--NC4' NC1'---------NN1 ATOM AH5' HN8 0.09 ! | \ / \ ATOM AH5s HN8 0.09 ! NH5' NC3'-NC2'NH1' ATOM AP P 1.50 ! / \ / \ ATOM AO1 ON3 -0.82 ! NO3' NH3'NO2'NH2' ATOM AO2 ON3 -0.82 ! | | ATOM AO5' ON2 -0.62 ! NH3T NH2T ATOM O3 ON2 -0.68 ATOM NP P 1.50 ATOM NO1 ON3 -0.82 ATOM NO2 ON3 -0.82 ATOM NO5' ON2 -0.62 ATOM NC5' CN8B -0.08 ATOM NH5s HN8 0.09 ATOM NH5' HN8 0.09 GROUP ATOM NC2' CN7B 0.14 ATOM NH2' HN7 0.09 ATOM NO2' ON5 -0.66 ATOM NH2T HN5 0.43 GROUP ATOM NC3' CN7 0.14 ATOM NH3' HN7 0.09 ATOM NO3' ON5 -0.66 ATOM NH3T HN5 0.43 GROUP ATOM NC1' CN7B 0.16 ATOM NH1' HN7 0.09 ATOM NC4' CN7 0.16 ATOM NH4' HN7 0.09 ATOM NO4' ON6B -0.50 GROUP ATOM NN1 NN2 -0.07 ATOM NC6 CN3B 0.16 ATOM NH6 HN3B 0.19 ATOM NC5 CN3 -0.10 ATOM NH5 HN3B 0.16 ATOM NC4 CN3A -0.05 ATOM NH4 HN3B 0.16 ATOM NC3 CN3 0.05 ATOM NC2 CN3B 0.18 ATOM NH2 HN3B 0.16 ATOM NC7 CN1A 0.68 ATOM NO7 ON1 -0.40 ATOM NN7 NN1 -0.82 ATOM NH71 HN1 0.34 ! trans to amide O ATOM NH72 HN1 0.36 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC5 NC6 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 ! adenine impropers IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 ! amide impropers IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 ! ring hydrogen impropers IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 DONO AH61 AN6 DONO AH62 AN6 DONO AH2T AO2' DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO2' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000 IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000 IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 PATCH FIRST NONE LAST NONE RESI NADH -2.00 ! reduced nicotinamide adenine dinucleotide, jjp1/adm jr. ! atom names correspond to pdb nomenclature ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! GROUP ! ATOM AC4' CN7 0.16 ! AH61 AH62 ATOM AH4' HN7 0.09 ! \ / ATOM AO4' ON6B -0.50 ! AN6 ATOM AC1' CN7B 0.16 ! | ATOM AH1' HN7 0.09 ! AC6 GROUP ! // \ ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NN4 -0.71 ! | || AC8-AH8 ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ ATOM AH8 HN3 0.12 ! / \\ / \ ATOM AN9 NN2 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NN3A -0.74 ! \ ATOM AC2 CN4 0.50 ! \ ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NN3A -0.75 ! | | | \ / \ \ ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CN2 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NN1 -0.77 ! \ / \ / \ ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HN1 0.38 ! \ | | GROUP ! \ AH3T AH2T ATOM AC2' CN7B 0.14 ! \ NH71 ATOM AH2' HN7 0.09 ! \ \ ATOM AO2' ON5 -0.66 ! \ NH72-NN7 NH4 NH42 ATOM AH2T HN5 0.43 ! \ \ \ / GROUP ! \ NC7 NC4 ATOM AC3' CN7 0.14 ! \ / \ / \ ATOM AH3' HN7 0.09 ! \ NO7 NC3 NC5-NH5 ATOM AO3' ON5 -0.66 ! \ | | ATOM AH3T HN5 0.43 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 GROUP ! \ | \ / \ \ / ATOM AC5' CN8B -0.08 ! NC5'--NC4' NC1'---------NN1 ATOM AH5' HN8 0.09 ! | \ / \ ATOM AH5s HN8 0.09 ! NH5' NC3'-NC2'NH1' ATOM AP P 1.50 ! / \ / \ ATOM AO1 ON3 -0.82 ! NO3' NH3'NO2'NH2' ATOM AO2 ON3 -0.82 ! | | ATOM AO5' ON2 -0.62 ! NH3T NH2T ATOM O3 ON2 -0.68 ATOM NP P 1.50 ATOM NO1 ON3 -0.82 ATOM NO2 ON3 -0.82 ATOM NO5' ON2 -0.62 ATOM NC5' CN8B -0.08 ATOM NH5s HN8 0.09 ATOM NH5' HN8 0.09 GROUP ATOM NC2' CN7B 0.14 ATOM NH2' HN7 0.09 ATOM NO2' ON5 -0.66 ATOM NH2T HN5 0.43 GROUP ATOM NC3' CN7 0.14 ATOM NH3' HN7 0.09 ATOM NO3' ON5 -0.66 ATOM NH3T HN5 0.43 GROUP ATOM NC1' CN7B 0.16 ATOM NH1' HN7 0.09 ATOM NC4' CN7 0.16 ATOM NH4' HN7 0.09 ATOM NO4' ON6B -0.50 GROUP ATOM NN1 NN2 -0.27 !N2 ATOM NC6 CN3C -0.06 !C3 ATOM NH6 HN6 0.17 !H4 ATOM NC5 CN3 -0.18 !C5 ATOM NH5 HN6 0.14 !H6 ATOM NC4 CN8 -0.28 !C7 ATOM NH4 HN8 0.09 !H8 ATOM NH42 HN8 0.09 !H17 ATOM NC3 CN3 0.36 !C9 ATOM NC2 CN3C -0.10 !C10 ATOM NH2 HN6 0.14 !H11 ATOM NC7 CN1A 0.55 !C12 ATOM NO7 ON1 -0.51 !O13 ATOM NN7 NN1 -0.72 !N14 ATOM NH71 HN1 0.26 !H15 ! trans to amide O ATOM NH72 HN1 0.32 !H16 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AH2T AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC4 NC5 NC6 NN1 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 DOUBLE NC2 NC3 NC5 NC6 ! adenine impropers IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 ! amide impropers IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 ! ring hydrogen impropers IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 DONO AH61 AN6 DONO AH62 AN6 DONO AH2T AO2' DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO2' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 IC AP O3 NP NO5' 1.5477 110.11 175.47 98.59 1.5945 IC AC5' AO5' AP O3 1.4379 124.23 -120.69 96.29 1.5477 IC AC5' AO5' AP AO2 1.4379 124.23 -4.20 104.25 1.4838 IC AH5S AC5' AC4' AC3' 1.1127 107.45 -172.00 111.64 1.5309 IC AP O3 NP NO1 1.5477 110.11 63.14 114.14 1.4739 IC AP O3 NP NO2 1.5477 110.11 -73.96 111.08 1.4835 IC AP AO5' AC5' AC4' 1.5968 124.23 104.17 111.45 1.5366 IC AO1 AP AO5' AC5' 1.4736 106.06 122.59 124.23 1.4379 IC AO5' AC5' AC4' AC3' 1.4379 111.45 -54.02 111.64 1.5309 IC AC5' AC4' AC3' AO3' 1.5366 111.64 117.91 108.23 1.4176 IC AH3T AO3' AC3' AC4' 0.9780 101.86 -77.83 108.23 1.5309 IC AO4' AC3' *AC4 AC5' 3.7210 30.68 12.44 22.46 6.0953 IC AC2' AC4' *AC3' AO3' 1.5171 107.22 -123.00 108.23 1.4176 IC AC4' AC3' AC2' AC1' 1.5309 107.22 -27.93 98.01 1.5397 IC AC3' AC2' AC1' AN9 1.5171 98.01 168.03 114.25 1.4756 IC AO4' AC1' AN9 AC4 1.4308 112.85 -160.05 123.87 1.3958 IC AC1' AC4 *AN9 AC8 1.4756 123.87 160.62 105.30 1.3614 IC AC4 AN9 AC8 AN7 1.3958 105.30 2.73 114.72 1.3222 IC AC8 AN9 AC4 AC5 1.3614 105.30 -0.85 105.33 1.3777 IC AC8 AN7 AC5 AC6 1.3222 102.89 -175.73 131.43 1.4163 IC AN7 AC5 AC6 AN1 1.3877 131.43 177.76 117.35 1.3499 IC AC5 AC6 AN1 AC2 1.4163 117.35 0.19 119.36 1.3330 IC AN9 AC5 *AC4 AN3 1.3958 105.33 -177.76 126.56 1.3567 IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 IC AN9 AN7 *AC8 AH8 1.3614 114.72 173.63 127.58 1.0942 IC AN1 AN3 *AC2 AH2 1.3330 128.86 179.26 114.95 1.0940 IC AC1' AC3' *AC2 AO2' 4.3577 16.73 79.16 23.49 5.5426 IC AH2' AO2' AC2' AC3' 2.0992 29.77 125.89 110.79 1.5171 IC AH2T AO2' AC2' AC3' 0.9759 105.90 7.59 110.79 1.5171 IC AO4' AC2' *AC1' AH1' 1.4308 104.32 -114.05 107.95 1.1153 IC AC1' AC3' *AC2 AH2' 4.3577 16.73 138.52 14.56 4.3331 IC AC2' AC4' *AC3' AH3' 1.5171 107.22 118.77 114.33 1.1023 IC AC3' AO4' *AC4 AH4' 4.6236 30.68 55.38 18.92 5.2267 IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 IC NC5' NO5' NP NO2 1.4351 125.31 34.31 105.69 1.4835 IC NH5S NC5' NO5' NP 1.1087 111.20 -6.79 125.31 1.5945 IC NH5' NC5' NO5' NP 1.1115 107.95 108.24 125.31 1.5945 IC NP NO5' NC5' NC4' 1.5945 125.31 -133.06 113.61 1.5644 IC NO5' NC5' NC4' NC3' 1.4351 113.61 37.01 114.92 1.5111 IC NC5' NC4' NC3' NC2' 1.5644 114.92 71.49 99.06 1.5369 IC NC4' NC3' NC2' NC1' 1.5111 99.06 54.76 97.08 1.5500 IC NC3' NC2' NC1' NO4' 1.5369 97.08 -39.12 103.14 1.4628 IC NC2' NC1' NO4' NC4' 1.5500 103.14 9.47 109.09 1.4960 IC NO2' NC2' NC1' NO4' 1.4207 114.02 -166.39 103.14 1.4628 IC NH2T NO2' NC2' NC1' 0.9638 100.52 -89.37 114.02 1.5500 IC NO4' NC2' *NC1' NH1' 1.4628 103.14 -111.22 105.40 1.1096 IC NC1' NC3' *NC2 NH2' 2.4663 46.96 -41.97 34.01 3.9460 IC NC2' NC4' *NC3 NH3' 3.9136 23.54 -115.76 16.12 3.6674 IC NC3' NO4' *NC4 NH4' 5.4003 24.61 -39.21 14.97 6.7904 IC NC4' NO5' *NC5 NH5' 5.9665 13.65 -41.47 15.17 7.7670 IC NC4' NO5' *NC5 NH5S 5.9665 13.65 -87.41 13.92 6.7251 IC NC3' NC2' NC1' NN1 1.5369 97.08 88.64 116.58 1.5502 IC NO3' NC3' NC2' NC1' 1.4176 119.76 -172.52 97.08 1.5500 IC NH3T NO3' NC3' NC2' 0.9717 103.61 17.81 119.76 1.5369 IC NC2' NC1' NN1 NC2 1.5500 116.58 -19.65 116.34 1.3499 IC NC1' NN1 NC2 NC3 1.5502 116.34 134.66 130.57 1.3607 IC NN1 NC2 NC3 NC4 1.3499 130.57 5.82 111.74 1.5356 IC NC2 NC3 NC4 NC5 1.3607 111.74 -1.05 119.26 1.5319 IC NC3 NC4 NC5 NC6 1.5356 119.26 -1.26 113.69 1.3745 IC NC4 NC5 NC6 NN1 1.5319 113.69 -0.29 128.15 1.3388 IC NC5 NC6 NN1 NC2 1.3745 128.15 4.14 116.26 1.3499 IC NN1 NC2 NC3 NC7 1.3499 130.57 -147.46 122.72 1.5282 IC NC2 NC3 NC7 NO7 1.3607 122.72 -140.47 119.41 1.2169 IC NC2 NC3 NC7 NN7 1.3607 122.72 46.61 116.68 1.3621 IC NO7 NC7 NN7 NH71 1.2169 123.49 -177.07 120.21 1.0093 IC NO7 NC7 NN7 NH72 1.2169 123.49 -4.94 119.16 1.0014 IC NC2 NC3 NC4 NH4 1.3607 111.74 -135.39 112.16 1.1099 IC NC2 NC3 NC4 NH42 1.3607 111.74 114.48 103.52 1.1129 IC NC3 NC4 NC5 NH5 1.5356 119.26 -171.18 122.65 1.0912 IC NC4 NC5 NC6 NH6 1.5319 113.69 179.92 118.00 1.0878 IC NC6 NN1 NC2 NH2 1.3388 116.26 162.03 117.47 1.0731 PATCH FIRST NONE LAST NONE RESI NADP -2.00 ! oxidized nicotinamide adenine dinucleotide, ! NADP+, adm jr. ! atom names correspond to pdb nomenclature ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! GROUP ! ATOM AC4' CN7 0.16 ! AH61 AH62 ATOM AH4' HN7 0.09 ! \ / ATOM AO4' ON6B -0.50 ! AN6 ATOM AC1' CN7B 0.16 ! | ATOM AH1' HN7 0.09 ! AC6 GROUP ! // \ ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NN4 -0.71 ! | || AC8-AH8 ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ ATOM AH8 HN3 0.12 ! / \\ / \ ATOM AN9 NN2 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NN3A -0.74 ! \ ATOM AC2 CN4 0.50 ! \ ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NN3A -0.75 ! | | | \ / \ \ ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CN2 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NN1 -0.77 ! \ / \ / \ ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HN1 0.38 ! \ | | GROUP ! \ AH3T AO1P=AP2==AO2P (-) ATOM AC2' CN7B 0.01 ! \ | NH71 ATOM AH2' HN7 0.09 ! \ AH2T-AO2T / ATOM AO2' ON2 -0.62 ! \ NH72-NN7 NH4 NH42 ATOM AP2 P 1.50 ! \ \ \ / ATOM AO1P ON3 -0.82 ! \ NC7 NC4 ATOM AO2P ON3 -0.82 ! \ / \ / \ ATOM AO2T ON4 -0.68 ! \ NO7 NC3 NC5-NH5 ATOM AH2T HN4 0.34 ! \ | | GROUP ! \ | | ATOM AC3' CN7 0.14 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 ATOM AH3' HN7 0.09 ! \ | \ / \ \ / ATOM AO3' ON5 -0.66 ! NC5'--NC4' NC1'--------NN1 ATOM AH3T HN5 0.43 ! | \ / \ GROUP ! NH5' NC3'-NC2'NH1' ATOM AC5' CN8B -0.08 ! / \ / \ ATOM AH5' HN8 0.09 ! NO3' NH3'NO2'NH2' ATOM AH5s HN8 0.09 ! | | ATOM AP P 1.50 ! NH3T NH2T ATOM AO1 ON3 -0.82 ! ATOM AO2 ON3 -0.82 ! ATOM AO5' ON2 -0.62 ! ATOM O3 ON2 -0.68 ATOM NP P 1.50 ATOM NO1 ON3 -0.82 ATOM NO2 ON3 -0.82 ATOM NO5' ON2 -0.62 ATOM NC5' CN8B -0.08 ATOM NH5s HN8 0.09 ATOM NH5' HN8 0.09 GROUP ATOM NC2' CN7B 0.14 ATOM NH2' HN7 0.09 ATOM NO2' ON5 -0.66 ATOM NH2T HN5 0.43 GROUP ATOM NC3' CN7 0.14 ATOM NH3' HN7 0.09 ATOM NO3' ON5 -0.66 ATOM NH3T HN5 0.43 GROUP ATOM NC1' CN7B 0.16 ATOM NH1' HN7 0.09 ATOM NC4' CN7 0.16 ATOM NH4' HN7 0.09 ATOM NO4' ON6B -0.50 GROUP ATOM NN1 NN2 -0.07 ATOM NC6 CN3B 0.16 ATOM NH6 HN3B 0.19 ATOM NC5 CN3 -0.10 ATOM NH5 HN3B 0.16 ATOM NC4 CN3A -0.05 ATOM NH4 HN3B 0.16 ATOM NC3 CN3 0.05 ATOM NC2 CN3B 0.18 ATOM NH2 HN3B 0.16 ATOM NC7 CN1A 0.68 ATOM NO7 ON1 -0.40 ATOM NN7 NN1 -0.82 ATOM NH71 HN1 0.34 ! trans to amide O ATOM NH72 HN1 0.36 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC5 NC6 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC5 NH5 NC6 NH6 BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 ! adenine impropers IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 ! amide impropers IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 ! ring hydrogen impropers IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 DONO AH61 AN6 DONO AH62 AN6 DONO AH2T AO2' DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO2' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 DONO AH2T AO2T ACCE AO2T ACCE AO1P ACCE AO2P ACCE AO2' IC AP O3 NP NO5' 1.4863 65.28 -169.00 98.59 1.5977 IC AC5' AO5' AP O3 1.4232 127.31 -165.10 103.27 1.4863 IC AC5' AO5' AP AO2 1.4232 127.31 73.33 111.48 1.4836 IC AH5S AC5' AC4' AC3' 0.9935 120.00 -58.20 111.58 1.6942 IC AP O3 NP NO1 1.4863 65.28 78.51 108.97 1.4756 IC AP O3 NP NO2 1.4863 65.28 -54.29 112.88 1.4636 IC AP AO5' AC5' AC4' 1.5901 127.31 121.29 111.63 1.5491 IC AO1 AP AO5' AC5' 1.5901 127.31 121.29 127.31 1.4232 IC AO5' AC5' AC4' AC3' 1.4232 111.63 -58.20 111.58 1.6942 IC AC5' AC4' AC3' AO3' 1.5491 111.58 128.42 114.19 1.4337 IC AH3T AO3' AC3' AC4' 0.9671 98.77 147.40 114.19 1.6942 IC AO4' AC3' *AC4 AC5' 1.8868 112.95 -118.10 111.58 1.5491 IC AC2' AC4' *AC3' AO3' 1.5097 93.22 -117.72 114.19 1.4337 IC AC4' AC3' AC2' AC1' 1.6942 93.22 -12.93 117.82 1.5415 IC AC3' AC2' AC1' AN9 1.5097 117.82 135.56 115.01 1.4847 IC AO4' AC1' AN9 AC4 1.3646 95.44 -90.72 125.96 1.4013 IC AC1' AC4 *AN9 AC8 1.4847 125.96 -176.52 105.34 1.3777 IC AC4 AN9 AC8 AN7 1.4013 105.34 -0.07 114.01 1.3282 IC AC8 AN9 AC4 AC5 1.3777 105.34 0.11 105.06 1.3782 IC AC8 AN7 AC5 AC6 1.3282 103.21 -179.92 130.78 1.4146 IC AN7 AC5 AC6 AN1 1.3814 130.78 -179.94 117.85 1.3482 IC AC5 AC6 AN1 AC2 1.4146 117.85 -0.14 118.87 1.3300 IC AN9 AC5 *AC4 AN3 1.4013 105.06 -179.67 126.14 1.3648 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AC5 AN1 *AC6 AN6 1.4146 117.85 179.89 119.69 1.3419 IC AN1 AC6 AN6 AH61 1.3482 119.69 -0.39 116.60 0.9912 IC AH61 AC6 *AN6 AH62 0.9912 116.60 -179.02 116.94 0.9978 IC AN9 AN7 *AC8 AH8 1.3777 114.01 -179.37 126.34 1.0962 IC AN1 AN3 *AC2 AH2 1.3300 129.42 179.97 114.82 1.0928 IC AC1' AC3' *AC2 AO2' 1.5415 117.82 -145.06 114.13 1.4294 IC AH2' AO2' AC2' AC3' 2.0386 31.12 -93.63 114.13 1.5097 IC AH2T AO2' AC2' AC3' 0.9953 99.36 -93.63 114.13 1.5097 IC AO4' AC2' *AC1' AH1' 1.3646 120.77 -114.99 109.65 1.1105 IC AC1' AC3' *AC2 AH2' 1.5415 117.82 108.23 86.44 1.0999 IC AC2' AC4' *AC3' AH3' 1.5097 93.22 117.28 111.94 1.1110 IC AC3' AO4' *AC4 AH4' 1.6942 112.95 -140.26 57.99 1.0000 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC AC4' AO5' *AC5 AH5' 1.5491 111.63 -123.75 111.23 1.1111 IC NC5' NO5' NP NO2 1.4451 128.40 -49.72 108.83 1.4636 IC NH5S NC5' NO5' NP 1.1110 109.50 115.00 128.40 1.5977 IC NH5' NC5' NO5' NP 1.1110 109.50 -115.00 128.40 1.5977 IC NP NO5' NC5' NC4' 1.5977 128.40 0.00 110.10 1.5160 IC NO5' NC5' NC4' NC3' 1.4451 110.10 0.00 108.50 1.5160 IC NC5' NC4' NC3' NC2' 1.5160 108.50 0.00 111.00 1.5160 IC NC4' NC3' NC2' NC1' 1.5160 111.00 0.00 105.50 1.5270 IC NC3' NC2' NC1' NO4' 1.5160 105.50 0.00 105.00 1.4100 IC NC2' NC1' NO4' NC4' 1.5270 105.00 0.00 117.86 1.4712 IC NO2' NC2' NC1' NO4' 1.4200 110.10 180.00 105.00 1.4100 IC NH2T NO2' NC2' NC1' 0.9600 106.00 180.00 110.10 1.5270 IC NO4' NC2' *NC1' NH1' 1.4100 105.00 -115.00 110.10 1.1110 IC NC1' NC3' *NC2 NH2' 1.5270 105.50 115.00 110.10 1.1110 IC NC2' NC4' *NC3 NH3' 1.5160 111.00 115.00 110.10 1.1110 IC NC3' NO4' *NC4 NH4' 1.5160 100.64 -115.00 107.24 1.1110 IC NC4' NO5' *NC5 NH5' 1.5160 110.10 -115.00 109.50 1.1110 IC NC4' NO5' *NC5 NH5S 1.5160 110.10 115.00 109.50 1.1110 IC NC3' NC2' NC1' NN1 1.5160 105.50 0.00 113.70 1.4800 IC NO3' NC3' NC2' NC1' 1.4200 110.10 180.00 105.50 1.5270 IC NH3T NO3' NC3' NC2' 0.9600 106.00 180.00 110.10 1.5160 IC NC2' NC1' NN1 NC2 1.5270 113.70 0.00 121.70 1.3150 IC NC1' NN1 NC2 NC3 1.4800 121.70 0.00 122.00 1.3500 IC NN1 NC2 NC3 NC4 1.3150 122.00 0.00 118.00 1.3600 IC NC2 NC3 NC4 NC5 1.3500 118.00 0.00 118.00 1.3600 IC NC3 NC4 NC5 NC6 1.3600 118.00 0.00 118.00 1.3500 IC NC4 NC5 NC6 NN1 1.3600 118.00 0.00 124.51 1.2199 IC NC5 NC6 NN1 NC2 1.3500 124.51 0.00 119.49 1.3150 IC NN1 NC2 NC3 NC7 1.3150 122.00 0.00 131.80 1.4800 IC NC2 NC3 NC7 NO7 1.3500 131.80 0.00 118.50 1.2300 IC NC2 NC3 NC7 NN7 1.3500 131.80 0.00 113.00 1.3600 IC NO7 NC7 NN7 NH71 1.2300 0.00 180.00 120.00 1.0000 IC NO7 NC7 NN7 NH72 1.2300 0.00 0.00 120.00 1.0000 IC NC2 NC3 NC4 NH4 1.3500 118.00 0.00 121.00 1.0900 IC NC3 NC4 NC5 NH5 1.3600 118.00 0.00 119.00 1.0900 IC NC4 NC5 NC6 NH6 1.3600 118.00 0.00 120.50 1.0900 IC NC6 NN1 NC2 NH2 1.2199 119.49 0.00 117.50 1.0900 IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000 IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000 IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000 IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000 IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000 PATCH FIRST NONE LAST NONE RESI NDPH -3.00 ! reduced nicotinamide adenine dinucleotide ! NADPH, VARNAI/adm jr. ! from RESI NADH and 3PHO ! checked for consistency with new NA params, adm jr., 9/98 ! note that differences with respect to published results exist ! due to new NA params ! GROUP ! ATOM AC4' CN7 0.16 ! AH61 AH62 ATOM AH4' HN7 0.09 ! \ / ATOM AO4' ON6B -0.50 ! AN6 ATOM AC1' CN7B 0.16 ! | ATOM AH1' HN7 0.09 ! AC6 GROUP ! // \ ATOM AC5 CN5 0.28 ! AN1 AC5--AN7\\ ATOM AN7 NN4 -0.71 ! | || AC8-AH8 ATOM AC8 CN4 0.34 ! AC2 AC4--AN9/ ATOM AH8 HN3 0.12 ! / \\ / \ ATOM AN9 NN2 -0.05 ! AH2 AN3 \ ! \ ATOM AN1 NN3A -0.74 ! \ ATOM AC2 CN4 0.50 ! \ ATOM AH2 HN3 0.13 ! NO1 AO1 AH5sAH4' AO4' \ ATOM AN3 NN3A -0.75 ! | | | \ / \ \ ATOM AC4 CN5 0.43 ! NO5'NP-O3--AP-AO5'-AC5'-AC4' AC1' ATOM AC6 CN2 0.46 ! \ | | | \ / \ ! \ NO2 AO2 AH5' AC3'-AC2' AH1' ATOM AN6 NN1 -0.77 ! \ / \ / \ ATOM AH61 HN1 0.38 ! \ AO3' AH3'AO2'AH2' ATOM AH62 HN1 0.38 ! \ | | GROUP ! \ AH3T AO1P=AP2==AO2P (-) ATOM AC2' CN7B 0.01 ! \ | NH71 ATOM AH2' HN7 0.09 ! \ AH2T-AO2T / ATOM AO2' ON2 -0.62 ! \ NH72-NN7 NH4 NH42 ATOM AP2 P 1.50 ! \ \ \ / ATOM AO1P ON3 -0.82 ! \ NC7 NC4 ATOM AO2P ON3 -0.82 ! \ / \ / \ ATOM AO2T ON4 -0.68 ! \ NO7 NC3 NC5-NH5 ATOM AH2T HN4 0.34 ! \ | | GROUP ! \ | | ATOM AC3' CN7 0.14 ! \ NH5s NH4'NO4' NH2-NC2 NC6-NH6 ATOM AH3' HN7 0.09 ! \ | \ / \ \ / ATOM AO3' ON5 -0.66 ! NC5'--NC4' NC1'--------NN1 ATOM AH3T HN5 0.43 ! | \ / \ GROUP ! NH5' NC3'-NC2'NH1' ATOM AC5' CN8B -0.08 ! / \ / \ ATOM AH5' HN8 0.09 ! NO3' NH3'NO2'NH2' ATOM AH5s HN8 0.09 ! | | ATOM AP P 1.50 ! NH3T NH2T ATOM AO1 ON3 -0.82 ! ATOM AO2 ON3 -0.82 ! ATOM AO5' ON2 -0.62 ! ATOM O3 ON2 -0.68 ATOM NP P 1.50 ATOM NO1 ON3 -0.82 ATOM NO2 ON3 -0.82 ATOM NO5' ON2 -0.62 ATOM NC5' CN8B -0.08 ATOM NH5s HN8 0.09 ATOM NH5' HN8 0.09 GROUP ATOM NC2' CN7B 0.14 ATOM NH2' HN7 0.09 ATOM NO2' ON5 -0.66 ATOM NH2T HN5 0.43 GROUP ATOM NC3' CN7 0.14 ATOM NH3' HN7 0.09 ATOM NO3' ON5 -0.66 ATOM NH3T HN5 0.43 GROUP ATOM NC1' CN7B 0.16 ATOM NH1' HN7 0.09 ATOM NC4' CN7 0.16 ATOM NH4' HN7 0.09 ATOM NO4' ON6B -0.50 GROUP ATOM NN1 NN2 -0.27 !N2 ATOM NC6 CN3C -0.06 !C3 ATOM NH6 HN6 0.17 !H4 ATOM NC5 CN3 -0.18 !C5 ATOM NH5 HN6 0.14 !H6 ATOM NC4 CN8 -0.28 !C7 ATOM NH4 HN8 0.09 !H8 ATOM NH42 HN8 0.09 !H17 ATOM NC3 CN3 0.36 !C9 ATOM NC2 CN3C -0.10 !C10 ATOM NH2 HN6 0.14 !H11 ATOM NC7 CN1A 0.55 !C12 ATOM NO7 ON1 -0.51 !O13 