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From: Alexis Salas (as2444_at_columbia.edu)
Date: Tue Mar 08 2005 - 14:29:43 CST
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Hi,
I working with the combine.tlc script, and membrane building from
feller99. But the lipid in the protein_membrane.pdb file is fragmented.
Now i make the new topology for DPPC (i don't like use PCGL+2PALM) for
use with the membrane_plugin, but the topology don't work. I used this
script for psfgen:
package require psfgen
topology /home/alsalas/Software/DATA_CHARMM27/top_DPPC_alsalas2005.inp
segment MEM { pdb dppc_alsalas.pdb}
coordpdb dppc_alsalas.pdb MEM
guesscoord
writepdb dppc_4.pdb
writepsf dppc_4.psf
mol load psf dppc_4.psf pdb dppc_4.pdb
,and fusion the top_dppc_alex.inp with top_all27_prot_lipid.top
I attach the files:
- top_dppc_alsalas.inp
- dppc_alsalas.pdb
- dppc_4.pdb (this is with problem extra atoms CA, COOH, NH3, total 9
atoms)
, thanks in advance for any suggestion.
Alexis Salas
PhD Student
Universidad de Concepción, CHILE
*>>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
*>>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
*from
*>>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
*>>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
*>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
*>>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
*and
* \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
* \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
* Alexander D. MacKerell Jr.
* August 1999
* All comments to ADM jr. email: alex,mmiris.ab.umd.edu
* telephone: 410-706-7442
*
27 1
!
! references
!
!PROTEINS
!
!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.;
!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.;
!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos,
!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III,
!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.;
!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom
!empirical potential for molecular modeling and dynamics Studies of
!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616.
!
!PHOSPHOTYROSINE
!
!Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D. and Lim, C.
!Structural Characterization of the Phosphotyrosine Binding Region of a
!High-Affinity aSH2 Domain-Phosphopeptide Complex by Molecular Dynamics
!Simulation and Chemical Shift Calculations. Journal of the American
!Chemical Society, 1996, 118: 11265-11277.
!
!IONS (see lipid and nucleic acid topology and parameter files for
!additional ions
!
!ZINC
!
!Roland H. Stote and Martin Karplus, Zinc Binding in Proteins and
!Solution: A Simple but Accurate Nonbonded Representation, PROTEINS:
!Structure, Function, and Genetics 23:12-31 (1995)
!
!references
!
!LIPIDS
!
!Feller, S. and MacKerell, Jr., A.D. manuscript in preparation
!
!and
!
!Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M.
!Empirical Potential Energy Function for Phospholipids: Criteria for
!Parameter Optimization and Applications, in "Biological Membranes: A
!Molecular Perspective from Computation and Experiment," K.M. Merz and
!B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81.
!
!new ALKANES
!
!Yin, D. and MacKerell, Jr. A.D. Combined Ab initio/Empirical Approach
!for the Optimization of Lennard-Jones Parameters. Journal of
!Computational Chemistry, 1998, 19: 334-338.
!
!ALKENES
!
!Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D.,
!Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration:
!Parameterization and Comparison with Diffraction Studies. Biophysical
!Journal, 73:2269-2279, 1997.
!
!new PHOSPHATE
!
!MacKerell, Jr., A.D. Influence of Water and Sodium on the Energetics
!of Dimethylphosphate and its Implications For DNA Structure, Journal
!de Chimie Physique, 1997, 94: 1436-1447.
!
!IONS
!
!all ions from Roux and coworkers
!
!Sodium
!
!Beglov, D. and Roux, B., Finite Representation of an Infinite
!Bulk System: Solvent Boundary Potential for Computer Simulations,
!Journal of Chemical Physics, 1994, 100: 9050-9063
!
MASS 1 H 1.00800 H ! polar H
MASS 2 HC 1.00800 H ! N-ter H
MASS 3 HA 1.00800 H ! nonpolar H
MASS 4 HT 1.00800 H ! TIPS3P WATER HYDROGEN
MASS 5 HP 1.00800 H ! aromatic H
MASS 6 HB 1.00800 H ! backbone H
MASS 7 HR1 1.00800 H ! his he1, (+) his HG,HD2
MASS 8 HR2 1.00800 H ! (+) his HE1
MASS 9 HR3 1.00800 H ! neutral his HG, HD2
MASS 10 HS 1.00800 H ! thiol hydrogen
MASS 11 HE1 1.00800 H ! for alkene; RHC=CR
MASS 12 HE2 1.00800 H ! for alkene; H2C=CR
MASS 20 C 12.01100 C ! carbonyl C, peptide backbone
MASS 21 CA 12.01100 C ! aromatic C
MASS 22 CT1 12.01100 C ! aliphatic sp3 C for CH
MASS 23 CT2 12.01100 C ! aliphatic sp3 C for CH2
MASS 24 CT3 12.01100 C ! aliphatic sp3 C for CH3
MASS 25 CPH1 12.01100 C ! his CG and CD2 carbons
MASS 26 CPH2 12.01100 C ! his CE1 carbon
MASS 27 CPT 12.01100 C ! trp C between rings
MASS 28 CY 12.01100 C ! TRP C in pyrrole ring
MASS 29 CP1 12.01100 C ! tetrahedral C (proline CA)
MASS 30 CP2 12.01100 C ! tetrahedral C (proline CB/CG)
MASS 31 CP3 12.01100 C ! tetrahedral C (proline CD)
MASS 32 CC 12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS 33 CD 12.01100 C ! carbonyl C, pres aspp,glup,ct1
MASS 34 CPA 12.01100 C ! heme alpha-C
MASS 35 CPB 12.01100 C ! heme beta-C
MASS 36 CPM 12.01100 C ! heme meso-C
MASS 37 CM 12.01100 C ! heme CO carbon
MASS 38 CS 12.01100 C ! thiolate carbon
MASS 39 CE1 12.01100 C ! for alkene; RHC=CR
MASS 40 CE2 12.01100 C ! for alkene; H2C=CR
MASS 50 N 14.00700 N ! proline N
MASS 51 NR1 14.00700 N ! neutral his protonated ring nitrogen
MASS 52 NR2 14.00700 N ! neutral his unprotonated ring nitrogen
MASS 53 NR3 14.00700 N ! charged his ring nitrogen
MASS 54 NH1 14.00700 N ! peptide nitrogen
MASS 55 NH2 14.00700 N ! amide nitrogen
MASS 56 NH3 14.00700 N ! ammonium nitrogen
MASS 57 NC2 14.00700 N ! guanidinium nitroogen
MASS 58 NY 14.00700 N ! TRP N in pyrrole ring
MASS 59 NP 14.00700 N ! Proline ring NH2+ (N-terminal)
MASS 60 NPH 14.00700 N ! heme pyrrole N
MASS 70 O 15.99900 O ! carbonyl oxygen
MASS 71 OB 15.99900 O ! carbonyl oxygen in acetic acid
MASS 72 OC 15.99900 O ! carboxylate oxygen
MASS 73 OH1 15.99900 O ! hydroxyl oxygen
MASS 74 OS 15.99940 O ! ester oxygen
MASS 75 OT 15.99940 O ! TIPS3P WATER OXYGEN
MASS 76 OM 15.99900 O ! heme CO/O2 oxygen
MASS 81 S 32.06000 S ! sulphur
MASS 82 SM 32.06000 S ! sulfur C-S-S-C type
MASS 83 SS 32.06000 S ! thiolate sulfur
MASS 85 HE 4.00260 HE ! helium
MASS 86 NE 20.17970 NE ! neon
MASS 90 CAL 40.08000 CA ! calcium 2+
MASS 91 ZN 65.37000 ZN ! zinc (II) cation
MASS 92 FE 55.84700 Fe ! heme iron 56
MASS 99 DUM 0.00000 H ! dummy atom
!lipids section
MASS 101 HL 1.008000 H ! polar H (equivalent to protein H)
MASS 102 HCL 1.008000 H ! charged H for PE (equivalent to protein HC)
!MASS 3 HT 1.008000 H ! TIPS3P WATER HYDROGEN
MASS 104 HOL 1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS 105 HAL1 1.008000 H ! alphatic proton
MASS 106 HAL2 1.008000 H ! alphatic proton
MASS 107 HAL3 1.008000 H ! alphatic proton
MASS 108 HEL1 1.008000 H ! for alkene; RHC=CR
MASS 109 HEL2 1.008000 H ! for alkene; H2C=CR
MASS 120 CL 12.011000 C ! carbonyl C (acetic acid/methyl acetate)
MASS 121 CTL1 12.011000 C ! sp3 carbon with 1 H (-CH1-)
MASS 122 CTL2 12.011000 C ! carbon of methylene group (-CH2-)
MASS 123 CTL3 12.011000 C ! carbon of methyl group (-CH3)
MASS 124 CTL5 12.011000 C ! carbon of methyl group (-CH3) for tetramethylammonium
MASS 125 CEL1 12.011000 C ! for alkene; RHC=CR
MASS 126 CEL2 12.011000 C ! for alkene; H2C=CR
MASS 140 NTL 14.007000 N ! ammonium nitrogen
MASS 141 NH3L 14.007000 N ! nitrogen phosphatidylethanolamine
MASS 160 OBL 15.999400 O ! acetic acid carboxyl oxygen (e. to protein OB)
MASS 161 OCL 15.999400 O ! acetate oxygen
!MASS 162 OT 15.999400 O ! TIPS3P WATER OXYGEN
MASS 163 OSL 15.999400 O ! Nucleic acid phosphate ester oxygen
MASS 164 O2L 15.999400 O ! Nucleic acid =O in phosphate or sulfate
MASS 165 OHL 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS 180 PL 30.974000 P ! phosphorus
MASS 185 SL 32.060000 S ! Sulfate sulfur
MASS 190 CLA 35.450000 CL ! CHLORIDE Anion
MASS 191 SOD 22.989770 NA ! Sodium Ion
MASS 192 MG 24.305000 MG ! Magnesium Ion
MASS 193 POT 39.102000 K ! Potassium Ion
!MASS 199 DUM 0.000000 H ! dummy atom
DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
DEFA FIRS NTER LAST CTER
AUTO ANGLES DIHE
RESI ALA 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB2
ATOM CB CT3 -0.27 ! | \
ATOM HB1 HA 0.09 ! | HB3
ATOM HB2 HA 0.09 ! O=C
ATOM HB3 HA 0.09 ! |
GROUP !
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA N HN N CA
BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
RESI ARG 1.00
GROUP
ATOM N NH1 -0.47 ! | HH11
ATOM HN H 0.31 ! HN-N |
ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE NH1-HH12
ATOM HA HB 0.09 ! | | | | | //(+)
GROUP ! HA-CA--CB--CG--CD--NE--CZ
ATOM CB CT2 -0.18 ! | | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 NH2-HH22
ATOM HB2 HA 0.09 ! O=C |
GROUP ! | HH21
ATOM CG CT2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CT2 0.20
ATOM HD1 HA 0.09
ATOM HD2 HA 0.09
ATOM NE NC2 -0.70
ATOM HE HC 0.44
ATOM CZ C 0.64
ATOM NH1 NC2 -0.80
ATOM HH11 HC 0.46
ATOM HH12 HC 0.46
ATOM NH2 NC2 -0.80
ATOM HH21 HC 0.46
ATOM HH22 HC 0.46
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG NE CD CZ NE
BOND NH2 CZ N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 CG HG1 CG HG2 CD HD1 CD HD2
BOND NE HE NH1 HH11 NH1 HH12 NH2 HH21 NH2 HH22
DOUBLE O C CZ NH1
IMPR N -C CA HN C CA +N O
IMPR CZ NH1 NH2 NE
DONOR HN N
DONOR HE NE
DONOR HH11 NH1
DONOR HH12 NH1
DONOR HH21 NH2
DONOR HH22 NH2
ACCEPTOR O C
IC -C CA *N HN 1.3496 122.4500 180.0000 116.6700 0.9973
IC -C N CA C 1.3496 122.4500 180.0000 109.8600 1.5227
IC N CA C +N 1.4544 109.8600 180.0000 117.1200 1.3511
IC +N CA *C O 1.3511 117.1200 180.0000 121.4000 1.2271
IC CA C +N +CA 1.5227 117.1200 180.0000 124.6700 1.4565
IC N C *CA CB 1.4544 109.8600 123.6400 112.2600 1.5552
IC N C *CA HA 1.4544 109.8600 -117.9300 106.6100 1.0836
IC N CA CB CG 1.4544 110.7000 180.0000 115.9500 1.5475
IC CG CA *CB HB1 1.5475 115.9500 120.0500 106.4000 1.1163
IC CG CA *CB HB2 1.5475 115.9500 -125.8100 109.5500 1.1124
IC CA CB CG CD 1.5552 115.9500 180.0000 114.0100 1.5384
IC CD CB *CG HG1 1.5384 114.0100 125.2000 108.5500 1.1121
IC CD CB *CG HG2 1.5384 114.0100 -120.3000 108.9600 1.1143
IC CB CG CD NE 1.5475 114.0100 180.0000 107.0900 1.5034
IC NE CG *CD HD1 1.5034 107.0900 120.6900 109.4100 1.1143
IC NE CG *CD HD2 1.5034 107.0900 -119.0400 111.5200 1.1150
IC CG CD NE CZ 1.5384 107.0900 180.0000 123.0500 1.3401
IC CZ CD *NE HE 1.3401 123.0500 180.0000 113.1400 1.0065
IC CD NE CZ NH1 1.5034 123.0500 180.0000 118.0600 1.3311
IC NE CZ NH1 HH11 1.3401 118.0600 -178.2800 120.6100 0.9903
IC HH11 CZ *NH1 HH12 0.9903 120.6100 171.1900 116.2900 1.0023
IC NH1 NE *CZ NH2 1.3311 118.0600 178.6400 122.1400 1.3292
IC NE CZ NH2 HH21 1.3401 122.1400 -174.1400 119.9100 0.9899
