*> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids << *>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<< *>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<< * All comments to ADM jr. via the CHARMM web site: www.charmm.org * parameter set discussion forum * 31 1 ! references ! !PROTEINS ! !MacKerell, A.D., Jr,. Feig, M., Brooks, C.L., III, Extending the !treatment of backbone energetics in protein force fields: limitations !of gas-phase quantum mechanics in reproducing protein conformational !distributions in molecular dynamics simulations, Journal of !Computational Chemistry, 25: 1400-1415, 2004. ! !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. ! !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) ! 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 13 HA1 1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 14 HA2 1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 15 HA3 1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 16 HF1 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) MASS 17 HF2 1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str) 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 41 CST 12.01100 C ! CO2 carbon MASS 42 CT 12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str) MASS 43 CT1x 12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 44 CT2x 12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 45 CT3x 12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) MASS 46 CN 12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str) MASS 47 CAP 12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 48 COA 12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str) MASS 49 C3 12.01100 C ! cyclopropyl carbon 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 61 NC 14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str) 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 77 OST 15.99900 O ! CO2 oxygen MASS 78 OCA 15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str) 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 87 CF1 12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 88 CF2 12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 89 CF3 12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str) MASS 90 FE 55.84700 Fe ! heme iron 56 MASS 91 CLAL 35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str) MASS 92 FA 18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str) MASS 93 F1 18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 94 F2 18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 95 F3 18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str) MASS 99 DUM 0.00000 H ! dummy atom !lipid 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 103 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 SOD 22.989770 NA ! Sodium Ion MASS 191 MG 24.305000 MG ! Magnesium Ion