ATOM NN7 NN1 -0.72 !N14 ATOM NH71 HN1 0.26 !H15 ! trans to amide O ATOM NH72 HN1 0.32 !H16 ! cis to amide O BOND AN1 AC2 AN3 AC4 AC5 AC6 BOND AC6 AN6 AC5 AN7 AC8 AN9 BOND AN9 AC4 AC2 AH2 AN6 AH61 AN6 AH62 AC8 AH8 DOUBLE AC6 AN1 AC2 AN3 AC4 AC5 AN7 AC8 BOND AN9 AC1' AC1' AC2' AC2' AC3' AC3' AC4' AC4' AO4' BOND AO4' AC1' AC1' AH1' AC2' AO2' AO2' AP2 AC2' AH2' BOND AC3' AH3' AC3' AO3' AO3' AH3T AC4' AH4' AC4' AC5' BOND AC5' AH5s AC5' AH5' AC5' AO5' AO5' AP AP AO1 BOND AP AO2 AP O3 O3 NP NP NO1 NP NO2 BOND NP NO5' NO5' NC5' NC5' NH5s NC5' NH5' NC5' NC4' BOND NC4' NO4' NO4' NC1' NC1' NC2' NC2' NC3' NC3' NC4' BOND NC1' NH1' NC2' NH2' NC2' NO2' NO2' NH2T NC3' NH3' BOND NC3' NO3' NO3' NH3T NC4' NH4' NC1' NN1 NN1 NC2 BOND NC3 NC4 NC5 NC6 BOND NC2 NH2 NC3 NC7 NC7 NO7 NC7 NN7 NN7 NH71 BOND NN7 NH72 NC4 NH4 NC4 NH42 NC5 NH5 NC6 NH6 BOND AP2 AO1P AP2 AO2P AP2 AO2T AO2T AH2T DOUBLE NC2 NC3 NC4 NC5 NC6 NN1 ! adenine impropers IMPR AN6 AC6 AH61 AH62 AC6 AN1 AC5 AN6 ! amide impropers IMPR NC7 NN7 NC3 NO7 NC7 NC3 NN7 NO7 IMPR NN7 NC7 NH71 NH72 NN7 NC7 NH72 NH71 ! ring hydrogen impropers IMPR NC6 NN1 NC5 NH6 NC5 NC6 NC4 NH5 IMPR NC4 NC5 NC3 NH4 NC2 NC3 NN1 NH2 DONO AH61 AN6 DONO AH62 AN6 DONO AH3T AO3' ACCE AN1 ACCE AN3 ACCE AN7 ACCE AO4' ACCE AO3' ACCE AO5' ACCE AO1 AP ACCE AO2 AP ACCE O3 ACCE NO1 NP ACCE NO2 NP ACCE NO5' ACCE NO4' ACCE NO3' ACCE NO2' ACCE NO7 DONO NH2T NO2' DONO NH3T NO3' DONO NH71 NN7 DONO NH72 NN7 DONO AH2T AO2T ACCE AO2T ACCE AO1P ACCE AO2P ACCE AO2' ! the following ICs will not totally IC BUILD NADPH IC AP O3 NP NO5' 1.5477 110.11 175.47 98.59 1.5945 IC AC5' AO5' AP O3 1.4379 124.23 -120.69 96.29 1.5477 IC AC5' AO5' AP AO2 1.4379 124.23 -4.20 104.25 1.4838 IC AH5S AC5' AC4' AC3' 1.1127 107.45 -172.00 111.64 1.5309 IC AP O3 NP NO1 1.5477 110.11 63.14 114.14 1.4739 IC AP O3 NP NO2 1.5477 110.11 -73.96 111.08 1.4835 IC AP AO5' AC5' AC4' 1.5968 124.23 104.17 111.45 1.5366 IC AO1 AP AO5' AC5' 1.4736 106.06 122.59 124.23 1.4379 IC AO5' AC5' AC4' AC3' 1.4379 111.45 -54.02 111.64 1.5309 IC AC5' AC4' AC3' AO3' 1.5366 111.64 117.91 108.23 1.4176 IC AH3T AO3' AC3' AC4' 0.9780 101.86 -77.83 108.23 1.5309 IC AO4' AC3' *AC4 AC5' 3.7210 30.68 12.44 22.46 6.0953 IC AC2' AC4' *AC3' AO3' 1.5171 107.22 -123.00 108.23 1.4176 IC AC4' AC3' AC2' AC1' 1.5309 107.22 -27.93 98.01 1.5397 IC AC3' AC2' AC1' AN9 1.5171 98.01 168.03 114.25 1.4756 IC AO4' AC1' AN9 AC4 1.4308 112.85 -160.05 123.87 1.3958 IC AC1' AC4 *AN9 AC8 1.4756 123.87 160.62 105.30 1.3614 IC AC4 AN9 AC8 AN7 1.3958 105.30 2.73 114.72 1.3222 IC AC8 AN9 AC4 AC5 1.3614 105.30 -0.85 105.33 1.3777 IC AC8 AN7 AC5 AC6 1.3222 102.89 -175.73 131.43 1.4163 IC AN7 AC5 AC6 AN1 1.3877 131.43 177.76 117.35 1.3499 IC AC5 AC6 AN1 AC2 1.4163 117.35 0.19 119.36 1.3330 IC AN9 AC5 *AC4 AN3 1.3958 105.33 -177.76 126.56 1.3567 IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 IC AC5 AN1 *AC6 AN6 1.4163 117.35 178.91 119.82 1.3439 IC AN1 AC6 AN6 AH61 1.3499 119.82 -2.82 115.89 0.9932 IC AH61 AC6 *AN6 AH62 0.9932 115.89 -173.48 118.52 0.9961 IC AN9 AN7 *AC8 AH8 1.3614 114.72 173.63 127.58 1.0942 IC AN1 AN3 *AC2 AH2 1.3330 128.86 179.26 114.95 1.0940 IC AO4' AC2' *AC1' AH1' 1.4308 104.32 -114.05 107.95 1.1153 IC AC1' AC3' *AC2 AH2' 4.3577 16.73 138.52 14.56 4.3331 IC AC2' AC4' *AC3' AH3' 1.5171 107.22 118.77 114.33 1.1023 IC AC3' AO4' *AC4 AH4' 4.6236 30.68 55.38 18.92 5.2267 IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 IC AC4' AO5' *AC5 AH5' 5.8410 8.40 125.34 12.50 6.6777 IC NC5' NO5' NP NO2 1.4351 125.31 34.31 105.69 1.4835 IC NH5S NC5' NO5' NP 1.1087 111.20 -6.79 125.31 1.5945 IC NH5' NC5' NO5' NP 1.1115 107.95 108.24 125.31 1.5945 IC NP NO5' NC5' NC4' 1.5945 125.31 -133.06 113.61 1.5644 IC NO5' NC5' NC4' NC3' 1.4351 113.61 37.01 114.92 1.5111 IC NC5' NC4' NC3' NC2' 1.5644 114.92 71.49 99.06 1.5369 IC NC4' NC3' NC2' NC1' 1.5111 99.06 54.76 97.08 1.5500 IC NC3' NC2' NC1' NO4' 1.5369 97.08 -39.12 103.14 1.4628 IC NC2' NC1' NO4' NC4' 1.5500 103.14 9.47 109.09 1.4960 IC NO2' NC2' NC1' NO4' 1.4207 114.02 -166.39 103.14 1.4628 IC NH2T NO2' NC2' NC1' 0.9638 100.52 -89.37 114.02 1.5500 IC NO4' NC2' *NC1' NH1' 1.4628 103.14 -111.22 105.40 1.1096 IC NC1' NC3' *NC2 NH2' 2.4663 46.96 -41.97 34.01 3.9460 IC NC2' NC4' *NC3 NH3' 3.9136 23.54 -115.76 16.12 3.6674 IC NC3' NO4' *NC4 NH4' 5.4003 24.61 -39.21 14.97 6.7904 IC NC4' NO5' *NC5 NH5' 5.9665 13.65 -41.47 15.17 7.7670 IC NC4' NO5' *NC5 NH5S 5.9665 13.65 -87.41 13.92 6.7251 IC NC3' NC2' NC1' NN1 1.5369 97.08 88.64 116.58 1.5502 IC NO3' NC3' NC2' NC1' 1.4176 119.76 -172.52 97.08 1.5500 IC NH3T NO3' NC3' NC2' 0.9717 103.61 17.81 119.76 1.5369 IC NC2' NC1' NN1 NC2 1.5500 116.58 -19.65 116.34 1.3499 IC NC1' NN1 NC2 NC3 1.5502 116.34 134.66 130.57 1.3607 IC NN1 NC2 NC3 NC4 1.3499 130.57 5.82 111.74 1.5356 IC NC2 NC3 NC4 NC5 1.3607 111.74 -1.05 119.26 1.5319 IC NC3 NC4 NC5 NC6 1.5356 119.26 -1.26 113.69 1.3745 IC NC4 NC5 NC6 NN1 1.5319 113.69 -0.29 128.15 1.3388 IC NC5 NC6 NN1 NC2 1.3745 128.15 4.14 116.26 1.3499 IC NN1 NC2 NC3 NC7 1.3499 130.57 -147.46 122.72 1.5282 IC NC2 NC3 NC7 NO7 1.3607 122.72 -140.47 119.41 1.2169 IC NC2 NC3 NC7 NN7 1.3607 122.72 46.61 116.68 1.3621 IC NO7 NC7 NN7 NH71 1.2169 123.49 -177.07 120.21 1.0093 IC NO7 NC7 NN7 NH72 1.2169 123.49 -4.94 119.16 1.0014 IC NC2 NC3 NC4 NH4 1.3607 111.74 -135.39 112.16 1.1099 IC NC2 NC3 NC4 NH42 1.3607 111.74 114.48 103.52 1.1129 IC NC3 NC4 NC5 NH5 1.5356 119.26 -171.18 122.65 1.0912 IC NC4 NC5 NC6 NH6 1.5319 113.69 179.92 118.00 1.0878 IC NC6 NN1 NC2 NH2 1.3388 116.26 162.03 117.47 1.0731 IC AC3' AC2' AO2' AP2 0.0000 000.00 180.00 000.00 0.0000 IC AC2' AO2' AP2 AO2T 0.0000 000.00 -39.52 000.00 0.0000 IC AO2T AO2' *AP2 AO1P 0.0000 000.00 -115.82 000.00 0.0000 IC AO2T AO2' *AP2 AO2P 0.0000 000.00 115.90 000.00 0.0000 IC AH2T AO2T AP2 AO2' 0.0000 000.00 180.00 000.00 0.0000 PATCH FIRST NONE LAST NONE ! below are residues and patches added for the 97/98 optimization ! and extension of the na all-atom parameters RESI THF 0.00 ! tetrahydrofuran, for MOLVIB ! GROUP ATOM O4' ON6 -0.50 ! H41' O4' H11' ATOM C4' CN8 0.07 ! \ / \ / ATOM C3' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM C2' CN8 -0.18 ! | | ATOM C1' CN8 0.07 ! H31'--C3'--C2'--H21' ATOM H11' HN8 0.09 ! / \ ATOM H12' HN8 0.09 ! H32' H22' ATOM H21' HN8 0.09 ! ATOM H22' HN8 0.09 ! ATOM H31' HN8 0.09 ! ATOM H32' HN8 0.09 ! ATOM H41' HN8 0.09 ! ATOM H42' HN8 0.09 ! BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' PATC FIRS NONE LAST NONE RESI THFM 0.00 ! Methyl-tetrahydrofuran GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN8 0.07 ! \ / ATOM C2' CN8 -0.18 ! H51'-C5' O4' H11' ATOM C3' CN8 -0.18 ! \ / \ / ATOM C4' CN8 0.16 ! H42'--C4' C1'--H12' ATOM H11' HN8 0.09 ! | | ATOM H12' HN8 0.09 ! H31'--C3'--C2'--H21' ATOM H21' HN8 0.09 ! / \ ATOM H22' HN8 0.09 ! H32' H22' ATOM H31' HN8 0.09 ! ATOM H32' HN8 0.09 ! ATOM H42' HN7 0.09 ! GROUP ! ATOM C5' CN9 -0.27 ! ATOM H51' HN9 0.09 ! ATOM H52' HN9 0.09 ! ATOM H53' HN9 0.09 ! BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H42' C5' H51' C5' H52' C5' H53' ! methyl- tetrahydrofuran guess conformation ! From Nicolas: the following guess conformation contains a ! mistake because it builds the H3' and H3'' atoms at the same point. ! So, I have commented out the following ic table !IC C4' O4' C1' C2' 1.4556 110.31 -14.32 105.78 1.5315 !IC O4' C1' C2' C3' 1.4200 105.78 32.55 102.71 1.5248 !IC C1' C2' C3' C4' 1.5315 102.71 -36.74 101.19 1.5432 !IC C2' C3' C4' O4' 1.5248 101.19 29.12 105.88 1.4556 !IC C3' C4' O4' C1' 1.5432 105.88 -9.56 110.31 1.4200 !IC H1' C1' C2' C3' 1.1024 109.82 -83.66 102.71 1.5248 !IC H1'' C1' C2' C3' 1.1024 109.82 154.66 102.71 1.5248 !IC H2' C2' C3' C4' 1.0992 111.36 -156.17 101.19 1.5432 !IC H2'' C2' C3' C4' 1.0994 109.88 81.56 101.19 1.5432 !IC H3' C3' C4' O4' 1.1016 110.76 146.70 105.88 1.4556 !IC H3'' C3' C4' O4' 1.1016 110.76 146.70 105.88 1.4556 !IC H4'' C4' O4' C1' 1.1012 107.70 -126.13 110.31 1.4200 !IC C5' C4' O4' C1' 1.4102 105.70 139.13 110.31 1.4200 !IC H51 C5' C4' O4' 1.0802 110.70 175.13 105.31 1.4556 !IC H52 C5' C4' O4' 1.0802 110.70 -63.99 105.31 1.4556 !IC H53 C5' C4' O4' 1.0802 110.70 55.99 105.31 1.4556 ! From Nicolas: the following ic table builds thfch3 in its ! energy minimized conformation, with the above ic table ('guess ! conformation as starting structure) !IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 !IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 !IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 !IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 !IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 !IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 !IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 !IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 !IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 !IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 !IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 !IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 !IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 !IC H51 C5' C4' O4' 1.1092 110.48 -179.98 108.43 1.4416 !IC H52 C5' C4' O4' 1.1104 110.01 -59.66 108.43 1.4416 !IC H53 C5' C4' O4' 1.1106 109.99 59.68 108.43 1.4416 PATC FIRS NONE LAST NONE RESI THFO 0.00 ! 