IC HH21 CZ *NH2 HH22 0.9899 119.9100 166.1600 116.8800 0.9914
RESI ASN 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 OD1 HD21 (cis to OD1)
ATOM HA HB 0.09 ! | | || /
GROUP ! HA-CA--CB--CG--ND2
ATOM CB CT2 -0.18 ! | | \
ATOM HB1 HA 0.09 ! | HB2 HD22 (trans to OD1)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CC 0.55
ATOM OD1 O -0.55
GROUP
ATOM ND2 NH2 -0.62
ATOM HD21 H 0.32
ATOM HD22 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND2 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 ND2 HD21 ND2 HD22
DOUBLE C O CG OD1
IMPR N -C CA HN C CA +N O
IMPR CG ND2 CB OD1 CG CB ND2 OD1
IMPR ND2 CG HD21 HD22 ND2 CG HD22 HD21
DONOR HN N
DONOR HD21 ND2
DONOR HD22 ND2
ACCEPTOR OD1 CG
ACCEPTOR O C
IC -C CA *N HN 1.3480 124.0500 180.0000 114.4900 0.9992
IC -C N CA C 1.3480 124.0500 180.0000 105.2300 1.5245
IC N CA C +N 1.4510 105.2300 180.0000 117.3800 1.3467
IC +N CA *C O 1.3467 117.3800 180.0000 120.3200 1.2282
IC CA C +N +CA 1.5245 117.3800 180.0000 124.8800 1.4528
IC N C *CA CB 1.4510 105.2300 121.1800 113.0400 1.5627
IC N C *CA HA 1.4510 105.2300 -115.5200 107.6300 1.0848
IC N CA CB CG 1.4510 110.9100 180.0000 114.3000 1.5319
IC CG CA *CB HB1 1.5319 114.3000 119.1700 107.8200 1.1120
IC CG CA *CB HB2 1.5319 114.3000 -123.7400 110.3400 1.1091
IC CA CB CG OD1 1.5627 114.3000 180.0000 122.5600 1.2323
IC OD1 CB *CG ND2 1.2323 122.5600 -179.1900 116.1500 1.3521
IC CB CG ND2 HD21 1.5319 116.1500 -179.2600 117.3500 0.9963
IC HD21 CG *ND2 HD22 0.9963 117.3500 178.0200 120.0500 0.9951
RESI ASP -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 OD1
ATOM HA HB 0.09 ! | | //
GROUP ! HA-CA--CB--CG
ATOM CB CT2 -0.28 ! | | \
ATOM HB1 HA 0.09 ! | HB2 OD2(-)
ATOM HB2 HA 0.09 ! O=C
ATOM CG CC 0.62 ! |
ATOM OD1 OC -0.76
ATOM OD2 OC -0.76
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB OD2 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2
DOUBLE O C CG OD1
IMPR N -C CA HN C CA +N O
!IMPR OD1 CB OD2 CG
IMPR CG CB OD2 OD1
DONOR HN N
ACCEPTOR OD1 CG
ACCEPTOR OD2 CG
ACCEPTOR O C
IC -C CA *N HN 1.3465 125.3100 180.0000 112.9400 0.9966
IC -C N CA C 1.3465 125.3100 180.0000 105.6300 1.5315
IC N CA C +N 1.4490 105.6300 180.0000 117.0600 1.3478
IC +N CA *C O 1.3478 117.0600 180.0000 120.7100 1.2330
IC CA C +N +CA 1.5315 117.0600 180.0000 125.3900 1.4484
IC N C *CA CB 1.4490 105.6300 122.3300 114.1000 1.5619
IC N C *CA HA 1.4490 105.6300 -116.4000 106.7700 1.0841
IC N CA CB CG 1.4490 111.1000 180.0000 112.6000 1.5218
IC CG CA *CB HB1 1.5218 112.6000 119.2200 109.2300 1.1086
IC CG CA *CB HB2 1.5218 112.6000 -121.6100 110.6400 1.1080
IC CA CB CG OD1 1.5619 112.6000 180.0000 117.9900 1.2565
IC OD1 CB *CG OD2 1.2565 117.9900 -170.2300 117.7000 1.2541
RESI CYS 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | |
GROUP ! HA-CA--CB--SG
ATOM CB CT2 -0.11 ! | | \
ATOM HB1 HA 0.09 ! | HB2 HG1
ATOM HB2 HA 0.09 ! O=C
ATOM SG S -0.23 ! |
ATOM HG1 HS 0.16
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA SG CB N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 SG HG1
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HG1 SG
ACCEPTOR O C
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
IC CA CB SG HG1 1.5584 113.8700 176.9600 97.1500 1.3341
RESI GLN 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1 HE21 (cis to OE1)
ATOM HA HB 0.09 ! | | | || /
GROUP ! HA-CA--CB--CG--CD--NE2
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HE22 (trans to OE1)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CC 0.55
ATOM OE1 O -0.55
GROUP
ATOM NE2 NH2 -0.62
ATOM HE21 H 0.32
ATOM HE22 H 0.30
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG NE2 CD
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2 NE2 HE21 NE2 HE22
DOUBLE O C CD OE1
IMPR N -C CA HN C CA +N O
IMPR CD NE2 CG OE1 CD CG NE2 OE1
IMPR NE2 CD HE21 HE22 NE2 CD HE22 HE21
DONOR HN N
DONOR HE21 NE2
DONOR HE22 NE2
ACCEPTOR OE1 CD
ACCEPTOR O C
IC -C CA *N HN 1.3477 123.9300 180.0000 114.4500 0.9984
IC -C N CA C 1.3477 123.9300 180.0000 106.5700 1.5180
IC N CA C +N 1.4506 106.5700 180.0000 117.7200 1.3463
IC +N CA *C O 1.3463 117.7200 180.0000 120.5900 1.2291
IC CA C +N +CA 1.5180 117.7200 180.0000 124.3500 1.4461
IC N C *CA CB 1.4506 106.5700 121.9100 111.6800 1.5538
IC N C *CA HA 1.4506 106.5700 -116.8200 107.5300 1.0832
IC N CA CB CG 1.4506 111.4400 180.0000 115.5200 1.5534
IC CG CA *CB HB1 1.5534 115.5200 120.9300 106.8000 1.1147
IC CG CA *CB HB2 1.5534 115.5200 -124.5800 109.3400 1.1140
IC CA CB CG CD 1.5538 115.5200 180.0000 112.5000 1.5320
IC CD CB *CG HG1 1.5320 112.5000 118.6900 110.4100 1.1112
IC CD CB *CG HG2 1.5320 112.5000 -121.9100 110.7400 1.1094
IC CB CG CD OE1 1.5534 112.5000 180.0000 121.5200 1.2294
IC OE1 CG *CD NE2 1.2294 121.5200 179.5700 116.8400 1.3530
IC CG CD NE2 HE21 1.5320 116.8400 -179.7200 116.8600 0.9959
IC HE21 CD *NE2 HE22 0.9959 116.8600 -178.9100 119.8300 0.9943
RESI GLU -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 OE1
ATOM HA HB 0.09 ! | | | //
GROUP ! HA-CA--CB--CG--CD
ATOM CB CT2 -0.18 ! | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 OE2(-)
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.28
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM CD CC 0.62
ATOM OE1 OC -0.76
ATOM OE2 OC -0.76
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG OE2 CD
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2
DOUBLE O C CD OE1
IMPR N -C CA HN C CA +N O
!IMPR OE1 CG OE2 CD
IMPR CD CG OE2 OE1
DONOR HN N
ACCEPTOR OE1 CD
ACCEPTOR OE2 CD
ACCEPTOR O C
IC -C CA *N HN 1.3471 124.4500 180.0000 113.9900 0.9961
IC -C N CA C 1.3471 124.4500 180.0000 107.2700 1.5216
IC N CA C +N 1.4512 107.2700 180.0000 117.2500 1.3501
IC +N CA *C O 1.3501 117.2500 180.0000 121.0700 1.2306
IC CA C +N +CA 1.5216 117.2500 180.0000 124.3000 1.4530
IC N C *CA CB 1.4512 107.2700 121.9000 111.7100 1.5516
IC N C *CA HA 1.4512 107.2700 -118.0600 107.2600 1.0828
IC N CA CB CG 1.4512 111.0400 180.0000 115.6900 1.5557
IC CG CA *CB HB1 1.5557 115.6900 121.2200 108.1600 1.1145
IC CG CA *CB HB2 1.5557 115.6900 -123.6500 109.8100 1.1131
IC CA CB CG CD 1.5516 115.6900 180.0000 115.7300 1.5307
IC CD CB *CG HG1 1.5307 115.7300 117.3800 109.5000 1.1053
IC CD CB *CG HG2 1.5307 115.7300 -121.9600 111.0000 1.1081
IC CB CG CD OE1 1.5557 115.7300 180.0000 114.9900 1.2590
IC OE1 CG *CD OE2 1.2590 114.9900 -179.1000 120.0800 1.2532
RESI GLY 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! N-H
ATOM CA CT2 -0.02 ! |
ATOM HA1 HB 0.09 ! |
ATOM HA2 HB 0.09 ! HA1-CA-HA2
GROUP ! |
ATOM C C 0.51 ! |
ATOM O O -0.51 ! C=O
! |
BOND N HN N CA C CA
BOND C +N CA HA1 CA HA2
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3475 122.8200 180.0000 115.6200 0.9992
IC -C N CA C 1.3475 122.8200 180.0000 108.9400 1.4971
IC N CA C +N 1.4553 108.9400 180.0000 117.6000 1.3479
IC +N CA *C O 1.3479 117.6000 180.0000 120.8500 1.2289
IC CA C +N +CA 1.4971 117.6000 180.0000 124.0800 1.4560
IC N C *CA HA1 1.4553 108.9400 117.8600 108.0300 1.0814
IC N C *CA HA2 1.4553 108.9400 -118.1200 107.9500 1.0817
PATCHING FIRS GLYP
RESI HSD 0.00 ! neutral HIS, proton on ND1
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / ||
GROUP ! HA-CA--CB--CG ||
ATOM CB CT2 -0.09 ! | | \\ ||
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
ATOM HB2 HA 0.09 ! O=C |
ATOM ND1 NR1 -0.36 ! | HD2
ATOM HD1 H 0.32
ATOM CG CPH1 -0.05
GROUP
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
ATOM NE2 NR2 -0.70
ATOM CD2 CPH1 0.22
ATOM HD2 HR3 0.10
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CE1 ND1
BOND NE2 CD2 N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 ND1 HD1 CD2 HD2 CE1 HE1
DOUBLE O C CG CD2 CE1 NE2
IMPR ND1 CG CE1 HD1 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
IMPR ND1 CE1 CG HD1 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HD1 ND1
ACCEPTOR NE2
ACCEPTOR O C
IC -C CA *N HN 1.3475 123.2700 180.0000 115.2100 0.9988
IC -C N CA C 1.3475 123.2700 180.0000 107.7000 1.5166
IC N CA C +N 1.4521 107.7000 180.0000 117.5700 1.3509
IC +N CA *C O 1.3509 117.5700 180.0000 120.2400 1.2273
IC CA C +N +CA 1.5166 117.5700 180.0000 123.7200 1.4545
IC N C *CA CB 1.4521 107.7000 122.4600 109.9900 1.5519
IC N C *CA HA 1.4521 107.7000 -117.4900 107.3700 1.0830
IC N CA CB CG 1.4521 112.1200 180.0000 114.0500 1.5041
IC CG CA *CB HB1 1.5041 114.0500 121.1700 109.0100 1.1118
IC CG CA *CB HB2 1.5041 114.0500 -122.3600 109.5300 1.1121
IC CA CB CG ND1 1.5519 114.0500 90.0000 124.1000 1.3783
IC ND1 CB *CG CD2 1.3783 124.1000 -171.2900 129.6000 1.3597
IC CB CG ND1 CE1 1.5041 124.1000 -173.2100 107.0300 1.3549
IC CB CG CD2 NE2 1.5041 129.6000 171.9900 110.0300 1.3817
IC NE2 ND1 *CE1 HE1 1.3166 111.6300 -179.6300 123.8900 1.0932
IC CE1 CG *ND1 HD1 1.3549 107.0300 -174.6500 126.2600 1.0005
IC NE2 CG *CD2 HD2 1.3817 110.0300 -177.8500 129.6300 1.0834
RESI HSE 0.00 ! neutral His, proton on NE2
GROUP
ATOM N NH1 -0.47 ! | HE1
ATOM HN H 0.31 ! HN-N __ /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / |
GROUP ! HA-CA--CB--CG |
ATOM CB CT2 -0.08 ! | | \\ |
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2
ATOM HB2 HA 0.09 ! O=C | \
ATOM ND1 NR2 -0.70 ! | HD2 HE2
ATOM CG CPH1 0.22
ATOM CE1 CPH2 0.25
ATOM HE1 HR1 0.13
GROUP
ATOM NE2 NR1 -0.36
ATOM HE2 H 0.32
ATOM CD2 CPH1 -0.05
ATOM HD2 HR3 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG
BOND NE2 CD2 N HN N CA
BOND C CA C +N NE2 CE1 CA HA CB HB1
BOND CB HB2 NE2 HE2 CD2 HD2 CE1 HE1
DOUBLE O C CD2 CG CE1 ND1
IMPR NE2 CD2 CE1 HE2 CD2 CG NE2 HD2 CE1 ND1 NE2 HE1
IMPR NE2 CE1 CD2 HE2 CD2 NE2 CG HD2 CE1 NE2 ND1 HE1
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HE2 NE2
ACCEPTOR ND1
ACCEPTOR O C
IC -C CA *N HN 1.3472 124.1600 180.0000 114.3600 0.9991
IC -C N CA C 1.3472 124.1600 180.0000 106.4300 1.5166
IC N CA C +N 1.4532 106.4300 180.0000 116.9700 1.3446
IC +N CA *C O 1.3446 116.9700 180.0000 120.6800 1.2290
IC CA C +N +CA 1.5166 116.9700 180.0000 124.9500 1.4505
IC N C *CA CB 1.4532 106.4300 123.5200 111.6700 1.5578
IC N C *CA HA 1.4532 106.4300 -116.4900 107.0800 1.0833
IC N CA CB CG 1.4532 112.8200 180.0000 116.9400 1.5109
IC CG CA *CB HB1 1.5109 116.9400 119.8000 107.9100 1.1114
IC CG CA *CB HB2 1.5109 116.9400 -124.0400 109.5000 1.1101
IC CA CB CG ND1 1.5578 116.9400 90.0000 120.1700 1.3859
IC ND1 CB *CG CD2 1.3859 120.1700 -178.2600 129.7100 1.3596
IC CB CG ND1 CE1 1.5109 120.1700 -179.2000 105.2000 1.3170
IC CB CG CD2 NE2 1.5109 129.7100 178.6600 105.8000 1.3782
IC NE2 ND1 *CE1 HE1 1.3539 111.7600 179.6900 124.5800 1.0929
IC CE1 CD2 *NE2 HE2 1.3539 107.1500 -178.6900 125.8600 0.9996
IC NE2 CG *CD2 HD2 1.3782 105.8000 -179.3500 129.8900 1.0809
RESI HSP 1.00 ! Protonated His
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 ND1--CE1
ATOM HA HB 0.09 ! | | / ||
GROUP ! HA-CA--CB--CG ||
ATOM CB CT2 -0.05 ! | | \\ ||
ATOM HB1 HA 0.09 ! | HB2 CD2--NE2(+)
ATOM HB2 HA 0.09 ! O=C | \
ATOM CD2 CPH1 0.19 ! | HD2 HE2
ATOM HD2 HR1 0.13
ATOM CG CPH1 0.19
GROUP
ATOM NE2 NR3 -0.51
ATOM HE2 H 0.44