MASS 192 POT 39.102000 K ! Potassium Ion! check masses MASS 193 CES 132.900000 CS ! Cesium Ion MASS 194 CAL 40.080000 CA ! Calcium Ion MASS 195 CLA 35.450000 CL ! Chloride Ion MASS 196 ZN 65.370000 ZN ! zinc (II) cation !the following masses must be added to the parent RTF for retinol/al MASS 212 CC1A 12.01100 C ! alkene conjugation MASS 213 CC1B 12.01100 C ! alkene conjugation MASS 214 CC2 12.01100 C ! alkene conjugation MASS 220 NS1 14.00700 N ! N for deprotonated Schiff's base MASS 221 NS2 14.00700 N ! N for protonated Schiff's base 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CD CG OE2 OE1 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 120.0000 112.5700 1.5360 IC CD1 CD2 *CG HG 1.5361 110.2600 120.0000 108.0200 1.1168 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 CMAP -C N CA C N CA C +N 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 ALAD 0.00 ! Alanine dipeptide, with CMAP term GROUP ATOM CL CT3 -0.27 ATOM HL1 HA 0.09 ATOM HL2 HA 0.09 ATOM HL3 HA 0.09 GROUP ATOM CLP C 0.51 ATOM OL O -0.51 GROUP ATOM NL NH1 -0.47 ATOM HL H 0.31 ATOM CA CT1 0.07 ATOM HA HB 0.09 GROUP ATOM CB CT3 -0.27 ! HL1 OL OR HR1 ATOM HB1 HA 0.09 ! \ || HL HA || HR / ATOM HB2 HA 0.09 ! \ || | | || | / ATOM HB3 HA 0.09 ! HL2---CL--CLP--NL--CA--CRP--NR---CR---HR2 GROUP ! / | \ ATOM CRP C 0.51 ! / HB1--CB--HB3 \ ATOM OR O -0.51 ! HL3 | HR3 GROUP ! HB2 ATOM NR NH1 -0.47 ATOM HR H 0.31 ATOM CR CT3 -0.11 ATOM HR1 HA 0.09 ATOM HR2 HA 0.09 ATOM HR3 HA 0.09 BOND CL CLP CLP NL NL CA BOND CA CRP CRP NR NR CR DOUBLE CLP OL CRP OR BOND NL HL NR HR BOND CA HA CA CB BOND CL HL1 CL HL2 CL HL3 BOND CB HB1 CB HB2 CB HB3 BOND CR HR1 CR HR2 CR HR3 IMPR CLP CL NL OL NL CLP CA HL IMPR CRP CA NR OR NR CRP CR HR CMAP CLP NL CA CRP NL CA CRP NR ic clp nl ca crp 0.0 0.0 180.0 0.0 0.0 ! Phi ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 ic hl nl ca crp 0.0 0.0 0.0 0.0 0.0 ic nl ca crp nr 0.0 0.0 180.0 0.0 0.0 ! Psi ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 ic nl ca crp or 0.0 0.0 0.0 0.0 0.0 ic cl clp nl ca 0.0 0.0 180.0 0.0 0.0 ! Omega Left ic nl cl *clp ol 0.0 0.0 180.0 0.0 0.0 ic ol clp nl ca 0.0 0.0 0.0 0.0 0.0 ic ca crp nr cr 0.0 0.0 180.0 0.0 0.0 ! Omega Right ic crp cr *nr hr 0.0 0.0 180.0 0.0 0.0 ic ca crp nr hr 0.0 0.0 180.0 0.0 0.0 ic nl crp *ca ha 0.0 0.0 240.0 0.0 0.0 ic nl crp *ca cb 0.0 0.0 120.0 0.0 0.0 ic hl1 cl clp nl 0.0 0.0 180.0 0.0 0.0 ic hl2 cl clp nl 0.0 0.0 60.0 0.0 0.0 ic hl3 cl clp ol 0.0 0.0 120.0 0.0 0.0 ic ha ca cb hb1 0.0 0.0 180.0 0.0 0.0 ic nl ca cb hb2 0.0 0.0 180.0 0.0 0.0 ic crp ca cb hb3 0.0 0.0 180.0 0.0 0.0 ic crp nr cr hr1 0.0 0.0 180.0 0.0 0.0 ic crp nr cr hr2 0.0 0.0 60.0 0.0 0.0 ic hr nr cr hr3 0.0 0.0 120.0 0.0 0.0 ic ca clp *nl hl 0.0 0.0 180.0 0.0 0.0 ic ca nr *crp or 0.0 0.0 180.0 0.0 0.0 ic hb1 hb2 *cb hb3 0.0 0.0 120.0 0.0 0.0 ic hl1 hl2 *cl hl3 0.0 0.0 240.0 0.0 0.0 ic hr1 hr2 *cr hr3 0.0 0.0 240.0 0.0 0.0 ic ha ca nl hl 0.0 0.0 240.0 0.0 0.0 patch first none last none 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, but not in NAMD 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 ! 