3'-hydroxyl-tetrahydrofuran ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' ON6 -0.50 ! H41' O4' H11' ATOM C1' CN7B 0.07 ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM C4' CN7 0.07 ! | | ATOM H11' HN7 0.09 ! H31'--C3'--C2'--H21' ATOM H12' HN7 0.09 ! / \ ATOM H21' HN8 0.09 ! O3' H22' ATOM H22' HN8 0.09 ! | ATOM H41' HN7 0.09 ! H32' ATOM H42' HN7 0.09 GROUP ATOM C3' CN7 0.14 ATOM H31' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' H32' !Nicolas: the following IC are for thf-oh as optimized via ab initio calculations IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE RESI THFI 0.00 ! imidazole analog with THF ring ! Sugar: transferred from thf; used for optimization of chi, therefore ! the sugar carbon atom types are not rigorously correct ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' ON6 -0.50 ! H41' O4' Imidazole ATOM C1' CN7B 0.16 ! \ / \ / ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C4' CN7 0.07 ! | | ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' ATOM H42' HN7 0.09 ! / \ GROUP ! H32' H22' ATOM C2' CN8 -0.18 ! ATOM H21' HN8 0.09 ! ATOM H22' HN8 0.09 ! GROUP ! ATOM C3' CN7 -0.18 ! ATOM H31' HN7 0.09 ! ATOM H32' HN7 0.09 ! GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / | ATOM ND1 NR1 -0.04 ! HG-CG | ATOM CE1 CPH2 0.25 ! \ | ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 BOND CE1 HE1 CD2 HD2 CG HG ! KEEPS HYDROGENS IN RING PLANE IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPR CG CD2 ND1 HG CG ND1 CD2 HG ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE RESI THMI 0.00 ! thf-ch3-imidazole ! C5' has been declared as CN8, and C3' as CN7, for compatibility ! with DNA, but these carbons are rigorously CN9 and CN8 respectively ! Atom types for aliphatic hydrogens based on nucleotide GROUP ! Sugar: transferred from thf ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.16 ! \ / ATOM H12' HN7 0.09 ! H51'-C5' O4' Imidazole ATOM C4' CN7 0.16 ! \ / \ / ATOM H42' HN7 0.09 ! H42'--C4' C1'--H12' GROUP ! | | ATOM C2' CN8 -0.18 ! H31'--C3'--C2'--H21' ATOM H21' HN8 0.09 ! / \ ATOM H22' HN8 0.09 ! H32' H22' GROUP ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H42' C4' C5' C5' H51' C5' H52' C5' H53' BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! KEEPS HYDROGENS IN RING PLANE IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPR CG CD2 ND1 HG CG ND1 CD2 HG ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE RESI THFC 0.00 ! THF-3'-OH-4'-CH3 ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN8 0.07 ! \ / ATOM H11' HN8 0.09 ! H51'-C5' O4' H11' ATOM H12' HN8 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CN8 -0.18 ! / \ ATOM H21' HN8 0.09 ! O3' H22' ATOM H22' HN8 0.09 ! | GROUP ! H32' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ATOM C5' CN9 -0.27 ATOM H51' HN9 0.09 ATOM H52' HN9 0.09 ATOM H53' HN9 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' BOND C1' H11' C1' H12' BOND C2' H21' C2' H22' BOND C3' H31' BOND C4' H42' BOND C5' H51' C5' H52' C5' H53' BOND O3' H32' PATC FIRS NONE LAST NONE RESI TH5P -2.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -2) ! Atom types for aliphatic hydrogens based on nucleotide GROUP ! O1P (-2) ATOM O4' ON6 -0.50 ! || ATOM C1' CN7B 0.07 ! O2P==P==O2P ATOM H1' HN7 0.09 ! | ATOM H1'' HN7 0.09 ! H5'' | ATOM C4' CN7 0.16 ! \ | ATOM H4'' HN7 0.09 ! H5'--C5' O4' H1' GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H4'--C4' C1'--H1'' ATOM H2' HN8 0.09 ! | | ATOM H2'' HN8 0.09 ! H3'--C3'--C2'--H2' GROUP ! / \ ATOM C3' CN7 -0.18 ! H3'' H2'' ATOM H3' HN7 0.09 ! ATOM H3'' HN7 0.09 GROUP ATOM C5' CN8B -0.18 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 GROUP ATOM O5' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TH5H 0.00 ! 5'-hydroxy-methyl-tetrahydrofuran (phosphate -2) ! Atom types for aliphatic hydrogens based on nucleotide ! H5T GROUP ! / ATOM O4' ON6 -0.50 ! H5'' O5' ATOM C1' CN7B 0.07 ! \ | ATOM H1' HN7 0.09 ! H5'--C5' O4' H1' ATOM H1'' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H4'--C4' C1'--H1'' ATOM H4'' HN7 0.09 ! | | GROUP ! H3'--C3'--C2'--H2' ATOM C2' CN8 -0.18 ! / \ ATOM H2' HN8 0.09 ! H3'' H2'' ATOM H2'' HN8 0.09 GROUP ATOM C3' CN7 -0.18 ATOM H3' HN7 0.09 ATOM H3'' HN7 0.09 GROUP ATOM C5' CN8B 0.05 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' H5T IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H5' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H5'' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 IC C4' C5' O5' H5T 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T5PH -1.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -1) ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM C5' CN8B -0.08 ! ATOM H5' HN8 0.09 ! O1P H5T ATOM H5'' HN8 0.09 ! || / ATOM O5' ON2 -0.62 ! O2P==P==O3P ATOM P P 1.50 ! | ATOM O1P ON3 -0.82 ! O5' ATOM O2P ON3 -0.82 ! | ATOM O3P ON4 -0.68 ! H5'' | ATOM H5T HN4 0.34 ! \ | GROUP ! H5'--C5' O4' H1' ATOM O4' ON6 -0.50 ! \ / \ / ATOM C1' CN7B 0.07 ! H4'--C4' C1'--H1'' ATOM H1' HN7 0.09 ! | | ATOM H1'' HN7 0.09 ! H3'--C3'--C2'--H2' ATOM C4' CN7 0.16 ! / \ ATOM H4'' HN7 0.09 ! H3'' H2'' GROUP ! ATOM C2' CN8 -0.18 ATOM H2' HN8 0.09 ATOM H2'' HN8 0.09 GROUP ATOM C3' CN7 -0.18 ATOM H3' HN7 0.09 ATOM H3'' HN7 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P O3P H5T IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC O4' C4' C5' H5' 0.0 0.0 180.0 0.0 0.0 IC O4' C4' C5' H5'' 0.0 0.0 -60.0 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 IC O5' P O3P H5T 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TH3P -2.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -2) ! used to fit epsilon ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.07 ! \ / ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | | ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CN8 -0.18 ! O3' H22' ATOM H21' HN8 0.09 ! | ATOM H22' HN8 0.09 ! O1P==P==O2P GROUP ! || ATOM C3' CN7 -0.09 ! O3P (-2) ATOM H31' HN7 0.09 ! GROUP ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran ! used to fit epsilon ! Atom types for aliphatic hydrogens based on nucleotide GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 ! ATOM H11' HN7 0.09 ! H41' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | | ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CN8 -0.18 ! O3' H22' ATOM H21' HN8 0.09 ! | ATOM H22' HN8 0.09 ! O1P==P==O2P GROUP ! | ATOM C3' CN7 0.01 ! O3T (-1) ATOM H31' HN7 0.09 ! \ ATOM O3' ON2 -0.62 ! H3T ATOM P P 1.50 ! ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI R3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran ! with O2' hydroxyl. Used to fit C2'-O2' torsion in RNA ! Atom types for aliphatic hydrogens based on RNA nucleotide GROUP ATOM O4' ON6B -0.50 ! ATOM C1' CN7B 0.07 ! ATOM H11' HN7 0.09 ! H41' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | | ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CN7B 0.14 ! O3' O2' ATOM H21' HN7 0.09 ! | | ATOM O2' ON5 -0.66 ! O1P==P==O2P H22' ATOM H22' HN5 0.43 ! | GROUP ! O3T (-1) ATOM C3' CN7 0.01 ! \ ATOM H31' HN7 0.09 ! H3T ATOM O3' ON2 -0.62 ! ATOM P P 1.50 ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC O2' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 IC H22' O2' C2' C3' 1.0822 110.88 0.00 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI A3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran ! with O2' hydroxyl in an arabinose (beta) conformation. ! The furanose ring contains atom type CN7C, specific of arabinose GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 ! ATOM H11' HN7 0.09 ! H41' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | | ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CN7C 0.14 ! O3' O2' O2' is beta ATOM H22' HN7 0.09 ! | | ATOM O2' ON5 -0.66 ! O1P==P==O2P H22' ATOM H21' HN5 0.43 ! | GROUP ! O3T (-1) ATOM C3' CN7 0.01 ! \ ATOM H31' HN7 0.09 ! H3T ATOM O3' ON2 -0.62 ! ATOM P P 1.50 ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H22' C2' O2' O2' H21' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H22' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 IC O2' C2' C3' C4' 1.0846 110.65 120.00 100.86 1.5211 IC H21' O2' C2' C3' 1.0822 110.88 120.00 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T3PM -1.00 ! 3'phosphate-hydroxyl-tetrahydrofuran (phosphate -1) ! capped with a methyl group. This is to investigate the differences ! between BI and BII forms of DNA ! C3T is defined as CN8B to miminck DNA GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 ! H41' O4' H11' ATOM H11' HN7 0.09 ! \ / \ / ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C4' CN7 0.07 ! | | ATOM H41' HN7 0.09 ! H31'--C3'--C2'--H21' ATOM H42' HN7 0.09 ! / \ GROUP ! O3' H22' ATOM C2' CN8 -0.18 ! | ATOM H21' HN8 0.09 ! O1P==P==O2P ATOM H22' HN8 0.09 ! | GROUP ! O3T (-1) ATOM C3' CN7 0.01 ! \ ATOM H31' HN7 0.09 ! C3T--H3T3 GROUP ! / \ ATOM O3' ON2 -0.57 ! H3T1 H3T2 ATOM P P 1.50 ! ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O3T ON2 -0.57 ATOM C3T CN8B -0.17 ATOM H3T1 HN8 0.09 ATOM H3T2 HN8 0.09 ATOM H3T3 HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T BOND C3T H3T1 C3T H3T2 C3T H3T3 IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000 IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000 IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000 IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000 IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000 IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000 PATC FIRS NONE LAST NONE RESI TM3P -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) ! This is the DNA version (the RNA version is RM3P, see below) GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.07 ! \ / ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CN8 -0.18 ! / \ ATOM H21' HN8 0.09 ! O3' H22' ATOM H22' HN8 0.09 ! | GROUP ! O1P==P==O2P ATOM C3' CN7 -0.09 ! || ATOM H31' HN7 0.09 ! O3P (-2) GROUP ! ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RM3P -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) ! This is the RNA version of TM3P: NOTE that it does NOT have a 2'hydroxyl to ! allow for the determination of the influence of the ring dihedrals on the ! sugar puckering energetics in the absence of the 2' hydroxyl GROUP ATOM O4' ON6B -0.50 ATOM C1' CN7B 0.07 ATOM H11' HN7 0.09 ATOM H12' HN7 0.09 ATOM C4' CN7 0.16 ATOM H42' HN7 0.09 GROUP ATOM C2' CN7B -0.18 ATOM H21' HN7 0.09 ATOM H22' HN7 0.09 GROUP ATOM C3' CN7 -0.09 ATOM H31' HN7 0.09 GROUP ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T35P -4.00 ! 5'-phosphate-3'-phosphate- ! methyl-tetrahydrofuran (phosphate -2) GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 ! O1P (-2) ATOM H1' HN7 0.09 ! || ATOM H1'' HN7 0.09 ! O2P==P==O2P ATOM C4' CN7 0.16 ! | ATOM H4'' HN7 0.09 ! H5'' O5' GROUP ! \ | ATOM C2' CN8 -0.18 ! H5'--C5' O4' H1' ATOM H2' HN8 0.09 ! \ / \ / ATOM H2'' HN8 0.09 ! H4'--C4' C1'--H1'' GROUP ! | | ATOM C3' CN7 -0.09 ! H3'--C3'--C2'--H2' ATOM H3' HN7 0.09 ! / \ GROUP ! O3' H22' ATOM O3' ON2 -0.40 ! | ATOM P3 P 1.10 ! O31P==P==O32P ATOM O31P ON3 -0.90 ! || ATOM O32P ON3 -0.90 ! O33P (-2) ATOM O33P ON3 -0.90 GROUP ATOM C5' CN8B -0.18 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 GROUP ATOM O5' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' O3' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P O3' P3 P3 O31P P3 O32P P3 O33P IC C4' O4' C1' C2' 1.4416 109.61 0.45 106.74 1.5328 IC O4' C1' C2' C3' 1.4471 106.74 -21.92 103.38 1.5200 IC C1' C2' C3' C4' 1.5328 103.38 33.49 102.18 1.5321 IC C2' C3' C4' O4' 1.5200 102.18 -34.11 105.43 1.4416 IC C3' C4' O4' C1' 1.5321 105.43 21.23 109.61 1.4471 IC H1' C1' C2' C3' 1.1099 113.03 -141.96 103.38 1.5200 IC H1'' C1' C2' C3' 1.1111 111.16 93.50 103.38 1.5200 IC H2' C2' C3' C4' 1.1135 109.13 -81.76 102.18 1.5321 IC H2'' C2' C3' C4' 1.1076 113.49 155.97 102.18 1.5321 IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 IC P3 C3' C4' O4' 1.5 112.41 -156.66 105.43 1.4416 IC C5' C4' C3' O3' 0.0 0.0 180.0 0.0 0.0 IC C4' C3' O3' P3 0.0 0.0 180.0 0.0 0.0 IC C3' O3' P3 O31P 0.0 0.0 -60.0 0.0 0.0 IC C3' O3' P3 O32P 0.0 0.0 180.0 0.0 0.0 IC C3' O3' P3 O33P 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI T2FU -2.00 ! THF with PO3 on c3, F (alpha, down) on c2 ! Charge distribution is preliminary GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 ! H41' O4' H11' ATOM C4' CN7 0.07 ! \ / \ / ATOM H11' HN7 0.09 ! H42'--C4' C1'--H12' ATOM H12' HN7 0.09 ! | | ATOM H41' HN7 0.09 ! H31'--C3'--C2'--F2' (alpha) ATOM H42' HN7 0.09 ! / \ GROUP ! O3' H22' ATOM C2' CN7C 0.14 ! | ATOM H22' HN7 0.09 ! O1P==P==O2P ATOM F2' FN1 -0.23 ! || GROUP ! O3P (-2) ATOM C3' CN7 -0.09 ! ATOM H31' HN7 0.09 GROUP ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' F2' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC F2' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TMFU -2.00 ! THF with ch3 on c4', opo3 on c3', F (beta, up) on c2' ! Caution: Charges are preliminary. Charge on fluorine was ! taken from Daxu Yin's thesis (monofluoroethane). GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.07 ! \ / ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | | GROUP ! H31'--C3'--C2'--F2' (beta) ATOM C2' CN7C 0.19 ! / \ ATOM H22' HN7 0.09 ! O3' H22' ATOM F2' FN1 -0.28 ! | GROUP ! O1P==P==O2P ATOM C3' CN7 -0.09 ! || ATOM H31' HN7 0.09 ! O3P (-2) GROUP ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' BOND C2' H22' C2' F2' BOND C3' O3' C3' H31' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' ! The following IC table is a guess from thfohch3 (Nicolas): IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 IC F2' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 180.00 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.00 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 -60.00 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 PATC FIRS NONE LAST NONE RESI T2FD -2.00 ! THF with methyl on c4', opo3 on c3, F (alpha, down) on c2 ! Charge distribution is preliminary GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 ! ATOM C4' CN7 0.07 ! H41' O4' H11' ATOM H11' HN7 0.09 ! \ / \ / ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | | ATOM H42' HN7 0.09 ! H31'--C3'--C2'--F2' (alpha) GROUP ! / \ ATOM C2' CN7C 0.14 ! O3' H22' ATOM H21' HN7 0.09 ! | ATOM F2' FN1 -0.23 ! O1P==P==O2P GROUP ! || ATOM C3' CN7 -0.09 ! O3P (-2) ATOM H31' HN7 0.09 GROUP ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' F2' C2' H21' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC F2' C2' C3' C4' 1.0846 110.65 -148.45 100.86 1.5211 IC H21' C2' C3' C4' 1.0822 110.88 91.68 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TMFD -2.00 ! Flourine on C2' (alpha, down) with ch3 on c4', opo3 on c3', oh on c2' ! Charge distribution is preliminary GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.07 ! \ / ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | | GROUP ! H31'--C3'--C2'--F2' (alpha) ATOM C2' CN7D 0.19 ! / \ ATOM H21' HN7 0.09 ! O3' H22' ATOM F2' FN1 -0.28 ! | GROUP ! O1P==P==O2P ATOM C3' CN7 -0.09 ! || ATOM H31' HN7 0.09 ! O3P (-2) GROUP ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' BOND C2' F2' C2' H21' BOND C3' O3' C3' H31' BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' ! The following IC table is a guess from thfohch3 (Nicolas): IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 IC F2' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 180.00 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.00 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 -60.00 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 PATC FIRS NONE LAST NONE RESI ARMO 0.00 ! ribose, thfch3ohoh, with the c2' hydroxyl in the beta configuration GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN8 0.07 ! \ / ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CN7 0.14 ! / \ ATOM H22' HN7 0.09 ! O3' O2' ATOM O2' ON5 -0.66 ! | | (beta) ATOM H21' HN5 0.43 ! H32' H22' GROUP ! ATOM C3' CN7 0.14 ATOM H31' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H11' C1' H12' BOND C2' O2' C2' H22' O2' H21' BOND C3' O3' O3' H32' C3' H31' BOND C4' C5' C5' H51' C5' H52' C5' H53' C4' H42' ! The following IC table is a guess from thfohch3 (Nicolas): IC C1' C2' C3' C4' 0.0 0.0 330.81 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 39.77 0.0 0.0 IC H11' C1' C2' C3' 0.0 0.0 129.38 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 251.29 0.0 0.0 IC O2' C2' C3' C4' 0.0 0.0 89.74 0.0 0.0 IC H21' O2' C2' C3' 0.0 0.0 90.00 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 209.60 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 161.48 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 280.72 0.0 0.0 IC H32' O3' C3' C4' 0.0 0.0 44.72 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 87.60 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 176.37 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 56.84 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 297.06 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 207.55 0.0 0.0 PATC FIRS NONE LAST NONE RESI THFA 0.00 ! THF-OH-CH3-IM GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C4' CN7 0.16 ! \ / ATOM H42' HN7 0.09 ! H51'-C5' O4' Imidazole ATOM C1' CN7B 0.16 ! \ / \ / ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' GROUP ! | | ATOM C2' CN8 -0.18 ! H31'--C3'--C2'--H21' ATOM H21' HN8 0.09 ! / \ ATOM H22' HN8 0.09 ! O3' H22' GROUP ! | ATOM H31' HN7 0.09 ! H32' ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' H53' BOND O3' H32' BOND C1' ND1 ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -59.66 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 59.68 0.0 0.0 PATC FIRS NONE LAST NONE RESI ARAO 0.00 ! arabinose sugar, oh alpha on c3', oh beta on c2' GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN8 0.07 ! ATOM H11' HN8 0.09 ! H41' O4' H11' ATOM H12' HN8 0.09 ! \ / \ / ATOM C4' CN8B 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN8 0.09 ! | | ATOM H42' HN8 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C2' CN7 