ATOM ND1 NR3 -0.51
ATOM HD1 H 0.44
ATOM CE1 CPH2 0.32
ATOM HE1 HR2 0.18
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB ND1 CG CE1 ND1
BOND NE2 CD2 N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 ND1 HD1 NE2 HE2 CD2 HD2 CE1 HE1
DOUBLE O C CD2 CG NE2 CE1
IMPR ND1 CG CE1 HD1 ND1 CE1 CG HD1
IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HD1 ND1
DONOR HE2 NE2
ACCEPTOR O C
IC -C CA *N HN 1.3489 123.9300 180.0000 118.8000 1.0041
IC -C N CA C 1.3489 123.9300 180.0000 112.0300 1.5225
IC N CA C +N 1.4548 112.0300 180.0000 116.4900 1.3464
IC +N CA *C O 1.3464 116.4900 180.0000 121.2000 1.2284
IC CA C +N +CA 1.5225 116.4900 180.0000 124.2400 1.4521
IC N C *CA CB 1.4548 112.0300 125.1300 109.3800 1.5533
IC N C *CA HA 1.4548 112.0300 -119.2000 106.7200 1.0832
IC N CA CB CG 1.4548 112.2500 180.0000 114.1800 1.5168
IC CG CA *CB HB1 1.5168 114.1800 122.5000 108.9900 1.1116
IC CG CA *CB HB2 1.5168 114.1800 -121.5100 108.9700 1.1132
IC CA CB CG ND1 1.5533 114.1800 90.0000 122.9400 1.3718
IC ND1 CB *CG CD2 1.3718 122.9400 -165.2600 128.9300 1.3549
IC CB CG ND1 CE1 1.5168 122.9400 -167.6200 108.9000 1.3262
IC CB CG CD2 NE2 1.5168 128.9300 167.1300 106.9300 1.3727
IC NE2 ND1 *CE1 HE1 1.3256 108.5000 178.3900 125.7600 1.0799
IC CE1 CD2 *NE2 HE2 1.3256 108.8200 -172.9400 125.5200 1.0020
IC CE1 CG *ND1 HD1 1.3262 108.9000 171.4900 126.0900 1.0018
IC NE2 CG *CD2 HD2 1.3727 106.9300 -174.4900 128.4100 1.0867
RESI ILE 0.00
GROUP
ATOM N NH1 -0.47 ! | HG21 HG22
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | CG2--HG23
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB HD1
ATOM CB CT1 -0.09 ! | \ /
ATOM HB HA 0.09 ! | CG1--CD--HD2
GROUP ! O=C / \ \
ATOM CG2 CT3 -0.27 ! | HG11 HG12 HD3
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM CG1 CT2 -0.18
ATOM HG11 HA 0.09
ATOM HG12 HA 0.09
GROUP
ATOM CD CT3 -0.27
ATOM HD1 HA 0.09
ATOM HD2 HA 0.09
ATOM HD3 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB CD CG1
BOND N HN N CA C CA C +N
BOND CA HA CB HB CG1 HG11 CG1 HG12 CG2 HG21
BOND CG2 HG22 CG2 HG23 CD HD1 CD HD2 CD HD3
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3470 124.1600 180.0000 114.1900 0.9978
IC -C N CA C 1.3470 124.1600 180.0000 106.3500 1.5190
IC N CA C +N 1.4542 106.3500 180.0000 117.9700 1.3465
IC +N CA *C O 1.3465 117.9700 180.0000 120.5900 1.2300
IC CA C +N +CA 1.5190 117.9700 180.0000 124.2100 1.4467
IC N C *CA CB 1.4542 106.3500 124.2200 112.9300 1.5681
IC N C *CA HA 1.4542 106.3500 -115.6300 106.8100 1.0826
IC N CA CB CG1 1.4542 112.7900 180.0000 113.6300 1.5498
IC CG1 CA *CB HB 1.5498 113.6300 114.5500 104.4800 1.1195
IC CG1 CA *CB CG2 1.5498 113.6300 -130.0400 113.9300 1.5452
IC CA CB CG2 HG21 1.5681 113.9300 -171.3000 110.6100 1.1100
IC HG21 CB *CG2 HG22 1.1100 110.6100 119.3500 110.9000 1.1102
IC HG21 CB *CG2 HG23 1.1100 110.6100 -120.0900 110.9700 1.1105
IC CA CB CG1 CD 1.5681 113.6300 180.0000 114.0900 1.5381
IC CD CB *CG1 HG11 1.5381 114.0900 122.3600 109.7800 1.1130
IC CD CB *CG1 HG12 1.5381 114.0900 -120.5900 108.8900 1.1141
IC CB CG1 CD HD1 1.5498 114.0900 -176.7800 110.3100 1.1115
IC HD1 CG1 *CD HD2 1.1115 110.3100 119.7500 110.6500 1.1113
IC HD1 CG1 *CD HD3 1.1115 110.3100 -119.7000 111.0200 1.1103
RESI LEU 0.00
GROUP
ATOM N NH1 -0.47 ! | HD11 HD12
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | HB1 CD1--HD13
ATOM HA HB 0.09 ! | | /
GROUP ! HA-CA--CB--CG-HG
ATOM CB CT2 -0.18 ! | | \
ATOM HB1 HA 0.09 ! | HB2 CD2--HD23
ATOM HB2 HA 0.09 ! O=C | \
GROUP ! | HD21 HD22
ATOM CG CT1 -0.09
ATOM HG HA 0.09
GROUP
ATOM CD1 CT3 -0.27
ATOM HD11 HA 0.09
ATOM HD12 HA 0.09
ATOM HD13 HA 0.09
GROUP
ATOM CD2 CT3 -0.27
ATOM HD21 HA 0.09
ATOM HD22 HA 0.09
ATOM HD23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD1 CG CD2 CG
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CG HG CD1 HD11
BOND CD1 HD12 CD1 HD13 CD2 HD21 CD2 HD22 CD2 HD23
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3474 124.3100 180.0000 114.2600 0.9979
IC -C N CA C 1.3474 124.3100 180.0000 106.0500 1.5184
IC N CA C +N 1.4508 106.0500 180.0000 117.9300 1.3463
IC +N CA *C O 1.3463 117.9300 180.0000 120.5600 1.2299
IC CA C +N +CA 1.5184 117.9300 180.0000 124.2600 1.4467
IC N C *CA CB 1.4508 106.0500 121.5200 112.1200 1.5543
IC N C *CA HA 1.4508 106.0500 -116.5000 107.5700 1.0824
IC N CA CB CG 1.4508 111.1900 180.0000 117.4600 1.5472
IC CG CA *CB HB1 1.5472 117.4600 120.9800 107.1700 1.1145
IC CG CA *CB HB2 1.5472 117.4600 -124.6700 108.9800 1.1126
IC CA CB CG CD1 1.5543 117.4600 180.0000 110.4800 1.5361
IC CD1 CB *CG CD2 1.5361 110.4800 -123.7500 112.5700 1.5360
IC CD1 CD2 *CG HG 1.5361 110.2600 -116.6300 108.0200 1.1168
!IC CD1 CB *CG HG 1.5361 110.4800 116.6300 108.6800 1.1168 old
IC CB CG CD1 HD11 1.5472 110.4800 177.3300 110.5400 1.1111
IC HD11 CG *CD1 HD12 1.1111 110.5400 119.9600 110.6200 1.1112
IC HD11 CG *CD1 HD13 1.1111 110.5400 -119.8500 110.6900 1.1108
IC CB CG CD2 HD21 1.5472 112.5700 178.9600 110.3200 1.1116
IC HD21 CG *CD2 HD22 1.1116 110.3200 119.7100 111.6900 1.1086
IC HD21 CG *CD2 HD23 1.1116 110.3200 -119.6100 110.4900 1.1115
RESI LYS 1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 HD1 HE1 HZ1
ATOM HA HB 0.09 ! | | | | | /
GROUP ! HA-CA--CB--CG--CD--CE--NZ--HZ2
ATOM CB CT2 -0.18 ! | | | | | \
ATOM HB1 HA 0.09 ! | HB2 HG2 HD2 HE2 HZ3
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM CD CT2 -0.18
ATOM HD1 HA 0.09
ATOM HD2 HA 0.09
GROUP
ATOM CE CT2 0.21
ATOM HE1 HA 0.05
ATOM HE2 HA 0.05
ATOM NZ NH3 -0.30
ATOM HZ1 HC 0.33
ATOM HZ2 HC 0.33
ATOM HZ3 HC 0.33
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD CG CE CD NZ CE
BOND N HN N CA C CA
BOND C +N CA HA CB HB1 CB HB2 CG HG1
BOND CG HG2 CD HD1 CD HD2 CE HE1 CE HE2
DOUBLE O C
BOND NZ HZ1 NZ HZ2 NZ HZ3
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HZ1 NZ
DONOR HZ2 NZ
DONOR HZ3 NZ
ACCEPTOR O C
IC -C CA *N HN 1.3482 123.5700 180.0000 115.1100 0.9988
IC -C N CA C 1.3482 123.5700 180.0000 107.2900 1.5187
IC N CA C +N 1.4504 107.2900 180.0000 117.2700 1.3478
IC +N CA *C O 1.3478 117.2700 180.0000 120.7900 1.2277
IC CA C +N +CA 1.5187 117.2700 180.0000 124.9100 1.4487
IC N C *CA CB 1.4504 107.2900 122.2300 111.3600 1.5568
IC N C *CA HA 1.4504 107.2900 -116.8800 107.3600 1.0833
IC N CA CB CG 1.4504 111.4700 180.0000 115.7600 1.5435
IC CG CA *CB HB1 1.5435 115.7600 120.9000 107.1100 1.1146
IC CG CA *CB HB2 1.5435 115.7600 -124.4800 108.9900 1.1131
IC CA CB CG CD 1.5568 115.7600 180.0000 113.2800 1.5397
IC CD CB *CG HG1 1.5397 113.2800 120.7400 109.1000 1.1138
IC CD CB *CG HG2 1.5397 113.2800 -122.3400 108.9900 1.1143
IC CB CG CD CE 1.5435 113.2800 180.0000 112.3300 1.5350
IC CE CG *CD HD1 1.5350 112.3300 122.2500 108.4100 1.1141
IC CE CG *CD HD2 1.5350 112.3300 -121.5900 108.1300 1.1146
IC CG CD CE NZ 1.5397 112.3300 180.0000 110.4600 1.4604
IC NZ CD *CE HE1 1.4604 110.4600 119.9100 110.5100 1.1128
IC NZ CD *CE HE2 1.4604 110.4600 -120.0200 110.5700 1.1123
IC CD CE NZ HZ1 1.5350 110.4600 179.9200 110.0200 1.0404
IC HZ1 CE *NZ HZ2 1.0404 110.0200 120.2700 109.5000 1.0402
IC HZ1 CE *NZ HZ3 1.0404 110.0200 -120.1300 109.4000 1.0401
RESI MET 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1 HG1 HE1
ATOM HA HB 0.09 ! | | | |
GROUP ! HA-CA--CB--CG--SD--CE--HE3
ATOM CB CT2 -0.18 ! | | | |
ATOM HB1 HA 0.09 ! | HB2 HG2 HE2
ATOM HB2 HA 0.09 ! O=C
GROUP ! |
ATOM CG CT2 -0.14
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
ATOM SD S -0.09
ATOM CE CT3 -0.22
ATOM HE1 HA 0.09
ATOM HE2 HA 0.09
ATOM HE3 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB SD CG CE SD
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CG HG1 CG HG2
BOND CE HE1 CE HE2 CE HE3
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3478 124.2100 180.0000 114.3900 0.9978
IC -C N CA C 1.3478 124.2100 180.0000 106.3100 1.5195
IC N CA C +N 1.4510 106.3100 180.0000 117.7400 1.3471
IC +N CA *C O 1.3471 117.7400 180.0000 120.6400 1.2288
IC CA C +N +CA 1.5195 117.7400 180.0000 124.5200 1.4471
IC N C *CA CB 1.4510 106.3100 121.6200 111.8800 1.5546
IC N C *CA HA 1.4510 106.3100 -116.9800 107.5700 1.0832
IC N CA CB CG 1.4510 111.2500 180.0000 115.9200 1.5460
IC CG CA *CB HB1 1.5460 115.9200 120.5600 106.9000 1.1153
IC CG CA *CB HB2 1.5460 115.9200 -124.8000 109.3800 1.1129
IC CA CB CG SD 1.5546 115.9200 180.0000 110.2800 1.8219
IC SD CB *CG HG1 1.8219 110.2800 120.5000 110.3400 1.1106
IC SD CB *CG HG2 1.8219 110.2800 -121.1600 109.6400 1.1119
IC CB CG SD CE 1.5460 110.2800 180.0000 98.9400 1.8206
IC CG SD CE HE1 1.8219 98.9400 -179.4200 110.9100 1.1111
IC HE1 SD *CE HE2 1.1111 110.9100 119.9500 111.0300 1.1115
IC HE1 SD *CE HE3 1.1111 110.9100 -119.9500 111.0900 1.1112
RESI PHE 0.00
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | |
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
ATOM HA HB 0.09 ! | | // \\
GROUP ! HA-CA--CB--CG CZ--HZ
ATOM CB CT2 -0.18 ! | | \ __ /
ATOM HB1 HA 0.09 ! | HB2 CD2--CE2
ATOM HB2 HA 0.09 ! O=C | |
GROUP ! | HD2 HE2
ATOM CG CA 0.00
GROUP
ATOM CD1 CA -0.115
ATOM HD1 HP 0.115
GROUP
ATOM CE1 CA -0.115
ATOM HE1 HP 0.115
GROUP
ATOM CZ CA -0.115
ATOM HZ HP 0.115
GROUP
ATOM CD2 CA -0.115
ATOM HD2 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG CE1 CD1
BOND CZ CE2 N HN
BOND N CA C CA C +N CA HA
BOND CB HB1 CB HB2 CD1 HD1 CD2 HD2 CE1 HE1
DOUBLE O C CD1 CG CZ CE1 CE2 CD2
BOND CE2 HE2 CZ HZ
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3476 123.8900 180.0000 114.4700 0.9987
IC -C N CA C 1.3476 123.8900 180.0000 106.3800 1.5229
IC N CA C +N 1.4504 106.3800 180.0000 117.6500 1.3483
IC +N CA *C O 1.3483 117.6500 180.0000 120.4900 1.2287
IC CA C +N +CA 1.5229 117.6500 180.0000 124.1000 1.4523
IC N C *CA CB 1.4504 106.3800 122.4900 112.4500 1.5594
IC N C *CA HA 1.4504 106.3800 -115.6300 107.0500 1.0832
IC N CA CB CG 1.4504 111.6300 180.0000 112.7600 1.5109
IC CG CA *CB HB1 1.5109 112.7600 118.2700 109.1000 1.1119
IC CG CA *CB HB2 1.5109 112.7600 -123.8300 111.1100 1.1113
IC CA CB CG CD1 1.5594 112.7600 90.0000 120.3200 1.4059
IC CD1 CB *CG CD2 1.4059 120.3200 -177.9600 120.7600 1.4062
IC CB CG CD1 CE1 1.5109 120.3200 -177.3700 120.6300 1.4006
IC CE1 CG *CD1 HD1 1.4006 120.6300 179.7000 119.6500 1.0814
IC CB CG CD2 CE2 1.5109 120.7600 177.2000 120.6200 1.4002
IC CE2 CG *CD2 HD2 1.4002 120.6200 -178.6900 119.9900 1.0811
IC CG CD1 CE1 CZ 1.4059 120.6300 -0.1200 119.9300 1.4004
IC CZ CD1 *CE1 HE1 1.4004 119.9300 -179.6900 120.0100 1.0808
IC CZ CD2 *CE2 HE2 1.4000 119.9600 -179.9300 119.8700 1.0811
IC CE1 CE2 *CZ HZ 1.4004 119.9800 179.5100 119.9700 1.0807
RESI PRO 0.00
GROUP ! HD1 HD2
ATOM N N -0.29 ! | \ /
ATOM CD CP3 0.00 ! N---CD HG1 ATOM CA CP1 0.02
ATOM HD1 HA 0.09 ! | \ /
ATOM HD2 HA 0.09 ! | CG
ATOM CA CP1 0.02 ! | / \
ATOM HA HB 0.09 ! HA-CA--CB HG2
GROUP ! | / \
ATOM CB CP2 -0.18 ! | HB1 HB2
ATOM HB1 HA 0.09 ! O=C
ATOM HB2 HA 0.09 ! |
GROUP
ATOM CG CP2 -0.18
ATOM HG1 HA 0.09
ATOM HG2 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND C CA C +N
BOND N CA CA CB CB CG CG CD N CD