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 RESI ZN2 2.00 ! Zinc ion, Roland Stote GROUP ATOM ZN ZN 2.00 PATCHING FIRST 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 (to create dipeptide) 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 CMAP CY N CA C N CA C NT 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 dipeptide) 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 CMAP CY N CA C N CA C NT 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 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 (HT1 is cis to O) BOND NT HT1 NT HT2 ! 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 IMPR NT C CAT HNT C CA NT O CMAP -C N CA C N CA C NT 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 statementand ! follow with AUTOgenerate ANGLes DIHEdrals command 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 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 and ! follow with AUTOgenerate ANGLes DIHEdrals command 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 DONOR HE2 OE2 IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000 PRES LSN 0.00 ! patch for neutral lysine based on methylamine ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command !delete atom and reassign charges DELETE ATOM HZ3 GROUP ATOM CE CT2 0.13 ATOM HE1 HA 0.075 ATOM HE2 HA 0.075 ATOM NZ NH2 -0.96 ATOM HZ1 HC 0.34 ATOM HZ2 HC 0.34 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 ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N !the need for the explicit specification of angles and dihedrals in !patches linking images has not been tested !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 DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS. ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command GROUP 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 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 ! use in a patch statement ! follow with AUTOgenerate ANGLes DIHEdrals command GROUP 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 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 ! 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 ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N 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 ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N 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 ! follow with AUTOgenerate ANGLes DIHEdrals command BOND 1C 2N 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 !lipid section 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 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) ! ! 