0.14 ! O3' O2' ATOM H22' HN7 0.09 ! | | (beta) ATOM O2' ON5 -0.66 ! H32' H22' ATOM H21' HN5 0.43 ! GROUP ATOM C3' CN7 0.14 ATOM H31' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41' BOND C4' H42' O2' H21' O3' H32' !Nicolas: the following IC are for thf-oh as optimized via ab initio calculations IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC O2' C2' C3' C4' 0.0000 0.00 91.68 0.0000 0.0000 IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE RESI ARIM 0.00 ! arabinose sugar with imidazole ! transferred from thf GROUP ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.16 ! H41' O4' Imidazole ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN8 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN8 0.09 ! | | ATOM H42' HN8 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM C3' CN8 -0.18 ! H32' O2' ATOM H31' HN8 0.09 ! | (beta) ATOM H32' HN8 0.09 ! H22' GROUP ATOM C2' CN7 0.14 ATOM H22' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H21' HN5 0.43 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C2' O2' C1' H12' C2' H22' C3' H31' C3' H32' O2' H21' BOND C4' H41' C4' H42' BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! KEEPS HYDROGENS IN RING PLANE IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPR CG CD2 ND1 HG CG ND1 CD2 HG ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 1.532 101.886 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC O2' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE RESI AR3P -2.00 ! arabinose sugar with phosphate on 3' (phosphate -2) GROUP ATOM O4' ON6 -0.50 ! H41' O4' H11' ATOM C1' CN8 0.07 ! \ / \ / ATOM C4' CN8B 0.07 ! H42'--C4' C1'--H12' ATOM H11' HN8 0.09 ! | | ATOM H12' HN8 0.09 ! H31'--C3'--C2'--H22' (alpha) ATOM H41' HN8 0.09 ! / \ ATOM H42' HN8 0.09 ! O3' O2' GROUP ! | | ATOM C2' CN7 0.14 ! O1P==P==O2P H21' ATOM H22' HN7 0.09 ! || ATOM O2' ON5 -0.66 ! O3P (-2) ATOM H21' HN5 0.43 GROUP ATOM C3' CN7 -0.09 ATOM H31' HN7 0.09 GROUP ATOM O3' ON5 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' O2' C2' H22' C3' H31' C4' H41' BOND C4' H42' O2' H21' O3' P P O1P P O2P P O3P IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC O2' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H21' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RIBO 0.00 ! ribose, both c2' and c3' hydroxyls are alpha GROUP ATOM O4' ON6 -0.50 ! H41' O4' H11' ATOM C1' CN8 0.07 ! \ / \ / ATOM C4' CN8B 0.07 ! H42'--C4' C1'--H12' ATOM H11' HN8 0.09 ! | | ATOM H12' HN8 0.09 ! H31'--C3'--C2'--H22' ATOM H41' HN8 0.09 ! / \ ATOM H42' HN8 0.09 ! O3' O2' GROUP ! | | ATOM C2' CN7 0.14 ! H32' H21' ATOM H21' HN7 0.09 ! ATOM O2' ON5 -0.66 ATOM H22' HN5 0.43 GROUP ATOM C3' CN7 0.14 ATOM H31' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' O2' C2' H21' C3' H31' C4' H41' BOND C4' H42' O2' H22' O3' H32' !Nicolas: the following IC are for thf-oh as optimized via ab initio calculations IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC O2' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H22' O2' C2' C3' 0.0 0.0 -60.0 0.0 0.0 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE RESI TMPM -1.00 ! 4'-methyl,3'-methylphosphate tetrahydrofuran (phosphate -1) !charges corrected by adm jr. 9/98 GROUP ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN8 0.07 ! \ / ATOM H11' HN8 0.09 ! H51'-C5' O4' H11' ATOM H12' HN8 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | | GROUP ! H31'--C3'--C2'--H21' ATOM C2' CN8 -0.18 ! / \ ATOM H21' HN8 0.09 ! O3' H22' ATOM H22' HN8 0.09 ! | GROUP ! O1P==P==O2P ATOM C3' CN7 0.01 ! | ATOM H31' HN7 0.09 ! O3P (-1) GROUP ! \ ATOM O3' ON2 -0.57 ! C3T--H3T3 ATOM P P 1.50 ! / \ ATOM O1P ON3 -0.78 ! H3T1 H3T2 ATOM O2P ON3 -0.78 ! ATOM O3P ON2 -0.57 ATOM C3T CN9 -0.17 ATOM H3T1 HN9 0.09 ATOM H3T2 HN9 0.09 ATOM H3T3 HN9 0.09 GROUP ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' C5' H53' IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TADE 0.00 ! thf with adenine ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 9-m-ade GROUP ATOM C5 CN5 0.28 ! H61 H62! ATOM N7 NN4 -0.71 ! \ / ATOM C8 CN4 0.34 ! N6 ATOM H8 HN3 0.12 ! | ATOM N9 NN2 -0.05 ! C6 ATOM C1' CN7B 0.16 ! // \ ATOM N1 NN3A -0.74 ! N1 C5--N7\\ ATOM C2 CN4 0.50 ! | || C8-H8 ATOM H2 HN3 0.13 ! C2 C4--N9/ ATOM N3 NN3A -0.75 ! / \\ / \ ATOM C4 CN5 0.43 ! H2 N3 \ ATOM C6 CN2 0.46 ! \ ATOM N6 NN1 -0.77 ! \ ATOM H61 HN1 0.38 ! \ ATOM H62 HN1 0.38 ! H42' O4' \ ATOM O4' ON6 -0.50 ! \ / \ \ ATOM H12' HN7 0.09 ! H41'-C4' C1' ATOM C4' CN7 0.07 ! \ / \ ATOM H41' HN7 0.09 ! H31'--C3'--C2' H12' ATOM H42' HN7 0.09 ! / / \ GROUP ! H32' H21' H22' ATOM C2' CN8 -0.18 ! ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TCYT 0.00 ! THF with cytosine ! Atom types for aliphatic atoms based on nucleotide !atom order to be consistent with 1-m-cyt GROUP ATOM N1 NN2 -0.13 ! ATOM C1' CN7B 0.16 ! H42 H41 ATOM C6 CN3 0.05 ! \ / ATOM H6 HN3 0.17 ! N4 ATOM C2 CN1 0.52 ! | ATOM O2 ON1C -0.49 ! C4 ATOM N3 NN3 -0.66 ! / \\ ATOM C4 CN2 0.65 ! H5-C5 N3 ATOM N4 NN1 -0.75 ! || | ATOM H41 HN1 0.37 ! H6-C6 C2 ATOM H42 HN1 0.33 ! \ / \\ ATOM C5 CN3 -0.13 ! N1 O2 ATOM H5 HN3 0.07 ! \ ATOM O4' ON6 -0.50 ! \ ATOM H12' HN7 0.09 ! \ ATOM C4' CN7 0.07 ! H42' O4' \ ATOM H41' HN7 0.09 ! \ / \ \ ATOM H42' HN7 0.09 ! H41'-C4' C1' GROUP ! \ / \ ATOM C2' CN8 -0.18 ! H31'--C3'--C2' H12' ATOM H21' HN8 0.09 ! / / \ ATOM H22' HN8 0.09 ! H32' H21' H22' GROUP ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N1 BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 BOND C2 N3 C4 C5 C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR C2 N1 N3 O2 C4 N3 C5 N4 IMPR N4 C4 H41 H42 BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TGUA 0.00 ! thf with guanine ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 9-m-gua GROUP ATOM N9 NN2B -0.02 ! O6 ATOM C4 CN5 0.26 ! || ATOM C1' CN7B 0.16 ! C6 ATOM N3 NN3G -0.74 ! / \ ATOM C2 CN2 0.75 ! H1-N1 C5--N7\\ ATOM N1 NN2G -0.34 ! | || C8-H8 ATOM H1 HN2 0.26 ! C2 C4--N9/ ATOM N2 NN1 -0.68 ! / \\ / \ ATOM H21 HN1 0.32 ! H21-N2 N3 \ ATOM H22 HN1 0.35 ! | \ ATOM C6 CN1 0.54 ! H22 \ ATOM O6 ON1 -0.51 ! \ ATOM C5 CN5G 0.00 ! H42' O4' \ ATOM N7 NN4 -0.60 ! \ / \ \ ATOM C8 CN4 0.25 ! H41'-C4' C1' ATOM H8 HN3 0.16 ! \ / \ ATOM O4' ON6 -0.50 ! H31'--C3'--C2' H12' ATOM H12' HN7 0.09 ! / / \ ATOM C4' CN7 0.07 ! H32' H21' H22' ATOM H41' HN7 0.09 ATOM H42' HN7 0.09 GROUP ATOM C2' CN8 -0.18 ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TTHY 0.00 ! THF with thymine on C1' ! Atom type for N1 changed from NN2 to NN2B, to adjust ! chi in thymine independantly of cytosine. ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 1-m-thy GROUP ATOM N1 NN2B -0.34 ! H51 O4 ATOM C1' CN7B 0.16 ! | || ATOM C6 CN3 0.17 ! H52-C5M C4 H3 ATOM H6 HN3 0.17 ! | \ / \ / ATOM C2 CN1T 0.51 ! H53 C5 N3 ATOM O2 ON1 -0.41 ! || | ATOM N3 NN2U -0.46 ! H6-C6 C2 ATOM H3 HN2 0.36 ! \ / \\ ATOM C4 CN1 0.50 ! N1 O2 ATOM O4 ON1 -0.45 ! \ ATOM C5 CN3T -0.15 ! \ ATOM C5M CN9 -0.11 ! \ ATOM H51 HN9 0.07 ! H42' O4' \ ATOM H52 HN9 0.07 ! \ / \ \ ATOM H53 HN9 0.07 ! H41'-C4' C1' ATOM O4' ON6 -0.50 ! \ / \ ATOM H12' HN7 0.09 ! H31'--C3'--C2' H12' ATOM C4' CN7 0.07 ! / / \ ATOM H41' HN7 0.09 ! H32' H21' H22' ATOM H42' HN7 0.09 GROUP ATOM C2' CN8 -0.18 ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N1 BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI TURA 0.00 ! THF with uracil on C1' ! Atom type for N1 changed from NN2 to NN2B, in order to adjust ! chi in uracil/thymine independantly of cytosine. ! Atom types for aliphatic atoms based on nucleotide ! atom order consistent with 1-m-thy GROUP ATOM N1 NN2B -0.34 ! O4 ATOM C1' CN7B 0.16 ! || ATOM C6 CN3 0.20 ! C4 H3 ATOM H6 HN3 0.14 ! / \ / ATOM C2 CN1T 0.55 ! H5-C5 N3 ATOM O2 ON1 -0.45 ! || | ATOM N3 NN2U -0.46 ! H6-C6 C2 ATOM H3 HN2 0.36 ! \ / \\ ATOM C4 CN1 0.53 ! N1 O2 ATOM O4 ON1 -0.48 ! \ ATOM C5 CN3 -0.15 ! \ ATOM H5 HN3 0.10 ! \ ATOM O4' ON6 -0.50 ! H42' O4' \ ATOM H12' HN7 0.09 ! \ / \ \ ATOM C4' CN7 0.07 ! H41'-C4' C1' ATOM H41' HN7 0.09 ! \ / \ ATOM H42' HN7 0.09 ! H31'--C3'--C2' H12' GROUP ! / / \ ATOM C2' CN8 -0.18 ! H32' H21' H22' ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42' BOND C1' N1 BOND N1 C2 N1 C6 BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 H5 C6 H6 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 ! ic table for thfim, from Nicolas: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI THAO 0.00 ! Nucleoside analogue with imidazole GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Imidazole GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | | ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \ ATOM H31' HN7 0.09 ! O3' H22' ATOM C3' CN7 0.14 ! | ATOM O3' ON5 -0.66 ! H32' ATOM H32' HN5 0.43 ! GROUP ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' ND1 BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! KEEPS HYDROGENS IN RING PLANE IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPR CG CD2 ND1 HG CG ND1 CD2 HG ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CG 0.0 0.0 90.