BOND HA CA HG1 CG HG2 CG HD1 CD HD2 CD HB1 CB HB2 CB
DOUBLE O C
IMPR N -C CA CD
IMPR C CA +N O
ACCEPTOR O C
IC -C CA *N CD 1.3366 122.9400 178.5100 112.7500 1.4624
IC -C N CA C 1.3366 122.9400 -76.1200 110.8600 1.5399
IC N CA C +N 1.4585 110.8600 180.0000 114.7500 1.3569
IC +N CA *C O 1.3569 114.7500 177.1500 120.4600 1.2316
IC CA C +N +CA 1.5399 116.1200 180.0000 124.8900 1.4517
IC N C *CA CB 1.4585 110.8600 113.7400 111.7400 1.5399
IC N C *CA HA 1.4585 110.8600 -122.4000 109.0900 1.0837
IC N CA CB CG 1.4585 102.5600 31.6100 104.3900 1.5322
IC CA CB CG CD 1.5399 104.3900 -34.5900 103.2100 1.5317
IC N CA CB HB1 1.4585 102.5600 -84.9400 109.0200 1.1131
IC N CA CB HB2 1.4585 102.5600 153.9300 112.7400 1.1088
IC CA CB CG HG1 1.5399 104.3900 -156.7200 112.9500 1.1077
IC CA CB CG HG2 1.5399 104.3900 81.2600 109.2200 1.1143
IC CB CG CD HD1 1.5322 103.2100 -93.5500 110.0300 1.1137
IC CB CG CD HD2 1.5322 103.2100 144.5200 110.0000 1.1144
PATCHING FIRS PROP
RESI SER 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | |
GROUP ! HA-CA--CB--OG
ATOM CB CT2 0.05 ! | | \
ATOM HB1 HA 0.09 ! | HB2 HG1
ATOM HB2 HA 0.09 ! O=C
ATOM OG OH1 -0.66 ! |
ATOM HG1 H 0.43
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA OG CB N HN N CA
BOND C CA C +N CA HA CB HB1
BOND CB HB2 OG HG1
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HG1 OG
ACCEPTOR OG
ACCEPTOR O C
IC -C CA *N HN 1.3474 124.3700 180.0000 114.1800 0.9999
IC -C N CA C 1.3474 124.3700 180.0000 105.8100 1.5166
IC N CA C +N 1.4579 105.8100 180.0000 117.7200 1.3448
IC +N CA *C O 1.3448 117.7200 180.0000 120.2500 1.2290
IC CA C +N +CA 1.5166 117.7200 180.0000 124.6300 1.4529
IC N C *CA CB 1.4579 105.8100 124.7500 111.4000 1.5585
IC N C *CA HA 1.4579 105.8100 -115.5600 107.3000 1.0821
IC N CA CB OG 1.4579 114.2800 180.0000 112.4500 1.4341
IC OG CA *CB HB1 1.4341 112.4500 119.3200 108.1000 1.1140
IC OG CA *CB HB2 1.4341 112.4500 -123.8600 110.3800 1.1136
IC CA CB OG HG1 1.5585 112.4500 165.9600 107.0800 0.9655
RESI THR 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | OG1--HG1
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB
ATOM CB CT1 0.14 ! | \
ATOM HB HA 0.09 ! | CG2--HG21
ATOM OG1 OH1 -0.66 ! O=C / \
ATOM HG1 H 0.43 ! | HG21 HG22
GROUP
ATOM CG2 CT3 -0.27
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA OG1 CB CG2 CB N HN
BOND N CA C CA C +N CA HA
BOND CB HB OG1 HG1 CG2 HG21 CG2 HG22 CG2 HG23
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HG1 OG1
ACCEPTOR OG1
ACCEPTOR O C
IC -C CA *N HN 1.3471 124.1200 180.0000 114.2600 0.9995
IC -C N CA C 1.3471 124.1200 180.0000 106.0900 1.5162
IC N CA C +N 1.4607 106.0900 180.0000 117.6900 1.3449
IC +N CA *C O 1.3449 117.6900 180.0000 120.3000 1.2294
IC CA C +N +CA 1.5162 117.6900 180.0000 124.6600 1.4525
IC N C *CA CB 1.4607 106.0900 126.4600 112.7400 1.5693
IC N C *CA HA 1.4607 106.0900 -114.9200 106.5300 1.0817
IC N CA CB OG1 1.4607 114.8100 180.0000 112.1600 1.4252
IC OG1 CA *CB HB 1.4252 112.1600 116.3900 106.1100 1.1174
IC OG1 CA *CB CG2 1.4252 112.1600 -124.1300 115.9100 1.5324
IC CA CB OG1 HG1 1.5693 112.1600 -179.2800 105.4500 0.9633
IC CA CB CG2 HG21 1.5693 115.9100 -173.6500 110.8500 1.1104
IC HG21 CB *CG2 HG22 1.1104 110.8500 119.5100 110.4100 1.1109
IC HG21 CB *CG2 HG23 1.1104 110.8500 -120.3900 111.1100 1.1113
RESI TRP 0.00
GROUP
ATOM N NH1 -0.47 ! | HE3
ATOM HN H 0.31 ! HN-N |
ATOM CA CT1 0.07 ! | HB1 CE3
ATOM HA HB 0.09 ! | | / \\
GROUP ! HA-CA--CB---CG-----CD2 CZ3-HZ3
ATOM CB CT2 -0.18 ! | | || || |
ATOM HB1 HA 0.09 ! | HB2 CD1 CE2 CH2-HH2
ATOM HB2 HA 0.09 ! O=C / \ / \ //
GROUP ! | HD1 NE1 CZ2
ATOM CG CY -0.03 ! | |
ATOM CD1 CA 0.035 ! HE1 HZ2
ATOM HD1 HP 0.115
ATOM NE1 NY -0.61
ATOM HE1 H 0.38
ATOM CE2 CPT 0.13
ATOM CD2 CPT -0.02
GROUP
ATOM CE3 CA -0.115
ATOM HE3 HP 0.115
GROUP
ATOM CZ3 CA -0.115
ATOM HZ3 HP 0.115
GROUP
ATOM CZ2 CA -0.115
ATOM HZ2 HP 0.115
GROUP
ATOM CH2 CA -0.115
ATOM HH2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG NE1 CD1
BOND CZ2 CE2
BOND N HN N CA C CA C +N
BOND CZ3 CH2 CD2 CE3 NE1 CE2 CA HA CB HB1
BOND CB HB2 CD1 HD1 NE1 HE1 CE3 HE3 CZ2 HZ2
BOND CZ3 HZ3 CH2 HH2
DOUBLE O C CD1 CG CE2 CD2 CZ3 CE3 CH2 CZ2
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HE1 NE1
ACCEPTOR O C
IC -C CA *N HN 1.3482 123.5100 180.0000 115.0200 0.9972
IC -C N CA C 1.3482 123.5100 180.0000 107.6900 1.5202
IC N CA C +N 1.4507 107.6900 180.0000 117.5700 1.3505
IC +N CA *C O 1.3505 117.5700 180.0000 121.0800 1.2304
IC CA C +N +CA 1.5202 117.5700 180.0000 124.8800 1.4526
IC N C *CA CB 1.4507 107.6900 122.6800 111.2300 1.5560
IC N C *CA HA 1.4507 107.6900 -117.0200 106.9200 1.0835
IC N CA CB CG 1.4507 111.6800 180.0000 115.1400 1.5233
IC CG CA *CB HB1 1.5233 115.1400 119.1700 107.8400 1.1127
IC CG CA *CB HB2 1.5233 115.1400 -124.7300 109.8700 1.1118
IC CA CB CG CD2 1.5560 115.1400 90.0000 123.9500 1.4407
IC CD2 CB *CG CD1 1.4407 123.9500 -172.8100 129.1800 1.3679
IC CD1 CG CD2 CE2 1.3679 106.5700 -0.0800 106.6500 1.4126
IC CG CD2 CE2 NE1 1.4407 106.6500 0.1400 107.8700 1.3746
IC CE2 CG *CD2 CE3 1.4126 106.6500 179.2100 132.5400 1.4011
IC CE2 CD2 CE3 CZ3 1.4126 120.8000 -0.2000 118.1600 1.4017
IC CD2 CE3 CZ3 CH2 1.4011 118.1600 0.1000 120.9700 1.4019
IC CE3 CZ3 CH2 CZ2 1.4017 120.9700 0.0100 120.8700 1.4030
IC CZ3 CD2 *CE3 HE3 1.4017 118.1600 -179.6200 121.8400 1.0815
IC CH2 CE3 *CZ3 HZ3 1.4019 120.9700 -179.8200 119.4500 1.0811
IC CZ2 CZ3 *CH2 HH2 1.4030 120.8700 -179.9200 119.5700 1.0811
IC CE2 CH2 *CZ2 HZ2 1.3939 118.4200 179.8700 120.0800 1.0790
IC CD1 CE2 *NE1 HE1 1.3752 108.8100 177.7800 124.6800 0.9767
IC CG NE1 *CD1 HD1 1.3679 110.1000 178.1000 125.4300 1.0820
RESI TYR 0.00
GROUP
ATOM N NH1 -0.47 ! | HD1 HE1
ATOM HN H 0.31 ! HN-N | |
ATOM CA CT1 0.07 ! | HB1 CD1--CE1
ATOM HA HB 0.09 ! | | // \\
GROUP ! HA-CA--CB--CG CZ--OH
ATOM CB CT2 -0.18 ! | | \ __ / \
ATOM HB1 HA 0.09 ! | HB2 CD2--CE2 HH
ATOM HB2 HA 0.09 ! O=C | |
GROUP ! | HD2 HE2
ATOM CG CA 0.00
GROUP
ATOM CD1 CA -0.115
ATOM HD1 HP 0.115
GROUP
ATOM CE1 CA -0.115
ATOM HE1 HP 0.115
GROUP
ATOM CZ CA 0.11
ATOM OH OH1 -0.54
ATOM HH H 0.43
GROUP
ATOM CD2 CA -0.115
ATOM HD2 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG CB CD2 CG CE1 CD1
BOND CZ CE2 OH CZ
BOND N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CD1 HD1 CD2 HD2
BOND CE1 HE1 CE2 HE2 OH HH
DOUBLE O C CD1 CG CE1 CZ CE2 CD2
IMPR N -C CA HN C CA +N O
DONOR HN N
DONOR HH OH
ACCEPTOR OH
ACCEPTOR O C
IC -C CA *N HN 1.3476 123.8100 180.0000 114.5400 0.9986
IC -C N CA C 1.3476 123.8100 180.0000 106.5200 1.5232
IC N CA C +N 1.4501 106.5200 180.0000 117.3300 1.3484
IC +N CA *C O 1.3484 117.3300 180.0000 120.6700 1.2287
IC CA C +N +CA 1.5232 117.3300 180.0000 124.3100 1.4513
IC N C *CA CB 1.4501 106.5200 122.2700 112.3400 1.5606
IC N C *CA HA 1.4501 106.5200 -116.0400 107.1500 1.0833
IC N CA CB CG 1.4501 111.4300 180.0000 112.9400 1.5113
IC CG CA *CB HB1 1.5113 112.9400 118.8900 109.1200 1.1119
IC CG CA *CB HB2 1.5113 112.9400 -123.3600 110.7000 1.1115
IC CA CB CG CD1 1.5606 112.9400 90.0000 120.4900 1.4064
IC CD1 CB *CG CD2 1.4064 120.4900 -176.4600 120.4600 1.4068
IC CB CG CD1 CE1 1.5113 120.4900 -175.4900 120.4000 1.4026
IC CE1 CG *CD1 HD1 1.4026 120.4000 178.9400 119.8000 1.0814
IC CB CG CD2 CE2 1.5113 120.4600 175.3200 120.5600 1.4022
IC CE2 CG *CD2 HD2 1.4022 120.5600 -177.5700 119.9800 1.0813
IC CG CD1 CE1 CZ 1.4064 120.4000 -0.1900 120.0900 1.3978
IC CZ CD1 *CE1 HE1 1.3978 120.0900 179.6400 120.5800 1.0799
IC CZ CD2 *CE2 HE2 1.3979 119.9200 -178.6900 119.7600 1.0798
IC CE1 CE2 *CZ OH 1.3978 120.0500 -178.9800 120.2500 1.4063
IC CE1 CZ OH HH 1.3978 119.6800 175.4500 107.4700 0.9594
RESI VAL 0.00
GROUP
ATOM N NH1 -0.47 ! | HG11 HG12
ATOM HN H 0.31 ! HN-N | /
ATOM CA CT1 0.07 ! | CG1--HG13
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB
ATOM CB CT1 -0.09 ! | \
ATOM HB HA 0.09 ! | CG2--HG21
GROUP ! O=C / \
ATOM CG1 CT3 -0.27 ! | HG21 HG22
ATOM HG11 HA 0.09
ATOM HG12 HA 0.09
ATOM HG13 HA 0.09
GROUP
ATOM CG2 CT3 -0.27
ATOM HG21 HA 0.09
ATOM HG22 HA 0.09
ATOM HG23 HA 0.09
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA CG1 CB CG2 CB N HN
BOND N CA C CA C +N CA HA
BOND CB HB CG1 HG11 CG1 HG12 CG1 HG13 CG2 HG21
BOND CG2 HG22 CG2 HG23
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3482 124.5700 180.0000 114.4100 0.9966
IC -C N CA C 1.3482 124.5700 180.0000 105.5400 1.5180
IC N CA C +N 1.4570 105.5400 180.0000 117.8300 1.3471
IC +N CA *C O 1.3471 117.8300 180.0000 120.7000 1.2297
IC CA C +N +CA 1.5180 117.8300 180.0000 124.0800 1.4471
IC N C *CA CB 1.4570 105.5400 122.9500 111.2300 1.5660
IC N C *CA HA 1.4570 105.5400 -117.2400 107.4600 1.0828
IC N CA CB CG1 1.4570 113.0500 180.0000 113.9700 1.5441
IC CG1 CA *CB CG2 1.5441 113.9700 123.9900 112.1700 1.5414
IC CG1 CA *CB HB 1.5441 113.9700 -119.1700 107.5700 1.1178
IC CA CB CG1 HG11 1.5660 113.9700 177.8300 110.3000 1.1114
IC HG11 CB *CG1 HG12 1.1114 110.3000 119.2500 111.6700 1.1097
IC HG11 CB *CG1 HG13 1.1114 110.3000 -119.4900 110.7000 1.1110
IC CA CB CG2 HG21 1.5660 112.1700 -177.7800 110.7100 1.1108
IC HG21 CB *CG2 HG22 1.1108 110.7100 120.0800 110.5600 1.1115
IC HG21 CB *CG2 HG23 1.1108 110.7100 -119.5500 111.2300 1.1098
RESI TIP3 0.000 ! tip3p water model, generate using noangle nodihedral
GROUP
ATOM OH2 OT -0.834
ATOM H1 HT 0.417
ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! the last bond is needed for shake
BOND OH2 H1 OH2 H2
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p
GROUP
ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup
ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup
ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup
BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p
ANGLE H1 OH2 H2 ! required
ACCEPTOR OH2
PATCHING FIRS NONE LAST NONE
RESI CAL 2.00 ! Calcium ion
GROUP
ATOM CAL CAL 2.00
PATCHING FIRST NONE LAST NONE
RESI ZN2 2.00 ! Zinc ion
GROUP
ATOM ZN ZN 2.00
PATCHING FIRST NONE LAST NONE
RESI HEME -2.00 ! 6-liganded planar heme
GROUP
ATOM FE FE 0.24 ! O2A O1A O2D O1D
ATOM NA NPH -0.18 ! \\ // \\ //
ATOM NB NPH -0.18 ! CGA CGD
ATOM NC NPH -0.18 ! | |
ATOM ND NPH -0.18 ! HBA1--CBA--HBA2 HA HBD1--CBD--HBD2
ATOM C1A CPA 0.12 ! | | |
ATOM C2A CPB -0.06 ! HAA1--CAA-HAA2 _CHA_ HAD1--CAD--HAD2
ATOM C3A CPB -0.06 ! | / \ |
ATOM C4A CPA 0.12 ! C2A---C1A C4D---C3D
ATOM C1B CPA 0.12 ! | | | |
ATOM C2B CPB -0.06 !HMA1\ | | | | /HMD1
ATOM C3B CPB -0.06 !HMA2-CMA--C3A NA ND C2D--CMD-HMD2
ATOM C4B CPA 0.12 !HMA3/ \ / \ / \ / \HMD3
ATOM C1C CPA 0.12 ! C4A \ / C1D
ATOM C2C CPB -0.06 ! / \ / \
ATOM C3C CPB -0.06 ! HB--CHB FE CHD--HD
ATOM C4C CPA 0.12 ! \ / \ /
ATOM C1D CPA 0.12 ! C1B / \ C4C HAC
ATOM C2D CPB -0.06 !HMB1\ / \ / \ / \ /
ATOM C3D CPB -0.06 !HMB2-CMB--C2B NB NC C3C--CAC
ATOM C4D CPA 0.12 !HMB3/ | | | | \\ /HBC1
GROUP ! | | | | CBC
ATOM CHA CPM -0.10 ! C3B---C4B C1C---C2C \HBC2
ATOM HA HA 0.10 ! | \_CHC_/ |
GROUP ! CAB | CMC--HMC3
ATOM CHB CPM -0.10 ! // \ HC / |
ATOM HB HA 0.10 ! CBB HAB HMC1 HMC2
GROUP ! / \
ATOM CHC CPM -0.10 ! HBB1 HBB2
ATOM HC HA 0.10 !