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 OLEO -1.00 ! oleic acid; combine with PCGL for DOPC, S.Feller and adm jr. ! GROUP ! O1 O2 (-) ATOM C1 CL 0.62 ! \\ / ATOM O1 OCL -0.76 ! C1 ATOM O2 OCL -0.76 ! | ATOM C2 CTL2 -0.28 ! | ATOM H2A HAL2 0.09 ! H2A---C2---H2B ATOM H2B HAL2 0.09 ! | GROUP ! ATOM C3 CTL2 -0.18 ! | ATOM H3A HAL2 0.09 ! H3A---C3---H3B ATOM H3B HAL2 0.09 ! | GROUP ! ATOM C4 CTL2 -0.18 ! | ATOM H4A HAL2 0.09 ! H4A---C4---H4B ATOM H4B HAL2 0.09 ! | GROUP ! ATOM C5 CTL2 -0.18 ! | ATOM H5A HAL2 0.09 ! H5A---C5---H5B ATOM H5B HAL2 0.09 ! | GROUP ! ATOM C6 CTL2 -0.18 ! | ATOM H6A HAL2 0.09 ! H6A---C6---H6B ATOM H6B HAL2 0.09 ! | GROUP ! ATOM C7 CTL2 -0.18 ! | ATOM H7A HAL2 0.09 ! H7A---C7---H7B ATOM H7B HAL2 0.09 ! | GROUP ! ATOM C8 CTL2 -0.18 ! | ATOM H8A HAL2 0.09 ! H8A---C8---H8B ATOM H8B HAL2 0.09 ! | GROUP ! ATOM C9 CEL1 -0.15 ! | ATOM H9A HEL1 0.15 ! H9A---C9 GROUP ! || ATOM C10 CEL1 -0.15 ! || ATOM H10A HEL1 0.15 ! H10A---C10 GROUP ! ATOM C11 CTL2 -0.18 ! | ATOM H11A HAL2 0.09 ! H11A---C11--H11B ATOM H11B HAL2 0.09 ! | GROUP ! ATOM C12 CTL2 -0.18 ! | ATOM H12A HAL2 0.09 ! H12A---C12--H12B ATOM H12B HAL2 0.09 ! | GROUP ! ATOM C13 CTL2 -0.18 ! | ATOM H13A HAL2 0.09 ! H13A---C13--H13B ATOM H13B HAL2 0.09 ! | GROUP ! ATOM C14 CTL2 -0.18 ! | ATOM H14A HAL2 0.09 ! H14A---C14--H14B ATOM H14B HAL2 0.09 ! | GROUP ! ATOM C15 CTL2 -0.18 ! | ATOM H15A HAL2 0.09 ! H15A---C15--H15B ATOM H15B HAL2 0.09 ! | GROUP ATOM C16 CTL2 -0.18 ! | ATOM H16A HAL2 0.09 ! H16A---C16--H16B ATOM H16B HAL2 0.09 ! | GROUP ! ATOM C17 CTL2 -0.18 ! | ATOM H17A HAL2 0.09 ! H17A---C17--H17B ATOM H17B HAL2 0.09 ! | GROUP ! ATOM C18 CTL3 -0.27 ! | ATOM H18A HAL3 0.09 ! H18A---C18--H18B ATOM H18B HAL3 0.09 ! | ATOM H18C HAL3 0.09 ! H18C ! bonding BOND C1 O1 C1 C2 BOND C2 C3 C2 H2A C2 H2B BOND C3 C4 C3 H3A C3 H3B BOND C4 C5 C4 H4A C4 H4B BOND C5 C6 C5 H5A C5 H5B BOND C6 C7 C6 H6A C6 H6B BOND C7 C8 C7 H7A C7 H7B BOND C8 C9 C8 H8A C8 H8B BOND C9 C10 C9 H9A BOND C10 C11 C10 H10A BOND C11 C12 C11 H11A C11 H11B BOND C12 C13 C12 H12A C12 H12B BOND C13 C14 C13 H13A C13 H13B BOND C14 C15 C14 H14A C14 H14B BOND C15 C16 C15 H15A C15 H15B BOND C16 C17 C16 H16A C16 H16B BOND C17 C18 C17 H17A C17 H17B BOND C18 H18C C18 H18A C18 H18B ! chain torsions IC O1 C1 C2 C3 0.0 0.0 180.0 0.0 0.0 IC C1 C2 C3 C4 0.0 0.0 180.0 0.0 0.0 IC C2 C3 C4 C5 0.0 0.0 180.0 0.0 0.0 IC C3 C4 C5 C6 0.0 0.0 180.0 0.0 0.0 IC C4 C5 C6 C7 0.0 0.0 180.0 0.0 0.0 IC C5 C6 C7 C8 0.0 0.0 180.0 0.0 0.0 IC C6 C7 C8 C9 0.0 0.0 180.0 0.0 0.0 IC C7 C8 C9 C10 0.0 0.0 180.0 0.0 0.0 IC C8 C9 C10 C11 0.0 0.0 0.0 0.0 0.0 IC C9 C10 C11 C12 0.0 0.0 180.0 0.0 0.0 IC C10 C11 C12 C13 0.0 0.0 180.0 0.0 0.0 IC C11 C12 C13 C14 0.0 0.0 180.0 0.0 0.0 IC C12 C13 C14 C15 0.0 0.0 180.0 0.0 0.0 IC C13 C14 C15 C16 0.0 0.0 180.0 0.0 0.0 IC C14 C15 C16 C17 0.0 0.0 180.0 0.0 0.0 IC