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSA 0.00 ! deoxy-nucleoside with adenine GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Adenine GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | | ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' ! Adenine atoms ! / \ GROUP ! O3' H22' ATOM C5 CN5 0.28 ! | ATOM N7 NN4 -0.71 ! H32' ATOM C8 CN4 0.34 ATOM H8 HN3 0.12 ATOM N9 NN2 -0.05 ATOM N1 NN3A -0.74 ATOM C2 CN4 0.50 ATOM H2 HN3 0.13 ATOM N3 NN3A -0.75 ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! Methyl group on C4' ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSG 0.00 ! nucleoside with guanine GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Guanine GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | | ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' ! Guanine atoms ! / \ GROUP ! O3' H22' ATOM N9 NN2B -0.02 ! | ATOM C4 CN5 0.26 ! H32' ATOM N3 NN3G -0.74 ATOM C2 CN2 0.75 ATOM N1 NN2G -0.34 ATOM H1 HN2 0.26 ATOM N2 NN1 -0.68 ATOM H21 HN1 0.32 ATOM H22 HN1 0.35 ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! C5' hydroxyl ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSC 0.00 ! nucleoside with cytosine GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Cytosine GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | | ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' ! Cytosine atoms ! / \ GROUP ! O3' H22' ATOM N1 NN2 -0.13 ! | ATOM C6 CN3 0.05 ! H32' ATOM H6 HN3 0.17 ATOM C2 CN1 0.52 ATOM O2 ON1C -0.49 ATOM N3 NN3 -0.66 ATOM C4 CN2 0.65 ATOM N4 NN1 -0.75 ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 ATOM C5 CN3 -0.13 ATOM H5 HN3 0.07 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! C5' hydroxyl ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N1 BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 BOND C2 N3 C4 C5 C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR N4 C4 H41 H42 C2 N1 N3 O2 C4 N3 C5 N4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUST 0.00 ! nucleoside with thymine GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Thymine GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | | ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' ! Atoms for thymine ! / \ GROUP ! O3' H22' ATOM N1 NN2B -0.34 ! | ATOM C6 CN3 0.17 ! H32' ATOM H6 HN3 0.17 ATOM C2 CN1T 0.51 ATOM O2 ON1 -0.41 ATOM N3 NN2U -0.46 ATOM H3 HN2 0.36 ATOM C4 CN1 0.50 ATOM O4 ON1 -0.45 ATOM C5 CN3T -0.15 ATOM C5M CN9 -0.11 ATOM H51 HN9 0.07 ATOM H52 HN9 0.07 ATOM H53 HN9 0.07 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! C5' hydroxyl ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N1 BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUSU 0.00 ! nucleoside with uracil GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Uracil GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | | ATOM H22' HN8 0.09 ! H31'--C3'--C2'--H21' ! Atoms for uracil ! / \ GROUP ! O3' H22' ATOM N1 NN2B -0.34 ! | ATOM C6 CN3 0.20 ! H32' ATOM H6 HN3 0.14 ATOM C2 CN1T 0.55 ATOM O2 ON1 -0.45 ATOM N3 NN2U -0.46 ATOM H3 HN2 0.36 ATOM C4 CN1 0.53 ATOM O4 ON1 -0.48 ATOM C5 CN3 -0.15 ATOM H5 HN3 0.10 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! C5' hydroxyl ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' N1 N1 C2 N1 C6 C2 O2 BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5 BOND C5 C6 C5 H5 C6 H6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUS 0.00 ! Ribonucleoside analogue with imidazole GROUP ATOM O4' ON6B -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Imidazole GROUP ! \ / \ / ATOM C2' CN7B 0.14 ! H42'--C4' C1'--H12' ATOM H21' HN7 0.09 ! | | ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' ATOM H22' HN5 0.43 ! / \ GROUP ! O3' O2' ATOM H31' HN7 0.09 ! | | ATOM C3' CN7 0.14 ! H32' H22' ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' BOND C4' H42' C5' H51' C5' H52' C5' O5' O5' H5T BOND O3' H32' BOND C1' ND1 BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! KEEPS HYDROGENS IN RING PLANE IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPR CG CD2 ND1 HG CG ND1 CD2 HG ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H22' O2' C2' C3' 0.0 0.0 -60.00 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 -93.14 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUA 0.00 ! ribo-nucleoside with adenine GROUP ATOM O4' ON6B -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Adenine GROUP ! \ / \ / ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C2' CN7B 0.14 ! | | ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' ATOM H22' HN5 0.43 ! / \ ! Adenine atoms ! O3' O2' GROUP ! | | ATOM C5 CN5 0.28 ! H32' H22' ATOM N7 NN4 -0.71 ATOM C8 CN4 0.34 ATOM H8 HN3 0.12 ATOM N9 NN2 -0.05 ATOM N1 NN3A -0.74 ATOM C2 CN4 0.50 ATOM H2 HN3 0.13 ATOM N3 NN3A -0.75 ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! C5' hydroxyl ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O2' H22' O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 150.8 113.71 1.4896 IC O4' C1' N9 C4 1.5251 108.6 229.5 125.5 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUG 0.00 ! ribo-nucleoside with guanine GROUP ATOM O4' ON6B -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Guanine GROUP ! \ / \ / ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C2' CN7B 0.14 ! | | ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' ATOM H22' HN5 0.43 ! / \ ! Guanine atoms ! O3' O2' GROUP ! | | ATOM N9 NN2B -0.02 ! H32' H22' ATOM C4 CN5 0.26 ATOM N3 NN3G -0.74 ATOM C2 CN2 0.75 ATOM N1 NN2G -0.34 ATOM H1 HN2 0.26 ATOM N2 NN1 -0.68 ATOM H21 HN1 0.32 ATOM H22 HN1 0.35 ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! C5' hydroxyl ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O2' H22' O3' H32' BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 DOUBLE C2 N3 C4 C5 N7 C8 C6 O6 IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374 BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI RNUC 0.00 ! ribo-nucleoside with cytosine GROUP ATOM O4' ON6B -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ | ATOM H12' HN7 0.09 !H52'--C5' O4' Cytosine GROUP ! \ / \ / ATOM H21' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C2' CN7B 0.14 ! | | ATOM O2' ON5 -0.66 ! H31'--C3'--C2'--H21' ATOM H22' HN5 0.43 ! / \ ! Cytosine atoms ! O3' O2' GROUP ! | | ATOM N1 NN2 -0.13 ! H32' H22' ATOM C6 CN3 0.05 ATOM H6 HN3 0.17 ATOM C2 CN1 0.52 ATOM O2 ON1C -0.49 ATOM N3 NN3 -0.66 ATOM C4 CN2 0.65 ATOM N4 NN1 -0.75 ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 ATOM C5 CN3 -0.13 ATOM H5 HN3 0.07 GROUP ! Hydroxyl group on C3' ATOM H31' HN7 0.09 ATOM C3' CN7 0.14 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43 GROUP ! Methyl group on C4' ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C3' O3' C1' H12' C2' H21' C2' O2' C3' H31' C4' H42' BOND C5' H51' C5' H52' C5' O5' O5' H5T BOND O2' H22' O3' H32' BOND C1' N1 BOND N1 C2 N1 C6 BOND C2 N3 C4 N4 N4 H41 N4 H42 BOND C4 C5 C5 H5 C6 H6 DOUBLE C2 O2 C5 C6 N3 C4 IMPR N4 C4 H41 H42 C2 N1 N3 O2 C4 N3 C5 N4 ! This IC table is only an initial guess: IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC O2' C2' C3' C4' 1.42 109.06 283.42 0.0 0.0 IC H22' O2' C2' C3' 0.98 109.05 283.42 0.0 0.0 IC O3' C3' C4' O4' 0.0 0.0 324.95 0.0 0.0 IC H32' O3' C3' C2' 0.0 0.0 -60.00 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 147.80 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364 IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 144.82 0.0 0.0 IC H51' C5' C4' O4' 0.0 0.0 -179.98 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 59.66 0.0 0.0 IC O5' C5' C4' O4' 0.0 0.0 -59.68 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NUCL -1.00 ! !WARNING: - The charge distribution on the imidazole is identical ! to the charge distribution on the imidazole in THFI, which is ! different from the charge distribution on the equivalent moiety ! in adenine. ! - The charge distribution on the sugar is identical to what ! it is in the DNA. ! - The charge' on the 3' end of the "backbone" is identical to ! what it is in the DNA, except for the terminal methyl group for which ! there is no DNA equivalent. ! - The charges on the 5' extremity of the backbone is as in the ! 