GROUP
ATOM CHD CPM -0.10
ATOM HD HA 0.10
GROUP
ATOM CMA CT3 -0.27
ATOM HMA1 HA 0.09
ATOM HMA2 HA 0.09
ATOM HMA3 HA 0.09
GROUP
ATOM CAA CT2 -0.18
ATOM HAA1 HA 0.09
ATOM HAA2 HA 0.09
GROUP
ATOM CBA CT2 -0.28
ATOM HBA1 HA 0.09
ATOM HBA2 HA 0.09
ATOM CGA CC 0.62
ATOM O1A OC -0.76
ATOM O2A OC -0.76
GROUP
ATOM CMB CT3 -0.27
ATOM HMB1 HA 0.09
ATOM HMB2 HA 0.09
ATOM HMB3 HA 0.09
GROUP
ATOM CAB C -0.20
ATOM HAB HA 0.20
GROUP
ATOM CBB C -0.20
ATOM HBB1 HA 0.10
ATOM HBB2 HA 0.10
GROUP
ATOM CMC CT3 -0.27
ATOM HMC1 HA 0.09
ATOM HMC2 HA 0.09
ATOM HMC3 HA 0.09
GROUP
ATOM CAC C -0.20
ATOM HAC HA 0.20
GROUP
ATOM CBC C -0.20
ATOM HBC1 HA 0.10
ATOM HBC2 HA 0.10
GROUP
ATOM CMD CT3 -0.27
ATOM HMD1 HA 0.09
ATOM HMD2 HA 0.09
ATOM HMD3 HA 0.09
GROUP
ATOM CAD CT2 -0.18
ATOM HAD1 HA 0.09
ATOM HAD2 HA 0.09
GROUP
ATOM CBD CT2 -0.28
ATOM HBD1 HA 0.09
ATOM HBD2 HA 0.09
ATOM CGD CC 0.62
ATOM O1D OC -0.76
ATOM O2D OC -0.76
BOND FE NA FE NB FE NC FE ND NA C1A
BOND C1A C2A C2A C3A C3A C4A NA C4A C2A CAA
BOND CAA CBA CBA CGA CGA O1A CGA O2A C3A CMA
BOND CHB C4A CHB C1B NB C1B C1B C2B C2B C3B
BOND C3B C4B NB C4B C2B CMB C3B CAB CAB CBB
BOND CHC C4B CHC C1C NC C1C C1C C2C C2C C3C
BOND C3C C4C NC C4C C2C CMC C3C CAC CAC CBC
BOND CHD C4C CHD C1D ND C1D C1D C2D C2D C3D
BOND C3D C4D ND C4D C2D CMD C3D CAD CAD CBD
BOND CBD CGD CGD O1D CGD O2D CHA C4D CHA C1A
BOND CHA HA CHB HB CHC HC CHD HD
BOND CAA HAA1 CAA HAA2 CBA HBA1 CBA HBA2
BOND CMA HMA1 CMA HMA2 CMA HMA3
BOND CMB HMB1 CMB HMB2 CMB HMB3
BOND CAB HAB CBB HBB1 CBB HBB2
BOND CMC HMC1 CMC HMC2 CMC HMC3
BOND CAC HAC CBC HBC1 CBC HBC2
BOND CMD HMD1 CMD HMD2 CMD HMD3
BOND CAD HAD1 CAD HAD2 CBD HBD1 CBD HBD2
IMPR C2A C1A C3A CAA C3A C2A C4A CMA C2B C1B C3B CMB
IMPR C3B C2B C4B CAB C2C C1C C3C CMC C3C C2C C4C CAC
IMPR C2D C1D C3D CMD C3D C2D C4D CAD
IMPR CGA CBA O2A O1A CGD CBD O2D O1D
IMPR C4A NA C1A C2A C1A NA C4A C3A
IMPR C4B NB C1B C2B C1B NB C4B C3B
IMPR C4C NC C1C C2C C1C NC C4C C3C
IMPR C4D ND C1D C2D C1D ND C4D C3D
IMPR NA C1A C2A C3A NA C4A C3A C2A
IMPR NB C1B C2B C3B NB C4B C3B C2B
IMPR NC C1C C2C C3C NC C4C C3C C2C
IMPR ND C1D C2D C3D ND C4D C3D C2D
IMPR NA C1A CHA C4D NA C4A CHB C1B
IMPR NB C1B CHB C4A NB C4B CHC C1C
IMPR NC C1C CHC C4B NC C4C CHD C1D
IMPR ND C1D CHD C4C ND C4D CHA C1A
IMPR CHA C1A C4D HA
IMPR CHB C1B C4A HB
IMPR CHC C1C C4B HC
IMPR CHD C1D C4C HD
IMPR C1A C2A CHA NA C4A C3A CHB NA
IMPR C1B C2B CHB NB C4B C3B CHC NB
IMPR C1C C2C CHC NC C4C C3C CHD NC
IMPR C1D C2D CHD ND C4D C3D CHA ND
IMPR NA C1A C4A FE
IMPR NB C1B C4B FE
IMPR NC C1C C4C FE
IMPR ND C1D C4D FE
IMPR CAB CBB C3B HAB HAB CAB CBB HBB2 CAB CBB HBB2 HBB1
IMPR CAC CBC C3C HAC HAC CAC CBC HBC2 CAC CBC HBC2 HBC1
ACCEPTOR NA
ACCEPTOR O1A ! CGA
ACCEPTOR O2A ! CGA
ACCEPTOR NB
ACCEPTOR NC
ACCEPTOR ND
ACCEPTOR O1D ! CGD
ACCEPTOR O2D ! CGD
IC FE NA C4A C3A 0.0000 0.0000 180.0000 0.0000 0.0000
IC C3A C4A NA C1A 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE NA C1A C2A 0.0000 0.0000 180.0000 0.0000 0.0000
IC C4A NA FE NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC NA FE NB C1B 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE NB C1B C2B 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2B C1B NB C4B 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE NB C4B C3B 0.0000 0.0000 180.0000 0.0000 0.0000
IC C4B NB FE NC 0.0000 0.0000 0.0000 0.0000 0.0000
IC NB FE NC C1C 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE NC C1C C2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2C C1C NC C4C 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE NC C4C C3C 0.0000 0.0000 180.0000 0.0000 0.0000
IC C4C NC FE ND 0.0000 0.0000 0.0000 0.0000 0.0000
IC NC FE ND C1D 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE ND C1D C2D 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2D C1D ND C4D 0.0000 0.0000 0.0000 0.0000 0.0000
IC FE ND C4D C3D 0.0000 0.0000 180.0000 0.0000 0.0000
IC C4A NA FE CHB 0.0000 0.0000 0.0000 0.0000 0.0000
IC NA FE CHB HB 0.0000 0.0000 0.0000 0.0000 0.0000
IC C4B NB FE CHC 0.0000 0.0000 0.0000 0.0000 0.0000
IC NB FE CHC HC 0.0000 0.0000 0.0000 0.0000 0.0000
IC C4C NC FE CHD 0.0000 0.0000 0.0000 0.0000 0.0000
IC NC FE CHD HD 0.0000 0.0000 0.0000 0.0000 0.0000
IC C4D ND FE CHA 0.0000 0.0000 0.0000 0.0000 0.0000
IC ND FE CHA HA 0.0000 0.0000 0.0000 0.0000 0.0000
IC C3B C1B *C2B CMB 0.0000 0.0000 180.0000 0.0000 0.0000
IC C4B C2B *C3B CAB 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2B C3B CAB CBB 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION
IC CHC C1C C2C CMC 0.0000 0.0000 0.0000 0.0000 0.0000
IC C4C C2C *C3C CAC 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2C C3C CAC CBC 0.0000 0.0000 -45.0000 0.0000 0.0000 ! PREVENTS VINYL COLLISION
IC C4D C2D *C3D CAD 0.0000 0.0000 180.0000 0.0000 0.0000
IC C3D C1D *C2D CMD 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2D C3D CAD CBD 0.0000 0.0000 -120.0000 0.0000 0.0000
IC C3D CAD CBD CGD 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAD CBD CGD O1D 0.0000 0.0000 0.0000 0.0000 0.0000
IC CAD CBD CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000
IC C4A C2A *C3A CMA 0.0000 0.0000 180.0000 0.0000 0.0000
IC C3A C1A *C2A CAA 0.0000 0.0000 180.0000 0.0000 0.0000
IC C1A C2A CAA CBA 0.0000 0.0000 120.0000 0.0000 0.0000
IC C2A CAA CBA CGA 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAA CBA CGA O1A 0.0000 0.0000 0.0000 0.0000 0.0000
IC CAA CBA CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000
IC C3C C1C *C2C CMC 0.0000 0.0000 180.0000 0.0000 0.0000
IC CBA O1A *CGA O2A 0.0000 0.0000 180.0000 0.0000 0.0000
IC CBD O1D *CGD O2D 0.0000 0.0000 180.0000 0.0000 0.0000
PATCHING FIRS NONE LAST NONE
PRES NTER 1.00 ! standard N-terminus
GROUP ! use in generate statement
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HT1
ATOM HT2 HC 0.33 ! (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT1 0.21 ! | \
ATOM HA HB 0.10 ! HA HT3
DELETE ATOM HN
BOND HT1 N HT2 N HT3 N
DONOR HT1 N
DONOR HT2 N
DONOR HT3 N
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
PRES GLYP 1.00 ! Glycine N-terminus
GROUP ! use in generate statement
ATOM N NH3 -0.30 !
ATOM HT1 HC 0.33 ! HA1 HT1
ATOM HT2 HC 0.33 ! | (+)/
ATOM HT3 HC 0.33 ! --CA--N--HT2
ATOM CA CT2 0.13 ! | \
ATOM HA1 HB 0.09 ! HA2 HT3
ATOM HA2 HB 0.09 !
DELETE ATOM HN
BOND HT1 N HT2 N HT3 N
DONOR HT1 N
DONOR HT2 N
DONOR HT3 N
IC HT1 N CA C 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT2 CA *N HT1 0.0000 0.0000 120.0000 0.0000 0.0000
IC HT3 CA *N HT2 0.0000 0.0000 120.0000 0.0000 0.0000
PRES PROP 1.00 ! Proline N-Terminal
GROUP ! use in generate statement
ATOM N NP -0.07 ! HA
ATOM HN1 HC 0.24 ! |
ATOM HN2 HC 0.24 ! -CA HN1
ATOM CD CP3 0.16 ! / \ /
ATOM HD1 HA 0.09 ! N(+)
ATOM HD2 HA 0.09 ! / \
ATOM CA CP1 0.16 ! -CD HN2
ATOM HA HB 0.09 ! | \
BOND HN1 N HN2 N ! HD1 HD2
DONOR HN1 N
DONOR HN2 N
IC HN1 CA *N CD 0.0000 0.0000 120.0000 0.0000 0.0000
IC HN2 CA *N HN1 0.0000 0.0000 120.0000 0.0000 0.0000
PRES ACE 0.00 ! acetylated N-terminus
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |
!
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA HN
ACCEPTOR OY CY
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
IC CY CA *N HN 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES ACP 0.00 ! acetylated N-terminus for proline
GROUP ! use in generate statement
ATOM CAY CT3 -0.27 !
ATOM HY1 HA 0.09 ! HY1 HY2 HY3
ATOM HY2 HA 0.09 ! \ | /
ATOM HY3 HA 0.09 ! CAY
GROUP ! |
ATOM CY C 0.51 ! CY=OY
ATOM OY O -0.51 ! |
!
BOND CY CAY CY N CAY HY1 CAY HY2 CAY HY3
DOUBLE OY CY
IMPR CY CAY N OY
IMPR N CY CA CD
ACCEPTOR OY CY
IC CY N CA C 0.0000 0.0000 -60.0000 0.0000 0.0000
IC CY CA *N CD 0.0000 0.0000 180.0000 0.0000 0.0000
IC CAY CY N CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC N CAY *CY OY 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY1 0.0000 0.0000 180.0000 0.0000 0.0000
IC OY CY CAY HY2 0.0000 0.0000 60.0000 0.0000 0.0000
IC OY CY CAY HY3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES CTER -1.00 ! standard C-terminus
GROUP ! use in generate statement
ATOM C CC 0.34 ! OT2(-)
ATOM OT1 OC -0.67 ! /
ATOM OT2 OC -0.67 ! -C
DELETE ATOM O ! \\
BOND C OT2 ! OT1
DOUBLE C OT1
!IMPR OT1 CA OT2 C
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
PRES CT1 0.00 ! methylated C-terminus from methyl acetate
GROUP ! use in generate statement
ATOM N NH1 -0.47 !
ATOM HN H 0.31 ! OT1
ATOM CA CT1 0.17 ! | //
ATOM HA HB 0.09 ! -N--CA--C HT1
ATOM C CD 0.63 ! | | \ /
ATOM OT1 OB -0.52 ! HN HA OT2--CT--HT2
ATOM OT2 OS -0.34 ! \
ATOM CT CT3 -0.14 ! HT3
ATOM HT1 HA 0.09 !
ATOM HT2 HA 0.09 !
ATOM HT3 HA 0.09 !
DELETE ATOM O
BOND C OT2 OT2 CT
BOND CT HT1 CT HT2 CT HT3
DOUBLE C OT1
IMPR C CA OT2 OT1
ACCEPTOR OT1 C
ACCEPTOR OT2 C
IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C OT2 CT 0.0000 0.0000 180.0000 0.0000 0.0000
IC C OT2 CT HT1 0.0000 0.0000 0.0000 0.0000 0.0000
IC C OT2 CT HT2 0.0000 0.0000 120.0000 0.0000 0.0000
IC C OT2 CT HT3 0.0000 0.0000 240.0000 0.0000 0.0000
PRES CT2 0.00 ! amidated C-terminus
GROUP ! use in generate statement
ATOM C CC 0.55 !
ATOM O O -0.55 ! |
GROUP ! O=C
ATOM NT NH2 -0.62 ! |
ATOM HT1 H 0.32 ! NT
ATOM HT2 H 0.30 ! / \
BOND C NT ! HT1 HT2
BOND NT HT1 NT HT2 !
DIHE CA C NT HT2 ! (HT1 is cis to O)
IMPR C NT CA O C CA NT O
IMPR NT C HT1 HT2 NT C HT2 HT1
DONOR HT1 NT
DONOR HT2 NT
IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C NT HT1 0.0000 0.0000 180.0000 0.0000 0.0000
IC HT1 C *NT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
PRES CT3 0.00 ! N-Methylamide C-terminus
GROUP ! use in generate statement
ATOM C C 0.51 !
ATOM O O -0.51 ! |
GROUP ! C=O
ATOM NT NH1 -0.47 ! |
ATOM HNT H 0.31 ! NT-HNT
ATOM CAT CT3 -0.11 ! |
ATOM HT1 HA 0.09 ! HT1-CAT-HT3
ATOM HT2 HA 0.09 ! |
ATOM HT3 HA 0.09 ! HT2
!
BOND C NT NT HNT NT CAT CAT HT1 CAT HT2 CAT HT3
DIHE CA C NT CAT
IMPR NT C CAT HNT C CA NT O
DONOR HNT NT
IC N CA C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC NT CA *C O 0.0000 0.0000 180.0000 0.0000 0.0000
IC C CAT *NT HNT 0.0000 0.0000 180.0000 0.0000 0.0000
IC CA C NT CAT 0.0000 0.0000 180.0000 0.0000 0.0000
IC C NT CAT HT1 0.0000 0.0000 60.0000 0.0000 0.0000
IC C NT CAT HT2 0.0000 0.0000 180.0000 0.0000 0.0000
IC C NT CAT HT3 0.0000 0.0000 -60.0000 0.0000 0.0000
PRES ASPP 0.00 ! patch for protonated aspartic acid, proton on od2
GROUP ! via acetic acid, use in a patch statement
ATOM CB CT2 -0.21 !
ATOM HB1 HA 0.09 ! HB1 OD1
ATOM HB2 HA 0.09 ! | //
ATOM CG CD 0.75 ! -CB--CG
ATOM OD1 OB -0.55 ! | \
ATOM OD2 OH1 -0.61 ! HB2 OD2-HD2
ATOM HD2 H 0.44 !
BOND OD2 HD2
ANGLE HD2 OD2 CG
DIHE HD2 OD2 CG OD1 HD2 OD2 CG CB
DONOR HD2 OD2
IC HD2 OD2 CG OD1 0.0000 0.0000 0.0000 0.0000 0.0000
PRES GLUP 0.00 ! patch for protonated glutamic acid, proton on oe2
GROUP ! via acetic acid, use in a patch statement
ATOM CG CT2 -0.21 !
ATOM HG1 HA 0.09 ! HG1 OE1
ATOM HG2 HA 0.09 ! | //
ATOM CD CD 0.75 ! -CG--CD
ATOM OE1 OB -0.55 ! | \
ATOM OE2 OH1 -0.61 ! HG2 OE2-HE2
ATOM HE2 H 0.44 !
BOND OE2 HE2
ANGLE HE2 OE2 CD
DIHE HE2 OE2 CD OE1 HE2 OE2 CD CG
DONOR HE2 OE2
IC HE2 OE2 CD OE1 0.0000 0.0000 0.0000 0.0000 0.0000
PRES LINK 0.00 ! linkage for IMAGES or for joining segments
! 1 refers to previous (N terminal)
! 2 refers to next (C terminal)
! use in a patch statement
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
PRES DISU -0.36 ! patch for disulfides. Patch must be 1-CYS and 2-CYS.
GROUP ! use in a patch statement
ATOM 1CB CT2 -0.10 !
ATOM 1SG SM -0.08 ! 2SG--2CB--
GROUP ! /
ATOM 2SG SM -0.08 ! -1CB--1SG
ATOM 2CB CT2 -0.10 !
DELETE ATOM 1HG1
DELETE ATOM 2HG1
BOND 1SG 2SG
ANGLE 1CB 1SG 2SG 1SG 2SG 2CB
DIHE 1HB1 1CB 1SG 2SG 1HB2 1CB 1SG 2SG
DIHE 2HB1 2CB 2SG 1SG 2HB2 2CB 2SG 1SG
DIHE 1CA 1CB 1SG 2SG 1SG 2SG 2CB 2CA
DIHE 1CB 1SG 2SG 2CB
!DIHE 1CB 1SG 2SG 2CB
IC 1CA 1CB 1SG 2SG 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CB 1SG 2SG 2CB 0.0000 0.0000 90.0000 0.0000 0.0000
IC 1SG 2SG 2CB 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
PRES HS2 0.00 ! Patch for neutral His, move proton from ND1 to NE2
GROUP ! use in a patch statement
ATOM CE1 CPH2 0.25 ! HE1
ATOM HE1 HR1 0.13 ! /
ATOM ND1 NR2 -0.70 ! HB1 ND1--CE1
ATOM CG CPH1 0.22 ! | / |
ATOM CB CT2 -0.08 ! -CB--CG |
ATOM HB1 HA 0.09 ! | \ |
ATOM HB2 HA 0.09 ! HB2 CD2--NE2
GROUP ! | \
ATOM NE2 NR1 -0.36 ! HD2 HE2
ATOM HE2 H 0.32
ATOM CD2 CPH1 -0.05
ATOM HD2 HR3 0.09
DELETE ATOM HD1
DELETE ACCE NE2
BOND NE2 HE2
ANGLE CD2 NE2 HE2 CE1 NE2 HE2
DIHE HE2 NE2 CE1 HE1 HE2 NE2 CE1 ND1 HE2 NE2 CD2 HD2
DIHE HE2 NE2 CD2 CG
IMPR NE2 CD2 CE1 HE2 NE2 CE1 CD2 HE2
DONOR HE2 NE2
ACCEPTOR ND1
IC CE1 CD2 *NE2 HE2 0.0000 0.0000 180.0000 0.0000 0.0000
RESI O2 0.00 ! O2 ligand for heme
GROUP
ATOM O1 OM 0.021
ATOM O2 OM -0.021
BOND O1 O2
PATCHING FIRS NONE LAST NONE
RESI CO 0.00 ! CO ligand for heme
GROUP
ATOM C CM 0.021
ATOM O OM -0.021
TRIPLE C O
PATCHING FIRS NONE LAST NONE
PRES FHEM 0.00 ! FIX UP THE HEME BY DELETING UNWANTED AUTOGENERATED ANGLES
! unliganded heme patch
DELETE ANGLE 1NA 1FE 1NC 1NB 1FE 1ND
PRES PHEM 0.00 ! Patch for HEME to His link.