C15 C16 C17 C18 0.0 0.0 180.0 0.0 0.0 ! impropers (from toplip.rtf ...) IC H2A C1 *C2 C3 0.0000 0.00 120.00 0.00 0.0000 IC H2B C1 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 IC H3A C2 *C3 C4 0.0000 0.00 120.00 0.00 0.0000 IC H3B C2 *C3 C4 0.0000 0.00 -120.00 0.00 0.0000 IC H4A C3 *C4 C5 0.0000 0.00 120.00 0.00 0.0000 IC H4B C3 *C4 C5 0.0000 0.00 -120.00 0.00 0.0000 IC H5A C4 *C5 C6 0.0000 0.00 120.00 0.00 0.0000 IC H5B C4 *C5 C6 0.0000 0.00 -120.00 0.00 0.0000 IC H6A C5 *C6 C7 0.0000 0.00 120.00 0.00 0.0000 IC H6B C5 *C6 C7 0.0000 0.00 -120.00 0.00 0.0000 IC H7A C6 *C7 C8 0.0000 0.00 120.00 0.00 0.0000 IC H7B C6 *C7 C8 0.0000 0.00 -120.00 0.00 0.0000 IC H8A C7 *C8 C9 0.0000 0.00 120.00 0.00 0.0000 IC H8B C7 *C8 C9 0.0000 0.00 -120.00 0.00 0.0000 IC H9A C8 *C9 C10 0.0000 0.00 180.00 0.00 0.0000 IC H10A C9 *C10 C11 0.0000 0.00 180.00 0.00 0.0000 IC H11A C10 *C11 C12 0.0000 0.00 120.00 0.00 0.0000 IC H11B C10 *C11 C12 0.0000 0.00 -120.00 0.00 0.0000 IC H12A C11 *C12 C13 0.0000 0.00 120.00 0.00 0.0000 IC H12B C11 *C12 C13 0.0000 0.00 -120.00 0.00 0.0000 IC H13A C12 *C13 C14 0.0000 0.00 120.00 0.00 0.0000 IC H13B C12 *C13 C14 0.0000 0.00 -120.00 0.00 0.0000 IC H14A C13 *C14 C15 0.0000 0.00 120.00 0.00 0.0000 IC H14B C13 *C14 C15 0.0000 0.00 -120.00 0.00 0.0000 IC H15A C14 *C15 C16 0.0000 0.00 120.00 0.00 0.0000 IC H15B C14 *C15 C16 0.0000 0.00 -120.00 0.00 0.0000 IC H16A C15 *C16 C17 0.0000 0.00 120.00 0.00 0.0000 IC H16B C15 *C16 C17 0.0000 0.00 -120.00 0.00 0.0000 IC H17A C16 *C17 C18 0.0000 0.00 120.00 0.00 0.0000 IC H17B C16 *C17 C18 0.0000 0.00 -120.00 0.00 0.0000 IC C16 C17 C18 H18A 0.0000 0.00 180.00 0.00 0.0000 IC H18A C17 *C18 H18B 0.0000 0.00 120.00 0.00 0.0000 IC H18A C17 *C18 H18C 0.0000 0.00 -120.00 0.00 0.0000 RESI DHA -1.00 ! docosahexaenoic acid; combine with PCGL ! and STEA to creat SDPC as follows !read sequence card !* modular generate of SDPC !* !3 !STEA PCGL DHA !GENERATE L001 FIRST none LAST none SETUP WARN !patch in the connectivity ! !patch est1 L001 2 L001 1 !patch est2 L001 2 L001 3 ! ATOM C1 CL 0.62 ! O1 O2 (-) ATOM O1 OCL -0.76 ! \\ / ATOM O2 OCL -0.76 ! C1 ATOM C2 CTL2 -0.28 ! | ATOM H2A HAL2 0.09 ! H2A---C2---H2B ATOM H2B HAL2 0.09 ! | GROUP ! ATOM C3 CTL2 -0.18 ! | ATOM H3A HAL2 0.09 ! H3A---C3---H3B ATOM H3B HAL2 0.09 ! | GROUP ! ATOM C4 CEL1 -0.15 ! | ATOM H4 HEL1 0.15 ! H4---C4 GROUP ! || ATOM C5 CEL1 -0.15 ! || ATOM H5 HEL1 0.15 ! H5---C5 GROUP ! | ATOM C6 CTL2 -0.18 ! | ATOM H6A HAL2 0.09 ! H6A---C6---H6B ATOM H6B HAL2 0.09 ! | GROUP ! ATOM C7 CEL1 -0.15 ! | ATOM H7 HEL1 0.15 ! H7---C7 GROUP ! || ATOM C8 CEL1 -0.15 ! || ATOM H8 HEL1 0.15 ! H8---C8 GROUP ! | ATOM C9 CTL2 -0.18 ! | ATOM H9A HAL2 0.09 ! H9A---C9---H9B ATOM H9B HAL2 0.09 ! | GROUP ! ATOM C10 CEL1 -0.15 ! | ATOM H10 HEL1 0.15 ! H10---C10 GROUP ! || ATOM C11 CEL1 -0.15 ! || ATOM H11 HEL1 0.15 ! H11---C11 GROUP ! | ATOM C12 CTL2 -0.18 ! | ATOM H12A HAL2 0.09 ! H12A---C12--H12B ATOM H12B HAL2 0.09 ! | GROUP ! ATOM C13 CEL1 -0.15 ! | ATOM H13 HEL1 0.15 ! H13---C13 GROUP ! || ATOM C14 CEL1 -0.15 ! || ATOM H14 HEL1 0.15 ! H14---C14 GROUP ! | ATOM C15 CTL2 -0.18 ! | ATOM H15A HAL2 0.09 ! H15A---C15--H15B ATOM H15B HAL2 0.09 ! | GROUP ! ATOM C16 CEL1 -0.15 ! | ATOM H16 HEL1 0.15 ! H16---C16 GROUP ! || ATOM C17 CEL1 -0.15 ! || ATOM H17 HEL1 0.15 ! H17---C17 GROUP ! | ATOM C18 CTL2 -0.18 ! | ATOM H18A HAL2 0.09 ! H18A---C18--H18B ATOM H18B HAL2 0.09 ! | GROUP ! ATOM C19 CEL1 -0.15 ! | ATOM H19 HEL1 0.15 ! H19---C19 GROUP ! || ATOM C20 CEL1 -0.15 ! || ATOM H20 HEL1 0.15 ! H20---C20 GROUP ! | ATOM C21 CTL2 -0.18 ! | ATOM H21A HAL2 0.09 ! H21A---C21--H21B ATOM H21B HAL2 0.09 ! | GROUP ! | ATOM C22 CTL3 -0.27 ! | ATOM H22A HAL3 0.09 ! H22A---C22--H22B ATOM H22B HAL3 0.09 ! | ATOM H22C HAL3 0.09 ! H22C ! bonding BOND C1 O1 C1 C2 BOND C2 C3 C2 H2A C2 H2B BOND C3 C4 C3 H3A C3 H3B BOND C4 C5 C4 H4 BOND C5 C6 C5 H5 BOND C6 C7 C6 H6A C6 H6B BOND C7 C8 C7 H7 BOND C8 C9 C8 H8 BOND C9 C10 C9 H9A C9 H9B BOND C10 C11 C10 H10 BOND C11 C12 C11 H11 BOND C12 C13 C12 H12A C12 H12B BOND C13 C14 C13 H13 BOND C14 C15 C14 H14 BOND C15 C16 C15 H15A C15 H15B BOND C16 C17 C16 H16 BOND C17 C18 C17 H17 BOND C18 C19 C18 H18A C18 H18B BOND C19 C20 C19 H19 BOND C20 C21 C20 H20 BOND C21 C22 C21 H21A C21 H21B BOND C22 H22C C22 H22A C22 H22B ! chain torsions, doubles in cis, singles in trans IC O1 C1 C2 C3 0.0 0.0 180.0 0.0 0.0 IC C1 C2 C3 C4 0.0 0.0 180.0 0.0 0.0 IC C2 C3 C4 C5 0.0 0.0 180.0 0.0 0.0 IC C3 C4 C5 C6 0.0 0.0 0.0 0.0 0.0 IC C4 C5 C6 C7 0.0 0.0 180.0 0.0 0.0 IC C5 C6 C7 C8 0.0 0.0 180.0 0.0 0.0 IC C6 C7 C8 C9 0.0 0.0 0.0 0.0 0.0 IC C7 C8 C9 C10 0.0 0.0 180.0 0.0 0.0 IC C8 C9 C10 C11 0.0 0.0 180.0 0.0 0.0 IC C9 C10 C11 C12 0.0 0.0 0.0 0.0 0.0 IC C10 C11 C12 C13 0.0 0.0 180.0 0.0 0.0 IC C11 C12 C13 C14 0.0 0.0 180.0 0.0 0.0 IC C12 C13 C14 C15 0.0 0.0 0.0 0.0 0.0 IC C13 C14 C15 C16 0.0 0.0 180.0 0.0 0.0 IC C14 C15 C16 C17 0.0 0.0 180.0 0.0 0.0 IC C15 C16 C17 C18 0.0 0.0 0.0 0.0 0.0 IC C16 C17 C18 C19 0.0 0.0 180.0 0.0 0.0 IC C17 C18 C19 C20 0.0 0.0 180.0 0.0 0.0 IC C18 C19 C20 C21 0.0 0.0 0.0 0.0 0.0 IC C19 C20 C21 C22 0.0 0.0 180.0 0.0 0.0 IC C3 C4 C5 H5 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C4 H4 0.0 0.0 180.0 0.0 0.0 IC C6 C7 C8 H8 0.0 0.0 180.0 0.0 0.0 IC C9 C8 C7 H7 0.0 0.0 180.0 0.0 0.0 IC C9 C10 C11 H11 0.0 0.0 180.0 0.0 0.0 IC C12 C11 C10 H10 0.0 0.0 180.0 0.0 0.0 IC C12 C13 C14 H14 0.0 0.0 180.0 0.0 0.0 IC C15 C14 C13 H13 0.0 0.0 180.0 0.0 0.0 IC C15 C16 C17 H17 0.0 0.0 180.0 0.0 0.0 IC C18 C17 C16 H16 0.0 0.0 180.0 0.0 0.0 IC C18 C19 C20 H20 0.0 0.0 180.0 0.0 0.0 IC C21 C20 C19 H19 0.0 0.0 180.0 0.0 0.0 ! impropers IC H2A C1 *C2 C3 0.0000 0.00 120.00 0.00 0.0000 IC H2B C1 