5TER patch used for the DNA. An alternative to that would be to use ! charges more similar to what is in non-terminal residues in DNA. GROUP ATOM O4' ON6 -0.50 ATOM C1' CN7B 0.16 ATOM H12' HN7 0.09 ATOM C4' CN7 0.16 ATOM H42' HN7 0.09 GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ! The following atom types use the parameters specifically developed ! for the imidazole ! Atom types for aliphatic atoms based on nucleotide ATOM CG CPH1 -0.05 ! C1' HE1 ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! | ! HD2 GROUP ! ATOM C2' CN8 -0.18 ! ATOM H21' HN8 0.09 ! H5T ATOM H22' HN8 0.09 ! | GROUP ! H52' O5' ATOM C3' CN7 0.01 ! \ / ATOM H31' HN7 0.09 ! H51'-C5' O4' Imidazole ATOM O3' ON2 -0.57 ! \ / \ / ATOM P P 1.50 ! H42'--C4' C1'--H12' ATOM O1P ON3 -0.78 ! | | ATOM O2P ON3 -0.78 ! H31'--C3'--C2'--H21' ATOM O3P ON2 -0.57 ! / \ ATOM C3T CN8B -0.17 ! O3' H22' ATOM H3T1 HN8 0.09 ! | ATOM H3T2 HN8 0.09 ! O1P==P==O2P ATOM H3T3 HN8 0.09 ! | GROUP ! O3P (-1) ATOM C5' CN8B 0.05 ! \ ATOM H51' HN8 0.09 ! C3T--H3T3 ATOM H52' HN8 0.09 ! / \ ATOM H5T HN5 0.43 ! H3T1 H3T2 ATOM O5' ON5 -0.66 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' BOND C5' O5' O5' H5T BOND C1' ND1 BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG DOUBLE CG CD2 CE1 NE2 ! KEEPS HYDROGENS IN RING PLANE IMPR ND1 CG CE1 C1' ND1 CE1 CG C1' IMPR CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPR CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPR CG CD2 ND1 HG CG ND1 CD2 HG IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 90.00 0.0 0.0 IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0 IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 PATC FIRS NONE LAST NONE RESI NADE -1.00 ! ! NADE is a nucleotide analogue similar to NUCL, except that the imidazole ! has been replaced by an adenine ! - The charge distribution on the sugar is identical to what ! it is in the DNA. ! - The charge' on the 3' end of the "backbone" is identical to ! what it is in the DNA, except for the terminal methyl group for which ! there is no DNA equivalent. ! - The charges on the 5' extremity of the backbone is as in the ! 5TER patch used for the DNA. An alternative to that would be to use ! charges more similar to what is actuallly in non-terminal residues in the ! DNA. GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C1' CN7B 0.16 ! | ATOM H12' HN7 0.09 ! H52' O5' ATOM C4' CN7 0.16 ! \ / ATOM H42' HN7 0.09 ! H51'-C5' O4' Adenine GROUP ! \ / \ / ATOM C5 CN5 0.30 ! H42'--C4' C1'--H12' ATOM N7 NN4 -0.69 ! | | ATOM C8 CN4 0.34 ! H31'--C3'--C2'--H21' ATOM H8 HN3 0.10 ! / \ ATOM N9 NN2 -0.06 ! O3' H22' ATOM N1 NN3A -0.74 ! | ATOM C2 CN4 0.50 ! O1P==P==O2P ATOM H2 HN3 0.13 ! | ATOM N3 NN3A -0.75 ! O3P (-1) ATOM C4 CN5 0.43 ! \ ATOM C6 CN2 0.44 ! C3T--H3T3 ATOM N6 NN1 -0.75 ! / \ ATOM H61 HN1 0.38 ! H3T1 H3T2 ATOM H62 HN1 0.37 GROUP ATOM C2' CN8 -0.18 ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP ATOM C3' CN7 0.01 ATOM H31' HN7 0.09 ATOM O3' ON2 -0.57 ATOM P P 1.50 ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O3P ON2 -0.57 ATOM C3T CN8B -0.17 ATOM H3T1 HN7 0.09 ATOM H3T2 HN7 0.09 ATOM H3T3 HN7 0.09 GROUP ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H5T HN5 0.43 ATOM O5' ON5 -0.66 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' BOND C5' O5' O5' H5T BOND C1' N9 BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 DOUBLE N1 C6 C2 N3 C4 C5 N7 C8 IMPR N6 C6 H61 H62 C6 N1 C5 N6 IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367 IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC H5T O5' C5' C4' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE RESI NTHY -1.00 ! ! NTHY is a nucleotide analogue similar to NUCL, except that the imidazole ! has been replaced by a thymine ! - The charge distribution on the sugar is identical to what ! it is in the DNA. ! - The charge' on the 3' end of the "backbone" is identical to ! what it is in the DNA, except for the terminal methyl group for which ! there is no DNA equivalent. ! - The charges on the 5' extremity of the backbone is as in the ! 5TER patch used for the DNA. An alternative to that would be to use ! charges more similar to what is actuallly in non-terminal residues in the ! DNA. GROUP ATOM O4' ON6 -0.50 ! H5T ATOM C1' CN7B 0.16 ! | ATOM H12' HN7 0.09 ! H52' O5' ATOM C4' CN7 0.16 ! \ / ATOM H42' HN7 0.09 ! H51'-C5' O4' Thymine GROUP ! \ / \ / ATOM N1 NN2B -0.34 ! H42'--C4' C1'--H12' ATOM C6 CN3 0.17 ! | | ATOM H6 HN3 0.17 ! H31'--C3'--C2'--H21' ATOM C2 CN1T 0.51 ! / \ ATOM O2 ON1 -0.41 ! O3' H22' ATOM N3 NN2U -0.46 ! | ATOM H3 HN2 0.36 ! O1P==P==O2P ATOM C4 CN1 0.50 ! | ATOM O4 ON1 -0.45 ! O3P (-1) ATOM C5 CN3T -0.15 ! \ ATOM C5M CN9 -0.11 ! C3T--H3T3 ATOM H51 HN9 0.07 ! / \ ATOM H52 HN9 0.07 ! H3T1 H3T2 ATOM H53 HN9 0.07 GROUP ATOM C2' CN8 -0.18 ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP ATOM C3' CN7 0.01 ATOM H31' HN7 0.09 ATOM O3' ON2 -0.57 ATOM P P 1.50 ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O3P ON2 -0.57 ATOM C3T CN8B -0.17 ATOM H3T1 HN7 0.09 ATOM H3T2 HN7 0.09 ATOM H3T3 HN7 0.09 GROUP ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H5T HN5 0.43 ATOM O5' ON5 -0.66 BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P BOND O3P C3T C3T H3T1 C3T H3T2 C3T H3T3 BOND C4' C5' C5' H51' C5' H52' BOND C5' O5' O5' H5T BOND C1' N1 BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53 DOUBLE C2 O2 C4 O4 C5 C6 IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC C3T O3P P O3' 0.0 0.0 180.0 0.0 0.0 IC H3T1 C3T O3P P 0.0 0.0 60.0 0.0 0.0 IC H3T2 C3T O3P P 0.0 0.0 -60.0 0.0 0.0 IC H3T3 C3T O3P P 0.0 0.0 180.0 0.0 0.0 IC C3' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE Remarks btn.top Remarks Created by XPLO2D V. 970709/2.6 at Wed Jul 9 22:35:01 1997 for user Remarks Auto-generated by XPLO2D from file btn.ppp Remarks You *MUST* check/edit MASSes and CHARges !!! Remarks Check DONOrs and ACCEptors Remarks Verify IMPRopers yourself Remarks DIHEdrals which are not flat are commented out set echo=false end { edit masses if necessary } MASS CX1 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS OX2 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS CX3 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS CX4 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS CX5 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS CX6 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS CX7 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS SX8 32.06600 ! assuming S -> 32.06600 + 1.008 * 0 (Hs) MASS CX9 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS CX10 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS NX11 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS CX12 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS OX13 15.99900 ! assuming O -> 15.99900 + 1.008 * 0 (Hs) MASS NX14 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS CX15 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) autogenerate angles=true end RESIdue BTN GROUp ATOM C11 TYPE CX1 CHARge 0.0 END ! Nr of Hs = 1 ATOM O11 TYPE OX2 CHARge 0.0 END ! Nr of Hs = 0 ATOM C10 TYPE CX3 CHARge 0.0 END ! Nr of Hs = 2 ATOM C9 TYPE CX4 CHARge 0.0 END ! Nr of Hs = 2 ATOM C8 TYPE CX5 CHARge 0.0 END ! Nr of Hs = 2 ATOM C7 TYPE CX6 CHARge 0.0 END ! Nr of Hs = 2 ATOM C2 TYPE CX7 CHARge 0.0 END ! Nr of Hs = 1 ATOM S1 TYPE SX8 CHARge 0.0 END ! Nr of Hs = 0 ATOM C6 TYPE CX9 CHARge 0.0 END ! Nr of Hs = 2 ATOM C5 TYPE CX10 CHARge 0.0 END ! Nr of Hs = 1 ATOM N1 TYPE NX11 CHARge 0.0 END ! Nr of Hs = 1 ATOM C3 TYPE CX12 CHARge 0.0 END ! Nr of Hs = 0 ATOM O3 TYPE OX13 CHARge 0.0 END ! Nr of Hs = 0 ATOM N2 TYPE NX14 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE CX15 CHARge 0.0 END ! Nr of Hs = 1 BOND C11 O11 BOND C11 C10 BOND C10 C9 BOND C9 C8 BOND C8 C7 BOND C7 C2 BOND C2 S1 BOND C2 C4 BOND S1 C6 BOND C6 C5 BOND C5 N1 BOND C5 C4 BOND N1 C3 BOND C3 O3 BOND C3 N2 BOND N2 C4 { edit these DIHEdrals if necessary } DIHEdral C4 C5 N1 C3 ! flat ? (0 degrees = cis) -0.47 DIHEdral C6 C5 C4 C2 ! flat ? (0 degrees = cis) -2.83 DIHEdral N1 C5 C4 N2 ! flat ? (0 degrees = cis) -0.42 DIHEdral C5 N1 C3 O3 ! flat ? (180 degrees = trans) 185.57 DIHEdral C5 N1 C3 N2 ! flat ? (0 degrees = cis) 1.24 DIHEdral N1 C3 N2 C4 ! flat ? (0 degrees = cis) -1.55 DIHEdral O3 C3 N2 C4 ! flat ? (180 degrees = trans) 174.12 DIHEdral C3 N2 C4 C5 ! flat ? (0 degrees = cis) 1.23 { edit these IMPRopers if necessary } IMPRoper C2 C7 S1 C4 ! chirality or flatness improper 36.34 IMPRoper C5 C6 N1 C4 ! chirality or flatness improper 38.96 IMPRoper C3 N2 O3 N1 ! chirality or flatness improper 2.92 IMPRoper C4 C2 C5 N2 ! chirality or flatness improper 37.09 { edit these DONOrs and ACCEptors if necessary } ACCEptor O11 C11 ! DONOr H?1 N1 ACCEptor O3 C3 ! DONOr H?1 N2 END { RESIdue BTN } Remarks btn.min.inp Remarks Created by XPLO2D V. 970709/2.6 at Wed Jul 9 22:35:02 1997 for user Remarks Auto-generated by XPLO2D from file btn.ppp Remarks Energy-minimisation input file for residue type BTN topology ! @tophcsdx.pro @btn.top end parameters ! @parhcsdx.pro @btn.par nbonds atom cdie shift eps=8.0 e14fac=0.4 cutnb=7.5 ctonnb=6.0 ctofnb=6.5 nbxmod=5 vswitch end remark dielectric constant eps set to 8.0 end flags exclude elec ? end segment name=" " chain coordinates @btn.pdb_clean end end coordinates @btn.pdb_clean ! Remarks Build hydrogens (if any) ! hbuild ! selection = (hydrogen and not known) ! phistep=45 ! end Remarks DELETE hydrogens and unknown atoms delete selection = (hydrogen or (not known)) end print threshold=0.02 bonds print threshold=3.0 angles print threshold=3.0 dihedrals print threshold=3.0 impropers Remarks Do Powell energy minimisation minimise powell nstep=250 drop=40.0 end write coordinates output=btn_min.pdb end write structure output=btn.psf end constraints interaction (not hydro) (not hydro) end print threshold=0.02 bonds print threshold=3.0 angles print threshold=3.0 dihedrals print threshold=3.0 impropers flags exclude * include vdw end energy end distance from=(not hydro) to=(not hydro) cutoff=2.6 end stop