! Patch residues must be 1-HIS, and 2-HEME.
DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND
BOND 1NE2 2FE
ANGLE 1CD2 1NE2 2FE 1CE1 1NE2 2FE 1NE2 2FE 2NA 1NE2 2FE 2NB
ANGLE 1NE2 2FE 2NC 1NE2 2FE 2ND
IC 1CD2 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CD2 1NE2 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1CE1 1NE2 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
PRES PLO2 0.00 ! Patch residue for Heme ligand. Residues must be
! 1-O2 , 2-HEME , and 3-HIS
! O1 of the oxygen is bonded to the iron.
BOND 1O1 2FE
ANGLE 1O2 1O1 2FE 1O1 2FE 2NA 1O1 2FE 2NB
ANGLE 1O1 2FE 2NC 1O1 2FE 2ND
DIHE 1O2 1O1 2FE 2NA
IC 1O2 1O1 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1O2 1O1 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000
PRES PLIG 0.00 ! Patch residue for Heme ligand. Residues must be,
! 1-CO , 2-HEME , and 3-HIS
BOND 1C 2FE
ANGLE 1C 2FE 3NE2
ANGLE 1O 1C 2FE 1C 2FE 2NA 1C 2FE 2NB
ANGLE 1C 2FE 2NC 1C 2FE 2ND
IC 1O 1C 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
IC 1O 1C 2FE 3NE2 0.0000 0.0000 0.0000 0.0000 0.0000
! patches for cyclic peptides
PRES LIG1 0.00000 ! linkage for cyclic peptide
! 1 refers to the C terminus which is a glycine
! 2 refers to the N terminus
! use in a patch statement, perform initial
! generation using first NONE last NONE
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA 1C 2N 2CA 2CB
DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
DIHE 1CA 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
PRES LIG2 0.00000 ! linkage for cyclic peptide
! 1 refers to the C terminus
! 2 refers to the N terminus which is a glycine
! use in a patch statement, perform initial
! generation using first NONE last NONE
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2
DIHE 1HA 1CA 1C 2N 1N 1CA 1C 2N 1CB 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
DIHE 1CA 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
PRES LIG3 0.00000 ! linkage for cyclic peptide
! 1 refers to the C terminus which is a glycine
! 2 refers to the N terminus which is a glycine
! use in a patch statement, perform initial
! generation using first NONE last NONE
BOND 1C 2N
ANGLE 1C 2N 2CA 1CA 1C 2N
ANGLE 1O 1C 2N 1C 2N 2HN
DIHE 1C 2N 2CA 2C 1C 2N 2CA 2HA1 1C 2N 2CA 2HA2
DIHE 1HA1 1CA 1C 2N 1N 1CA 1C 2N 1HA2 1CA 1C 2N
DIHE 1CA 1C 2N 2HN 1CA 1C 2N 2CA
DIHE 1O 1C 2N 2HN 1O 1C 2N 2CA
DIHE 1CA 1C 2N 2CA
IMPR 2N 1C 2CA 2HN 1C 1CA 2N 1O
IC 1N 1CA 1C 2N 0.0000 0.0000 180.0000 0.0000 0.0000
IC 2N 1CA *1C 1O 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1CA 1C 2N 2CA 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2N 2CA 2C 0.0000 0.0000 180.0000 0.0000 0.0000
IC 1C 2CA *2N 2HN 0.0000 0.0000 180.0000 0.0000 0.0000
RESI DUM 0.00 ! DUMMY ATOM
GROUP
ATOM DUM DUM 0.00
PATCHING FIRST NONE LAST NONE
!END
!phosphotyrosine information deleted
!
!lipids section
RESI MAS 0.00 ! methylacetate
GROUP !
ATOM C1 CTL3 -0.17 ! H22
ATOM C CL 0.63 ! |
ATOM OM OSL -0.34 ! H21-C2-H23
ATOM C2 CTL3 -0.14 ! \
ATOM O OBL -0.52 ! OM
ATOM H11 HAL3 0.09 ! /
ATOM H12 HAL3 0.09 ! O=C
ATOM H13 HAL3 0.09 ! |
ATOM H21 HAL3 0.09 ! H11-C1-H13
ATOM H22 HAL3 0.09 ! |
ATOM H23 HAL3 0.09 ! H12
BOND C1 C C OM OM C2
DOUBLE C O
BOND C1 H11 C1 H12 C1 H13
BOND C2 H21 C2 H22 C2 H23
IMPR C OM C1 O
! internal coordinates from experiment for heavy atoms
IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437
IC O C OM C2 1.200 125.9 0.0 114.8 1.437
IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334
IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334
IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334
IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334
IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334
IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334
RESI ETAC 0.00 ! Ethylacetate
! H213
GROUP ! |
ATOM C1 CTL3 -0.17 ! H211-C21-H212
ATOM C CL 0.63 ! /
ATOM OM OSL -0.34 ! H22-C2-H23
ATOM C2 CTL2 -0.05 ! \
ATOM O OBL -0.52 ! OM
ATOM H11 HAL3 0.09 ! /
ATOM H12 HAL3 0.09 ! O=C
ATOM H13 HAL3 0.09 ! \
ATOM H22 HAL2 0.09 ! H11-C1-H13
ATOM H23 HAL2 0.09 ! |
GROUP ! H12
ATOM C21 CTL3 -0.27
ATOM H211 HAL3 0.09
ATOM H212 HAL3 0.09
ATOM H213 HAL3 0.09
BOND C1 C C OM OM C2
DOUBLE C O
BOND C1 H11 C1 H12 C1 H13
BOND C2 C21 C2 H22 C2 H23
BOND C21 H211 C21 H212 C21 H213
IMPR C OM C1 O
! internal coordinates from experiment for heavy atoms
IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437
IC O C OM C2 1.200 125.9 0.0 114.8 1.437
IC H11 C1 C OM 1.1 108.9 180.0 109.0 1.334
IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334
IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334
IC C21 C2 OM C 1.520 109.94 180.0 114.8 1.334
IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334
IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334
IC H211 C21 C2 OM 1.1 108.90 180.0 116.7 1.437
IC H212 C21 C2 OM 1.1 108.90 60.0 116.7 1.437
IC H213 C21 C2 OM 1.1 108.90 -60.0 116.7 1.437
RESI MPRO 0.00 ! Methylpropionate
GROUP !
ATOM C1 CTL2 -0.08 ! H22
ATOM C CL 0.63 ! |
ATOM OM OSL -0.34 ! H21-C2-H23
ATOM C2 CTL3 -0.14 ! \
ATOM O OBL -0.52 ! OM
ATOM H12 HAL2 0.09 ! /
ATOM H13 HAL2 0.09 ! O=C
ATOM H21 HAL3 0.09 ! \
ATOM H22 HAL3 0.09 ! H12-C1-H13
ATOM H23 HAL3 0.09 ! /
GROUP ! H112-C11-H111
ATOM C11 CTL3 -0.27 ! |
ATOM H111 HAL3 0.09 ! H113
ATOM H112 HAL3 0.09 !
ATOM H113 HAL3 0.09 !
BOND C1 C C OM C O OM C2
BOND C1 C11 C1 H12 C1 H13
BOND C11 H111 C11 H112 C11 H113
BOND C2 H21 C2 H22 C2 H23
IMPR C OM C1 O
! internal coordinates from experiment for heavy atoms
IC C1 C OM C2 1.520 109.0 180.0 114.8 1.437
IC O C OM C2 1.200 125.9 0.0 114.8 1.437
IC C11 C1 C OM 1.520 108.9 180.0 109.0 1.334
IC H12 C1 C OM 1.1 109.75 60.4 109.0 1.334
IC H13 C1 C OM 1.1 109.75 -60.4 109.0 1.334
IC H21 C2 OM C 1.0788 109.94 180.0 114.8 1.334
IC H22 C2 OM C 1.0802 110.50 60.5 114.8 1.334
IC H23 C2 OM C 1.0802 110.50 -60.5 114.8 1.334
IC H111 C11 C1 C 1.1 109.75 180.0 109.0 1.520
IC H112 C11 C1 C 1.1 109.75 60.4 109.0 1.520
IC H113 C11 C1 C 1.1 109.75 -60.4 109.0 1.520
RESI ACEH 0.00 ! acetic acid
! atoms in proper order for molvib input
GROUP !
ATOM C2 CTL3 -0.30 !
ATOM C1 CL 0.75 ! H21 O2
ATOM H21 HAL3 0.09 ! \ //
ATOM H22 HAL3 0.09 ! H22-C2--C1
ATOM H23 HAL3 0.09 ! / \
ATOM O2 OBL -0.55 ! H23 O1-HO1
ATOM O1 OHL -0.61 !
ATOM HO1 HOL 0.44 !
BOND C1 O1 O1 HO1 C1 C2 C2 H21 C2 H22 C2 H23
DOUBLE C1 O2
IMPR C1 O1 C2 O2
IC O2 C1 C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000
IC HO1 O1 C1 O2 0.0000 0.0000 0.0000 0.0000 0.0000
IC HO1 O1 C1 C2 0.0000 0.0000 180.0000 0.0000 0.0000
IC O1 C1 C2 H21 0.0000 0.0000 180.0000 0.0000 0.0000
IC O1 C1 C2 H22 0.0000 0.0000 60.0000 0.0000 0.0000
IC O1 C1 C2 H23 0.0000 0.0000 -60.0000 0.0000 0.0000
RESI DMPA -1.00 ! Dimethylphosphate
GROUP !
ATOM P1 PL 1.50 !
ATOM O3 O2L -0.78 !
ATOM O4 O2L -0.78 ! H11
ATOM O1 OSL -0.57 ! |
ATOM O2 OSL -0.57 ! H13- C1-H12
! \
ATOM C1 CTL3 -0.17 ! (-) O3 O1
ATOM H11 HAL3 0.09 ! \ /
ATOM H12 HAL3 0.09 ! P1 (+)
ATOM H13 HAL3 0.09 ! / \
! (-) O4 O2
ATOM C2 CTL3 -0.17 ! /
ATOM H21 HAL3 0.09 ! H23-C2-H22
ATOM H22 HAL3 0.09 ! |
ATOM H23 HAL3 0.09 ! H21
!
BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1 O2 C2
BOND C1 H11 C1 H12 C1 H13 C2 H21 C2 H22 C2 H23
! IC FOR THE g,g conformation (3-21G* opt. structure)
IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356
IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357
IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357
IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356
IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343
IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343
IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343
IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344
IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344
IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344
RESI MP_1 -1.00 ! Methylphosphate, anionic
GROUP !
! atom order for molvib
ATOM C1 CTL3 -0.17 !
ATOM O1 OSL -0.62 ! H11
ATOM P1 PL 1.50 ! |
ATOM O2 OHL -0.68 ! H13--C1--H12
ATOM O3 O2L -0.82 ! |
ATOM O4 O2L -0.82 ! O1
ATOM H11 HAL3 0.09 ! |
ATOM H12 HAL3 0.09 ! O4==P1==O3 (-)
ATOM H13 HAL3 0.09 ! |
ATOM H2 HOL 0.34 ! O2
! \
! H2
BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1
BOND C1 H11 C1 H12 C1 H13 O2 H2
IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000
IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000
IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000
IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000
IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000
IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000
IC H2 O2 P1 O1 0.0000 000.00 000.0 000.00 0.0000
RESI MP_2 -2.00 ! Methylphosphate, dianionic
GROUP !
ATOM P1 PL 1.10 !
ATOM O1 OSL -0.40 ! H11
ATOM O2 O2L -0.90 ! |
ATOM O3 O2L -0.90 ! H13--C1--H12
ATOM O4 O2L -0.90 ! |
GROUP ! O1
ATOM C1 CTL3 -0.27 ! |
ATOM H11 HAL3 0.09 ! (-) O4--P1(+)--O3 (-)
ATOM H12 HAL3 0.09 ! |
ATOM H13 HAL3 0.09 ! O2 (-)
!
BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C1
BOND C1 H11 C1 H12 C1 H13
IC O3 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000
IC O4 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000
IC O2 P1 O1 C1 0.0000 000.00 000.0 000.00 0.0000
IC H11 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000
IC H12 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000
IC H13 C1 O1 P1 0.0000 000.00 000.0 000.00 0.0000
! dummy to analyze cetain angles
IC O3 P1 O4 O1 0.0 0.0 0.0 0.0 0.0
RESI MSO4 -1.00 ! Methylsulfate
GROUP !
ATOM S SL 1.33 ! OS2(-1)
ATOM OS1 OSL -0.28 ! |
ATOM OS2 O2L -0.65 ! (-1) OS2--S(+2)--OS4 (-1)
ATOM OS3 O2L -0.65 ! |
ATOM OS4 O2L -0.65 ! OS1
ATOM C1 CTL3 -0.37 ! \
ATOM H11 HAL3 0.09 ! H11-C1-H13
ATOM H12 HAL3 0.09 ! |
ATOM H13 HAL3 0.09 ! H12
!
BOND S OS1 S OS2 S OS3 S OS4 OS1 C1
BOND C1 H11 C1 H12 C1 H13
ACCE OS1
ACCE OS2
ACCE OS3
ACCE OS4
IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS2 S OS2 OS3 0.0000 0.0000 -60.0000 0.0000 0.0000
IC OS3 S OS1 OS4 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS1 S OS3 OS2 0.0000 0.0000 60.0000 0.0000 0.0000
IC C1 OS1 S OS2 0.0000 0.0000 60.0000 0.0000 0.0000
IC S OS1 C1 OS3 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS1 S OS4 OS2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OS1 S OS2 OS3 0.0000 0.0000 180.0000 0.0000 0.0000
IC OS1 S OS3 OS2 0.0000 0.0000 180.0000 0.0000 0.0000
IC OS4 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS4 S OS3 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS3 S OS2 OS1 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS4 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS2 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000
IC OS3 S OS1 C1 0.0000 0.0000 60.0000 0.0000 0.0000
Resi BUTA 0.00 ! BUTANE
Group
Atom h11 HAL3 0.09 ! H2
Atom h12 HAL3 0.09 ! |
Atom h13 HAL3 0.09 ! H1-C1-H3
Atom c1 CTL3 -0.27 ! |
Group ! |
Atom h21 HAL2 0.09 ! H4-C2-H5
Atom h22 HAL2 0.09 ! |
Atom c2 CTL2 -0.18 ! |
Group ! |
Atom h31 HAL2 0.09 ! H6-C3-H7
Atom h32 HAL2 0.09 ! |
atom c3 CTL2 -0.18 ! |
Group ! |
atom h41 HAL3 0.09 ! H8-C4-H10
atom h42 HAL3 0.09 ! |
atom h43 HAL3 0.09 ! H9
atom c4 CTL3 -0.27 !