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 IC H3A C2 *C3 C4 0.0000 0.00 120.00 0.00 0.0000 IC H3B C2 *C3 C4 0.0000 0.00 -120.00 0.00 0.0000 IC H6A C5 *C6 C7 0.0000 0.00 120.00 0.00 0.0000 IC H6B C5 *C6 C7 0.0000 0.00 -120.00 0.00 0.0000 IC H9A C8 *C9 C10 0.0000 0.00 120.00 0.00 0.0000 IC H9B C8 *C9 C10 0.0000 0.00 -120.00 0.00 0.0000 IC H12A C11 *C12 C13 0.0000 0.00 120.00 0.00 0.0000 IC H12B C11 *C12 C13 0.0000 0.00 -120.00 0.00 0.0000 IC H15A C14 *C15 C16 0.0000 0.00 120.00 0.00 0.0000 IC H15B C14 *C15 C16 0.0000 0.00 -120.00 0.00 0.0000 IC H18A C17 *C18 C19 0.0000 0.00 120.00 0.00 0.0000 IC H18B C17 *C18 C19 0.0000 0.00 -120.00 0.00 0.0000 IC H21A C20 *C21 C22 0.0000 0.00 120.00 0.00 0.0000 IC H21B C20 *C21 C22 0.0000 0.00 -120.00 0.00 0.0000 IC C20 C21 C22 H22A 0.0000 0.00 180.00 0.00 0.0000 IC H22A C21 *C22 H22B 0.0000 0.00 120.00 0.00 0.0000 IC H22A C21 *C22 H22C 0.0000 0.00 -120.00 0.00 0.0000 RESI STEA -1.00 ! stearoyl acid chain; combine with PCGL for DSPC ATOM C1 CL 0.62 ! O1 O2 (-) ATOM O1 OCL -0.76 ! \\ / ATOM O2 OCL -0.76 ! C1 ATOM C2 CTL2 -0.28 ! | ATOM H2A HAL2 0.09 ! H2A---C2---H2B ATOM H2B HAL2 0.09 ! | GROUP ! ATOM C3 CTL2 -0.18 ! | ATOM H3A HAL2 0.09 ! H3A---C3---H3B ATOM H3B HAL2 0.09 ! | GROUP ! ATOM C4 CTL2 -0.18 ! | ATOM H4A HAL2 0.09 ! H4A---C4---H4B ATOM H4B HAL2 0.09 ! | GROUP ! ATOM C5 CTL2 -0.18 ! | ATOM H5A HAL2 0.09 ! H5A---C5---H5B ATOM H5B HAL2 0.09 ! | GROUP ! ATOM C6 CTL2 -0.18 ! | ATOM H6A HAL2 0.09 ! H6A---C6---H6B ATOM H6B HAL2 0.09 ! | GROUP ! ATOM C7 CTL2 -0.18 ! | ATOM H7A HAL2 0.09 ! H7A---C7---H7B ATOM H7B HAL2 0.09 ! | GROUP ! ATOM C8 CTL2 -0.18 ! | ATOM H8A HAL2 0.09 ! H8A---C8---H8B ATOM H8B HAL2 0.09 ! | GROUP ! ATOM C9 CTL2 -0.18 ! | ATOM H9A HAL2 0.09 ! H9A---C9---H9B ATOM H9B HAL2 0.09 ! | GROUP ! ATOM C10 CTL2 -0.18 ! | ATOM H10A HAL2 0.09 ! H10A---C10--H10B ATOM H10B HAL2 0.09 ! | GROUP ! ATOM C11 CTL2 -0.18 ! | ATOM H11A HAL2 0.09 ! H11A---C11--H11B ATOM H11B HAL2 0.09 ! GROUP ! ATOM C12 CTL2 -0.18 ! | ATOM H12A HAL2 0.09 ! H12A---C12--H12B ATOM H12B HAL2 0.09 ! | GROUP ! ATOM C13 CTL2 -0.18 ! | ATOM H13A HAL2 0.09 ! H13A---C13--H13B ATOM H13B HAL2 0.09 ! | GROUP ! ATOM C14 CTL2 -0.18 ! | ATOM H14A HAL2 0.09 ! H14A---C14--H14B ATOM H14B HAL2 0.09 ! | GROUP ! ATOM C15 CTL2 -0.18 ! | ATOM H15A HAL2 0.09 ! H15A---C15--H15B ATOM H15B HAL2 0.09 ! | GROUP ! ATOM C16 CTL2 -0.18 ! | ATOM H16A HAL2 0.09 ! H16A---C16--H16B ATOM H16B HAL2 0.09 ! | GROUP ATOM C17 CTL2 -0.18 ! | ATOM H17A HAL2 0.09 ! H17A---C17--H17B ATOM H17B HAL2 0.09 ! | GROUP ATOM C18 CTL3 -0.27 ! | ATOM H18A HAL3 0.09 ! H18A---C18--H18B ATOM H18B HAL3 0.09 ! | ATOM H18C HAL3 0.09 ! H18C ! bonding BOND C1 O1 C1 C2 BOND C2 C3 C2 H2A C2 H2B BOND C3 C4 C3 H3A C3 H3B BOND C4 C5 C4 H4A C4 H4B BOND C5 C6 C5 H5A C5 H5B BOND C6 C7 C6 H6A C6 H6B BOND C7 C8 C7 H7A C7 H7B BOND C8 C9 C8 H8A C8 H8B BOND C9 