Bond h11 c1 h12 c1 h13 c1 c1 c2
Bond h21 c2 h22 c2 c2 c3
Bond h31 c3 h32 c3 c3 c4
Bond h41 c4 h42 c4 h43 c4
ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00
ic c2 c3 c4 h41 0.00 0.00 180.0 0.00 0.00
ic c3 h41 *c4 h42 0.00 0.00 120.0 0.00 0.00
ic c3 h41 *c4 h43 0.00 0.00 -120.0 0.00 0.00
ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00
ic c2 h11 *c1 h12 0.00 0.00 120.0 0.00 0.00
ic c2 h11 *c1 h13 0.00 0.00 -120.0 0.00 0.00
ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00
ic c1 c3 *c2 h22 0.00 0.00 -120.0 0.00 0.00
ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00
ic c2 c4 *c3 h32 0.00 0.00 -120.0 0.00 0.00
Resi HEXA 0.00 ! hexane
Group
Atom h11 HAL3 0.09 ! H2
Atom h12 HAL3 0.09 ! |
Atom h13 HAL3 0.09 ! H1-C1-H3
Atom c1 CTL3 -0.27 ! |
Group ! |
Atom h21 HAL2 0.09 ! H4-C2-H5
Atom h22 HAL2 0.09 ! |
Atom c2 CTL2 -0.18 ! |
Group ! |
Atom h31 HAL2 0.09 ! H6-C3-H7
Atom h32 HAL2 0.09 ! |
atom c3 CTL2 -0.18 ! |
Group ! |
atom h41 HAL2 0.09 ! H8-C4-H10
atom h42 HAL2 0.09 ! |
atom c4 CTL2 -0.18 ! |
Group ! |
atom h51 HAL2 0.09 ! H51-C5-H152
atom h52 HAL2 0.09 ! |
atom c5 CTL2 -0.18 ! |
Group ! |
atom h61 HAL2 0.09 ! H61-C4-H62
atom h62 HAL2 0.09 ! |
atom h63 HAL2 0.09 ! H63
atom c6 CTL2 -0.27 !
Bond h11 c1 h12 c1 h13 c1 c1 c2
Bond h21 c2 h22 c2 c2 c3
Bond h31 c3 h32 c3 c3 c4
Bond h41 c4 h42 c4 c4 c5
Bond h51 c5 h52 c5 c5 c6
Bond h61 c6 h62 c6 c6 h63
ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00
ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00
ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00
ic c3 c2 c1 h11 0.00 0.00 180.0 0.00 0.00
ic h11 c2 *c1 h12 0.00 0.00 120.0 0.00 0.00
ic h11 c2 *c1 h13 0.00 0.00 240.0 0.00 0.00
ic c1 c3 *c2 h21 0.00 0.00 120.0 0.00 0.00
ic c1 c3 *c2 h22 0.00 0.00 240.0 0.00 0.00
ic c2 c4 *c3 h31 0.00 0.00 120.0 0.00 0.00
ic c2 c4 *c3 h32 0.00 0.00 240.0 0.00 0.00
ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00
ic c3 c5 *c4 h42 0.00 0.00 240.0 0.00 0.00
ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00
ic c4 c6 *c5 h52 0.00 0.00 240.0 0.00 0.00
ic c4 c5 c6 h61 0.00 0.00 180.0 0.00 0.00
ic h61 c5 *c6 h62 0.00 0.00 120.0 0.00 0.00
ic h61 c5 *c6 h63 0.00 0.00 240.0 0.00 0.00
Resi ETHE 0.00 ! ethylene, yin/adm jr.
Group
Atom c1 cel2 -0.42 !
Atom h11 hel2 0.21 ! H11 H21
Atom h12 hel2 0.21 ! \ /
Group ! C1=C2
Atom c2 cel2 -0.42 ! / \
Atom h21 hel2 0.21 ! H12 H22
Atom h22 hel2 0.21 !
Bond c1 h11 c1 h12
Double c1 c2
Bond c2 h21 c2 h22
IMPR c1 c2 h12 h11
IMPR c1 c2 h11 h12
IMPR c2 c1 h22 h21
IMPR c2 c1 h21 h22
ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0
ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0
ic h22 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0
ic c1 c2 h21 h22 0.00 0.00 180.0 0.0 0.0
patc firs none last none
Resi PRPE 0.00 ! propene, yin/adm jr.
Group
Atom c1 cel2 -0.42 !
Atom h11 hel2 0.21 ! H11 H21
Atom h12 hel2 0.21 ! \ /
Group ! C1=C2 H31
Atom c2 cel1 -0.15 ! / \ /
Atom h21 HEL1 0.15 ! H12 C3
Group ! / \
Atom c3 ctl3 -0.27 ! H33 H32
Atom h31 HAL3 0.09 !
Atom h32 HAL3 0.09 !
Atom h33 HAL3 0.09 !
Bond c1 h11 c1 h12
Double c1 c2
Bond c2 h21
Bond c2 c3
bond c3 h31 c3 h32 c3 h33
ic h11 c1 c2 h21 0.00 0.00 180.0 0.0 0.0
ic h12 c2 *c1 h11 0.00 0.00 180.0 0.0 0.0
ic c3 c1 *c2 h21 0.00 0.00 180.0 0.0 0.0
ic h31 c3 c2 c1 0.00 0.00 0.0 0.0 0.0
ic h32 c3 c2 c1 0.00 0.00 120.0 0.0 0.0
ic h33 c3 c2 c1 0.00 0.00 -120.0 0.0 0.0
patc firs none last none
Resi BTE1 0.00 ! 1-Butene, yin/adm jr.
Group
Atom c1 cel2 -0.42 !
Atom h11 hel2 0.21 ! H11 H21 H41
Atom h12 hel2 0.21 ! \ / |
Group ! C1=C2 C4-H42
Atom c2 cel1 -0.15 ! / \ / \
Atom h21 HEL1 0.15 ! H12 C3 H43
Group ! / \
Atom c3 ctl2 -0.18 ! H31 H32
Atom h31 HAL2 0.09 !
Atom h32 HAL2 0.09 !
Group
Atom c4 ctl3 -0.27
Atom h41 HAL3 0.09
Atom h42 HAL3 0.09
Atom h43 HAL3 0.09
BOND c1 h11 c1 h12
Double c1 c2
BOND c2 h21
BOND c2 c3
BOND c3 h31 c3 h32
BOND c3 c4
BOND c4 h41 c4 h42 c4 h43
ic c1 c2 c3 c4 0.00 0.00 0.0 0.00 0.00
ic h11 c1 c2 c3 0.00 0.00 180.0 0.00 0.00
ic h12 c1 c2 c3 0.00 0.00 0.0 0.00 0.00
ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00
ic h31 c2 *c3 c4 0.00 0.00 120.0 0.00 0.00
ic h32 c2 *c3 c4 0.00 0.00 -120.0 0.00 0.00
ic h41 c4 c3 c2 0.00 0.00 180.0 0.00 0.00
ic h42 c4 c3 c2 0.00 0.00 60.0 0.00 0.00
ic h43 c4 c3 c2 0.00 0.00 -60.0 0.00 0.00
patc firs none last none
Resi BTE2 0.00 ! 2-Butene, yin/adm jr.
Group
Atom c1 ctl3 -0.27 ! H12 H13
Atom h11 HAL3 0.09 ! \ |
Atom h12 HAL3 0.09 ! H13-C1 H31
Atom h13 HAL3 0.09 ! \ /
Group ! C2=C3
Atom c2 cel1 -0.15 ! / \
Atom h21 HEL1 0.15 ! H21 C4-H41
Group ! | \
Atom c3 cel1 -0.15 ! H43 H42
Atom h31 HEL1 0.15 !
Group
Atom c4 ctl3 -0.27
Atom h41 HAL3 0.09
Atom h42 HAL3 0.09
Atom h43 HAL3 0.09
BOND c1 h11 c1 h12 c1 h13
BOND c1 c2
BOND c2 h21
DOUBLE c2 c3
BOND c3 h31
BOND c3 c4
BOND c4 h41 c4 h42 c4 h43
ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00
ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00
ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00
ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00
ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00
ic h31 c4 *c3 c2 0.00 0.00 120.0 0.00 0.00
ic h41 c4 c3 c2 0.00 0.00 0.0 0.00 0.00
ic h42 c4 c3 c2 0.00 0.00 120.0 0.00 0.00
ic h43 c4 c3 c2 0.00 0.00 -120.0 0.00 0.00
patc firs none last none
Resi HXE2 0.00 ! 2-hexene, yin/adm jr.
Group
Atom c1 ctl3 -0.27 ! H12 H13
Atom h11 HAL3 0.09 ! \ |
Atom h12 HAL3 0.09 ! H13-C1 H31 H51 H52
Atom h13 HAL3 0.09 ! \ / \ /
Group ! C2=C3 C5 H61
Atom c2 cel1 -0.15 ! / \ / \ /
Atom h21 HEL1 0.15 ! H21 C4 C6-H62
Group ! / \ \
Atom c3 cel1 -0.15 ! H41 H42 H63
Atom h31 HEL1 0.15 !
Group
Atom c4 ctl2 -0.18
Atom h41 HAL2 0.09
Atom h42 HAL2 0.09
Group
Atom c5 ctl2 -0.18
Atom h51 HAL2 0.09
Atom h52 HAL2 0.09
Group
Atom c6 ctl3 -0.27
Atom h61 HAL3 0.09
Atom h62 HAL3 0.09
Atom h63 HAL3 0.09
BOND c1 h11 c1 h12 c1 h13
BOND c1 c2
BOND c2 h21
DOUBLE c2 c3
BOND c3 h31
BOND c3 c4
BOND c4 h41 c4 h42
BOND c4 c5 c5 h51 c5 h52
BOND c5 c6 c6 h61 c6 h62 c6 h63
! all trans
ic c1 c2 c3 c4 0.00 0.00 180.0 0.00 0.00
ic h11 c1 c2 c3 0.00 0.00 0.0 0.00 0.00
ic h12 c1 c2 c3 0.00 0.00 120.0 0.00 0.00
ic h13 c1 c2 c3 0.00 0.00 -120.0 0.00 0.00
ic h21 c1 *c2 c3 0.00 0.00 180.0 0.00 0.00
ic h31 c4 *c3 c2 0.00 0.00 120.0 0.00 0.00
ic c2 c3 c4 c5 0.00 0.00 180.0 0.00 0.00
ic c3 c5 *c4 h41 0.00 0.00 120.0 0.00 0.00
ic c3 c5 *c4 h42 0.00 0.00 -120.0 0.00 0.00
ic c3 c4 c5 c6 0.00 0.00 180.0 0.00 0.00
ic c4 c6 *c5 h51 0.00 0.00 120.0 0.00 0.00
ic c4 c6 *c5 h52 0.00 0.00 -120.0 0.00 0.00
ic h61 c6 c5 c4 0.00 0.00 180.0 0.00 0.00
ic h62 c6 c5 c4 0.00 0.00 60.0 0.00 0.00
ic h63 c6 c5 c4 0.00 0.00 300.0 0.00 0.00
patc firs none last none
!RESI TIP3 0.00 ! TIPS3P WATER MODEL
! ! GENERATE USING NOANGLE NODIHEDRAL
!GROUP !
!ATOM OH2 OT -0.834
!ATOM H1 HT 0.417
!ATOM H2 HT 0.417
!BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE
!ANGLE H1 OH2 H2 ! REQUIRED
!ACCEPTOR OH2
!PATCHING FIRS NONE LAST NONE
!RESI TP3M 0.000 ! "mmff" water model, as an analog of tip3p
!GROUP
!ATOM OH2 OT -0.834 ! these charges are replaced by the mmff setup
!ATOM H1 HT 0.417 ! these charges are replaced by the mmff setup
!ATOM H2 HT 0.417 ! these charges are replaced by the mmff setup
!BOND OH2 H1 OH2 H2 ! omits the H1-H2 bond, which is needed for shake with tip3p
!ANGLE H1 OH2 H2 ! required
!ACCEPTOR OH2
!PATCHING FIRS NONE LAST NONE
RESI SOD 1.00 ! Sodium Ion
GROUP
ATOM SOD SOD 1.00
PATCHING FIRST NONE LAST NONE
RESI CLA -1.00 ! Chloride Anion
GROUP
ATOM CLA CLA -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 DUM 0.00 ! DUMMY ATOM
!GROUP
!ATOM DUM DUM 0.00
!PATCHING FIRST NONE LAST NONE
RESI NC4 1.00 ! tetramethylammonium
GROUP !
ATOM N NTL -0.60 ! H32
ATOM C1 CTL5 -0.35 ! |
ATOM C2 CTL5 -0.35 ! H31-C3-H33
ATOM C3 CTL5 -0.35 ! H23 | H41
ATOM C4 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! H22-C2------N------C4-H42 (+)
ATOM H12 HL 0.25 ! | | |
ATOM H13 HL 0.25 ! H21 | H43
ATOM H21 HL 0.25 ! H11-C1-H13
ATOM H22 HL 0.25 ! |
ATOM H23 HL 0.25 ! H12
ATOM H31 HL 0.25
ATOM H32 HL 0.25
ATOM H33 HL 0.25
ATOM H41 HL 0.25
ATOM H42 HL 0.25
ATOM H43 HL 0.25
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 H13
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
! internal are wrong
IC C2 N C1 H11 0.0000 0.0000 180.0000 0.0000 0.0000
IC C2 N C1 H12 0.0000 0.0000 -60.0000 0.0000 0.0000
IC C2 N C1 H13 0.0000 0.0000 60.0000 0.0000 0.0000
IC C2 C1 *N C3 0.0000 0.0000 120.0000 0.0000 0.0000
IC C2 C1 *N C4 0.0000 0.0000 -120.0000 0.0000 0.0000
IC C3 N C2 H21 0.0000 0.0000 0.0000 0.0000 0.0000
IC C3 N C2 H22 0.0000 0.0000 -120.0000 0.0000 0.0000
IC C3 N C2 H23 0.0000 0.0000 120.0000 0.0000 0.0000
IC C4 N C3 H31 0.0000 0.0000 0.0000 0.0000 0.0000
IC C4 N C3 H32 0.0000 0.0000 -120.0000 0.0000 0.0000
IC C4 N C3 H33 0.0000 0.0000 120.0000 0.0000 0.0000
IC C1 N C4 H41 0.0000 0.0000 0.0000 0.0000 0.0000
IC C1 N C4 H42 0.0000 0.0000 -120.0000 0.0000 0.0000
IC C1 N C4 H43 0.0000 0.0000 120.0000 0.0000 0.0000
RESI NC5 1.00 ! tetramethylammonium ethyl analog
GROUP
ATOM N NTL -0.60 !
ATOM C1 CTL2 -0.10 ! |
ATOM C2 CTL5 -0.35 ! -C3-
ATOM C3 CTL5 -0.35 ! |
ATOM C4 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! -C2---N---C4- (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! |
ATOM H22 HL 0.25 ! -C1-
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! -C5-
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25
ATOM H42 HL 0.25
ATOM H43 HL 0.25
GROUP
ATOM C5 CTL3 -0.27
ATOM H51 HAL3 0.09
ATOM H52 HAL3 0.09
ATOM H53 HAL3 0.09
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52 C5 H53
! ab-initio HF/6-31G* structure
IC C4 N C1 C5 1.4967 107.80 180.00 115.98 1.5217
IC C5 C1 N C2 1.5217 115.98 -61.05 111.12 1.4950
IC C5 C1 N C3 1.5217 115.98 61.05 111.12 1.4950
IC C4 N C1 H11 1.4967 107.80 57.27 105.76 1.0809
IC C4 N C1 H12 1.4967 107.80 -57.27 105.76 1.0809
IC C1 N C2 H21 1.5176 111.12 -174.50 108.75 1.0795
IC C1 N C2 H22 1.5176 111.12 65.81 109.69 1.0773
IC C1 N C2 H23 1.5176 111.12 -54.79 109.07 1.0797
IC C1 N C3 H31 1.5176 111.12 174.50 108.75 1.0795
IC C1 N C3 H32 1.5176 111.12 -65.81 109.69 1.0773
IC C1 N C3 H33 1.5176 111.12 54.79 109.07 1.0797
IC C1 N C4 H41 1.5176 107.80 180.00 109.11 1.0793
IC C1 N C4 H42 1.5176 107.80 60.03 109.12 1.0793
IC C1 N C4 H43 1.5176 107.80 -60.03 109.12 1.0793
IC N C1 C5 H51 1.5176 115.98 180.00 107.05 1.0836
IC N C1 C5 H52 1.5176 115.98 62.29 112.91 1.0820
IC N C1 C5 H53 1.5176 115.98 -62.29 112.91 1.0820
RESI CHOL 1.00 ! choline
GROUP !
ATOM N NTL -0.60 !
ATOM C1 CTL2 -0.10 ! |
ATOM C2 CTL5 -0.35 ! -C3-
ATOM C3 CTL5 -0.35 ! |
ATOM C4 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! -C2---N---C4- (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! |
ATOM H22 HL 0.25 ! -C1-
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! |
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25 ! |
ATOM H42 HL 0.25 ! |
ATOM H43 HL 0.25 ! |
GROUP ! |
ATOM C5 CTL2 0.05 ! |
ATOM H51 HAL2 0.09 ! -C5-
ATOM H52 HAL2 0.09 ! |
ATOM OH1 OHL -0.66 ! OH1---HO1
ATOM HO1 HOL 0.43 !