C10 C9 H9A C9 H9B BOND C10 C11 C10 H10A C10 H10B BOND C11 C12 C11 H11A C11 H11B BOND C12 C13 C12 H12A C12 H12B BOND C13 C14 C13 H13A C13 H13B BOND C14 C15 C14 H14A C14 H14B BOND C15 C16 C15 H15A C15 H15B BOND C16 C17 C16 H16A C16 H16B BOND C17 C18 C17 H17A C17 H17B BOND C18 H18C C18 H18A C18 H18B ! chain torsions IC O1 C1 C2 C3 0.0 0.0 180.0 0.0 0.0 IC C1 C2 C3 C4 0.0 0.0 180.0 0.0 0.0 IC C2 C3 C4 C5 0.0 0.0 180.0 0.0 0.0 IC C3 C4 C5 C6 0.0 0.0 180.0 0.0 0.0 IC C4 C5 C6 C7 0.0 0.0 180.0 0.0 0.0 IC C5 C6 C7 C8 0.0 0.0 180.0 0.0 0.0 IC C6 C7 C8 C9 0.0 0.0 180.0 0.0 0.0 IC C7 C8 C9 C10 0.0 0.0 180.0 0.0 0.0 IC C8 C9 C10 C11 0.0 0.0 180.0 0.0 0.0 IC C9 C10 C11 C12 0.0 0.0 180.0 0.0 0.0 IC C10 C11 C12 C13 0.0 0.0 180.0 0.0 0.0 IC C11 C12 C13 C14 0.0 0.0 180.0 0.0 0.0 IC C12 C13 C14 C15 0.0 0.0 180.0 0.0 0.0 IC C13 C14 C15 C16 0.0 0.0 180.0 0.0 0.0 IC C14 C15 C16 C17 0.0 0.0 180.0 0.0 0.0 IC C15 C16 C17 C18 0.0 0.0 180.0 0.0 0.0 ! impropers IC H2A C1 *C2 C3 0.0000 0.00 120.00 0.00 0.0000 IC H2B C1 *C2 C3 0.0000 0.00 -120.00 0.00 0.0000 IC H3A C2 *C3 C4 0.0000 0.00 120.00 0.00 0.0000 IC H3B C2 *C3 C4 0.0000 0.00 -120.00 0.00 0.0000 IC H4A C3 *C4 C5 0.0000 0.00 120.00 0.00 0.0000 IC H4B C3 *C4 C5 0.0000 0.00 -120.00 0.00 0.0000 IC H5A C4 *C5 C6 0.0000 0.00 120.00 0.00 0.0000 IC H5B C4 *C5 C6 0.0000 0.00 -120.00 0.00 0.0000 IC H6A C5 *C6 C7 0.0000 0.00 120.00 0.00 0.0000 IC H6B C5 *C6 C7 0.0000 0.00 -120.00 0.00 0.0000 IC H7A C6 *C7 C8 0.0000 0.00 120.00 0.00 0.0000 IC H7B C6 *C7 C8 0.0000 0.00 -120.00 0.00 0.0000 IC H8A C7 *C8 C9 0.0000 0.00 120.00 0.00 0.0000 IC H8B C7 *C8 C9 0.0000 0.00 -120.00 0.00 0.0000 IC H9A C8 *C9 C10 0.0000 0.00 120.00 0.00 0.0000 IC H9B C8 *C9 C10 0.0000 0.00 -120.00 0.00 0.0000 IC H10A C9 *C10 C11 0.0000 0.00 120.00 0.00 0.0000 IC H10B C9 *C10 C11 0.0000 0.00 -120.00 0.00 0.0000 IC H11A C10 *C11 C12 0.0000 0.00 120.00 0.00 0.0000 IC H11B C10 *C11 C12 0.0000 0.00 -120.00 0.00 0.0000 IC H12A C11 *C12 C13 0.0000 0.00 120.00 0.00 0.0000 IC H12B C11 *C12 C13 0.0000 0.00 -120.00 0.00 0.0000 IC H13A C12 *C13 C14 0.0000 0.00 120.00 0.00 0.0000 IC H13B C12 *C13 C14 0.0000 0.00 -120.00 0.00 0.0000 IC H14A C13 *C14 C15 0.0000 0.00 120.00 0.00 0.0000 IC H14B C13 *C14 C15 0.0000 0.00 -120.00 0.00 0.0000 IC H15A C14 *C15 C16 0.0000 0.00 120.00 0.00 0.0000 IC H15B C14 *C15 C16 0.0000 0.00 -120.00 0.00 0.0000 IC H16A C15 *C16 C17 0.0000 0.00 120.00 0.00 0.0000 IC H16B C15 *C16 C17 0.0000 0.00 -120.00 0.00 0.0000 IC H17A C16 *C17 C18 0.0000 0.00 120.00 0.00 0.0000 IC H17B C16 *C17 C18 0.0000 0.00 -120.00 0.00 0.0000 IC C16 C17 C18 H18A 0.0000 0.00 180.00 0.00 0.0000 IC H18A C17 *C18 H18B 0.0000 0.00 120.00 0.00 0.0000 IC H18A C17 *C18 H18C 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 IMPR 2C1 1O1 2C2 2O1 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 IMPR 2C1 1O2 2C2 2O1 END