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND C5 OH1 OH1 HO1
! ab-initio HF/6-31G* geometry of gauche conformer
IC C4 N C1 C5 1.4964 107.76 161.60 116.58 1.5208
IC C5 C1 N C2 1.5208 116.58 -80.13 111.04 1.5031
IC C5 C1 N C3 1.5208 116.58 42.05 111.71 1.4945
IC N C1 C5 OH1 1.5158 116.58 56.02 109.57 1.3947
IC C1 C5 OH1 HO1 1.5208 109.57 169.05 110.84 0.9491
IC C2 N C1 H11 1.5031 111.04 158.76 106.72 1.0813
IC C3 N C1 H12 1.4945 111.71 165.25 106.14 1.0802
IC C1 N C2 H21 1.5158 111.04 -179.38 108.21 1.0796
IC C3 N C2 H22 1.4945 109.20 -63.85 109.22 1.0746
IC C4 N C2 H23 1.4964 108.15 57.69 108.56 1.0794
IC C1 N C3 H31 1.5158 111.71 173.42 108.53 1.0794
IC C2 N C3 H32 1.5031 109.20 177.22 109.23 1.0800
IC C4 N C3 H33 1.4964 108.88 174.14 109.12 1.0773
IC C1 N C4 H41 1.5158 107.76 175.04 109.01 1.0793
IC C2 N C4 H42 1.5031 108.15 -64.86 109.05 1.0796
IC C3 N C4 H43 1.4945 108.88 56.40 109.30 1.0794
IC N C1 C5 H51 1.5158 116.58 176.61 105.66 1.0855
IC N C1 C5 H52 1.5158 116.58 -67.32 110.89 1.0847
RESI ACHO 1.00 ! acetylcholine
GROUP !
ATOM N NTL -0.60 !
ATOM C1 CTL2 -0.10 ! |
ATOM C2 CTL5 -0.35 ! -C3-
ATOM C3 CTL5 -0.35 ! |
ATOM C4 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! -C2---N---C4- (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! |
ATOM H22 HL 0.25 ! -C1-
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! |
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25 ! |
ATOM H42 HL 0.25 ! |
ATOM H43 HL 0.25 ! |
GROUP ! |
ATOM C5 CTL2 -0.05 ! -C5-
ATOM OM OSL -0.34 ! |
ATOM C CL 0.63 ! OM
ATOM C7 CTL3 -0.17 ! /
ATOM O OBL -0.52 ! O==C
ATOM H51 HAL2 0.09 ! |
ATOM H52 HAL2 0.09 ! --C7--
ATOM H71 HAL3 0.09 ! |
ATOM H72 HAL3 0.09 !
ATOM H73 HAL3 0.09 !
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND C7 C C OM OM C5
DOUBLE C O
BOND C7 H71 C7 H72 C7 H73
IMPR C OM C7 O
IC C4 N C1 C5 0.0000 000.00 161.60 000.00 0.0000
IC C5 C1 N C2 0.0000 000.00 -80.13 000.00 0.0000
IC C5 C1 N C3 0.0000 000.00 42.05 000.00 0.0000
IC C2 N C1 H11 0.0000 000.00 158.76 000.00 0.0000
IC C3 N C1 H12 0.0000 000.00 165.25 000.00 0.0000
IC C1 N C2 H21 0.0000 000.00 -179.38 000.00 0.0000
IC C3 N C2 H22 0.0000 000.00 -63.85 000.00 0.0000
IC C4 N C2 H23 0.0000 000.00 57.69 000.00 0.0000
IC C1 N C3 H31 0.0000 000.00 173.42 000.00 0.0000
IC C2 N C3 H32 0.0000 000.00 177.22 000.00 0.0000
IC C4 N C3 H33 0.0000 000.00 174.14 000.00 0.0000
IC C1 N C4 H41 0.0000 000.00 175.04 000.00 0.0000
IC C2 N C4 H42 0.0000 000.00 -64.86 000.00 0.0000
IC C3 N C4 H43 0.0000 000.00 56.40 000.00 0.0000
IC N C1 C5 H51 0.0000 000.00 180.00 000.00 0.0000
IC N C1 C5 H52 0.0000 000.00 -60.0 000.00 0.0000
IC N C1 C5 OM 0.0000 000.00 72.0 000.00 0.0000
IC C1 C5 OM C 0.0000 000.00 166.9 000.00 0.0000
IC C7 C OM C5 0.0000 000.00 20.0 000.00 0.0000
IC O C OM C5 0.0000 000.00 -160.0 000.00 0.0000
IC H71 C7 C OM 0.0000 000.00 180.0 000.00 0.0000
IC H72 C7 C OM 0.0000 000.00 60.4 000.00 0.0000
IC H73 C7 C OM 0.0000 000.00 -60.4 000.00 0.0000
RESI PC 0.00 ! phosphatidylcholine
GROUP !
ATOM N NTL -0.60 !
ATOM C1 CTL2 -0.10 ! |
ATOM C2 CTL5 -0.35 ! -C3-
ATOM C3 CTL5 -0.35 ! |
ATOM C4 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! -C2---N---C4- (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! |
ATOM H22 HL 0.25 ! -C1-
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! |
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25 ! |
ATOM H42 HL 0.25 ! |
ATOM H43 HL 0.25 ! |
GROUP ! |
ATOM C5 CTL2 -0.08 ! |
ATOM H51 HAL2 0.09 ! H52---C5---H51
ATOM H52 HAL2 0.09 ! |
GROUP ! |
ATOM P1 PL 1.50 ! (-) O3 O1
ATOM O3 O2L -0.78 ! \ /
ATOM O4 O2L -0.78 ! P1 (+)
ATOM O1 OSL -0.57 ! / \
ATOM O2 OSL -0.57 ! (-) O4 O2
GROUP ! |
ATOM C6 CTL3 -0.17 ! |
ATOM H61 HAL3 0.09 ! H63-C6-H62
ATOM H62 HAL3 0.09 ! |
ATOM H63 HAL3 0.09 ! H61
!
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND P1 O1 P1 O2 P1 O3 P1 O4 O1 C5 O2 C6
BOND C6 H61 C6 H62 C6 H63
IC C4 N C1 C5 0.0000 000.00 112.00 000.00 0.0000
IC C5 C1 N C2 0.0000 000.00 -121.00 000.00 0.0000
IC C5 C1 N C3 0.0000 000.00 0.00 000.00 0.0000
IC C2 N C1 H11 0.0000 000.00 120.00 000.00 0.0000
IC C3 N C1 H12 0.0000 000.00 120.00 000.00 0.0000
IC C1 N C2 H21 0.0000 000.00 180.00 000.00 0.0000
IC C3 N C2 H22 0.0000 000.00 -60.00 000.00 0.0000
IC C4 N C2 H23 0.0000 000.00 60.00 000.00 0.0000
IC C1 N C3 H31 0.0000 000.00 180.00 000.00 0.0000
IC C2 N C3 H32 0.0000 000.00 180.00 000.00 0.0000
IC C4 N C3 H33 0.0000 000.00 180.00 000.00 0.0000
IC C1 N C4 H41 0.0000 000.00 180.00 000.00 0.0000
IC C2 N C4 H42 0.0000 000.00 -60.00 000.00 0.0000
IC C3 N C4 H43 0.0000 000.00 60.00 000.00 0.0000
IC N C1 C5 H51 0.0000 000.00 -150.00 000.00 0.0000
IC N C1 C5 H52 0.0000 000.00 100.00 000.00 0.0000
IC N C1 C5 O1 0.0000 000.00 -30.00 000.00 0.0000
IC C1 C5 O1 P1 0.0000 000.00 130.00 000.00 0.0000
IC C5 O1 P1 O2 0.0000 000.00 -160.0 000.00 0.0000
IC O3 P1 O1 C5 0.0000 000.00 80.00 000.00 0.0000
IC O4 P1 O1 C5 0.0000 000.00 -60.00 000.00 0.0000
IC O1 P1 O2 C6 0.0000 000.00 180.00 000.00 0.0000
IC H61 C6 O2 P1 0.0000 000.00 0.00 000.00 0.0000
IC H62 C6 O2 P1 0.0000 000.00 120.00 000.00 0.0000
IC H63 C6 O2 P1 0.0000 000.00 -120.00 000.00 0.0000
RESI GPC 0.00 ! glycerolphosphorylcholine
GROUP !
ATOM N NTL -0.60 !
ATOM C1 CTL2 -0.10 ! |
ATOM C2 CTL5 -0.35 ! -C3-
ATOM C3 CTL5 -0.35 ! |
ATOM C4 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! -C2---N---C4- (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! |
ATOM H22 HL 0.25 ! -C1-
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! |
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25 ! |
ATOM H42 HL 0.25 ! |
ATOM H43 HL 0.25 ! |
GROUP ! |
ATOM C5 CTL2 -0.08 ! |
ATOM H51 HAL2 0.09 ! H51---C5---H52
ATOM H52 HAL2 0.09 ! |
ATOM P PL 1.50 ! (-) O3 O1
ATOM O3 O2L -0.78 ! \ /
ATOM O4 O2L -0.78 ! P (+)
ATOM O1 OSL -0.57 ! / \
ATOM O2 OSL -0.57 ! (-) O4 O2
ATOM CG1 CTL2 -0.08 ! |
ATOM HG11 HAL2 0.09 ! HG11-CG1-HG12
ATOM HG12 HAL2 0.09 ! |
GROUP ! |
ATOM CG2 CTL1 0.14 ! |
ATOM HG21 HAL1 0.09 ! HG21-CG2-OG2-HO2
ATOM OG2 OHL -0.66 ! |
ATOM HO2 HOL 0.43 ! |
GROUP ! |
ATOM CG3 CTL2 0.05 ! |
ATOM HG31 HAL2 0.09 ! HG31-CG3-OG3-HO3
ATOM HG32 HAL2 0.09 ! |
ATOM OG3 OHL -0.66 ! HG32
ATOM HO3 HOL 0.43 !
BOND CG1 O2 CG1 HG11 CG1 HG12
BOND CG2 CG1 CG2 HG21 CG2 OG2 OG2 HO2
BOND CG3 CG2 CG3 HG31 CG3 HG32 CG3 OG3 OG3 HO3
BOND N C1 N C2 N C3 N C4
BOND C1 H11 C1 H12 C1 C5
BOND C2 H21 C2 H22 C2 H23
BOND C3 H31 C3 H32 C3 H33
BOND C4 H41 C4 H42 C4 H43
BOND C5 H51 C5 H52
BOND P O1 P O2 P O3 P O4 O1 C5
! internal coordinates for analysis
! see H.Hauser,I.Pascher,R.H.Pearson,S.Sundell, BBA 650, 21-51 (1981)
! glycerol backbone
IC O2 CG1 CG2 CG3 0. 0. 0. 0. 0. ! t1
IC O2 CG1 CG2 OG2 0. 0. 0. 0. 0. ! t2
IC CG1 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3
IC OG2 CG2 CG3 OG3 0. 0. 0. 0. 0. ! t3
!
! zwitterionic headgroup
IC P O2 CG1 CG2 0. 0. 0. 0. 0. ! a1
IC O1 P O2 CG1 0. 0. 0. 0. 0. ! a2
IC O2 P O1 C5 0. 0. 0. 0. 0. ! a3
IC C1 C5 O1 P 0. 0. 0. 0. 0. ! a4
IC N C1 C5 O1 0. 0. 0. 0. 0. ! a5
IC C2 N C1 C5 0. 0. 0. 0. 0. ! a6
IC C3 N C1 C5 0. 0. 0. 0. 0. ! a6
IC C4 N C1 C5 0. 0. 0. 0. 0. ! a6
IC O1 O2 *P O3 0. 0. 120. 0. 0.
IC O1 O2 *P O4 0. 0. -120. 0. 0.
RESI LPPC 0.00 ! deoxylysophosphatidylcholine
! Polar Head and glycerol backbone
GROUP ! H15B
ATOM N NTL -0.60 ! |
ATOM C13 CTL5 -0.35 ! H15A-C15-H15C
ATOM H13A HL 0.25 ! |
ATOM H13B HL 0.25 ! H13B | H14A
ATOM H13C HL 0.25 ! | | |
ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+)
ATOM H14A HL 0.25 ! | | |
ATOM H14B HL 0.25 ! H13C | H14C
ATOM H14C HL 0.25 ! |
ATOM C15 CTL5 -0.35 ! |
ATOM H15A HL 0.25 ! | alpha6
ATOM H15B HL 0.25 ! |
ATOM H15C HL 0.25 ! |
ATOM C12 CTL2 -0.10 ! H12A--C12---H12B
ATOM H12A HL 0.25 ! |
ATOM H12B HL 0.25 ! |
GROUP ! alpha5
ATOM C11 CTL2 -0.08 ! |
ATOM H11A HAL2 0.09 ! H11A--C11---H11B
ATOM H11B HAL2 0.09 ! | alpha4
ATOM P PL 1.50 ! (-) O13 O12
ATOM O13 O2L -0.78 ! \ / alpha3
ATOM O14 O2L -0.78 ! P (+)
ATOM O11 OSL -0.57 ! / \ alpha2
ATOM O12 OSL -0.57 ! (-) O14 O11
ATOM C1 CTL2 -0.08 ! | alpha1
ATOM HA HAL2 0.09 ! HA---C1---HB
ATOM HB HAL2 0.09 ! | theta1
GROUP ! |
ATOM C2 CTL2 -0.18 ! HR---C2----HS
ATOM HS HAL2 0.09 ! |
ATOM HR HAL2 0.09 ! |
GROUP ! |
ATOM C3 CTL2 -0.05 ! HX---C3---HY
ATOM HX HAL2 0.09 ! |
ATOM HY HAL2 0.09 ! | gamma1
ATOM O31 OSL -0.34 ! O32 O31
ATOM C31 CL 0.63 ! \\ / gamma2
ATOM O32 OBL -0.52 ! C31
ATOM C32 CTL2 -0.08 ! | gamma3
ATOM H2X HAL2 0.09 ! H2X---C32---H2Y
ATOM H2Y HAL2 0.09 ! |
GROUP !
ATOM C33 CTL2 -0.18 ! |
ATOM H3X HAL2 0.09 ! H3X---C33---H3Y
ATOM H3Y HAL2 0.09 ! |
GROUP !
ATOM C34 CTL2 -0.18 ! |
ATOM H4X HAL2 0.09 ! H4X---C34---H4Y
ATOM H4Y HAL2 0.09 ! |
GROUP !
ATOM C35 CTL2 -0.18 ! |
ATOM H5X HAL2 0.09 ! H5X---C35---H5Y
ATOM H5Y HAL2 0.09 ! |
GROUP !
ATOM C36 CTL2 -0.18 ! |
ATOM H6X HAL2 0.09 ! H6X---C36---H6Y
ATOM H6Y HAL2 0.09 ! |
GROUP !
ATOM C37 CTL2 -0.18 ! |
ATOM H7X HAL2 0.09 ! H7X---C37---H7Y
ATOM H7Y HAL2 0.09 ! |
GROUP !
ATOM C38 CTL2 -0.18 ! |
ATOM H8X HAL2 0.09 ! H8X---C38---H8Y
ATOM H8Y HAL2 0.09 ! |
GROUP !
ATOM C39 CTL2 -0.18 ! |
ATOM H9X HAL2 0.09 ! H9X---C39---H9Y
ATOM H9Y HAL2 0.09 ! |
GROUP !
ATOM C310 CTL2 -0.18 ! |
ATOM H10X HAL2 0.09 ! H10X---C310--H10Y
ATOM H10Y HAL2 0.09 ! |
GROUP !
ATOM C311 CTL2 -0.18 ! |
ATOM H11X HAL2 0.09 ! H11X---C311--H11Y
ATOM H11Y HAL2 0.09 ! |
GROUP !
ATOM C312 CTL3 -0.27 ! |
ATOM H12X HAL3 0.09 ! H12X---C312--H12Y
ATOM H12Y HAL3 0.09 ! |
ATOM H12Z HAL3 0.09 ! H12Z
!
! Polar Head
BOND N C13 N C14 N C15
BOND C13 H13A C13 H13B C13 H13C
BOND C14 H14A C14 H14B C14 H14C
BOND C15 H15A C15 H15B C15 H15C
BOND N C12
BOND C12 H12A C12 H12B C12 C11
BOND C11 H11A C11 H11B C11 O12
BOND O12 P P O11 P O13 P O14
! Glycerol Backbone
BOND C1 HA C1 HB C1 C2 C1 O11
BOND C2 HS C2 HR C2 C3
BOND C3 HX C3 HY C3 O31
! Chain #3
BOND O31 C31
BOND C31 C32
DOUBLE C31 O32
BOND C32 H2X C32 H2Y C32 C33
BOND C33 H3X C33 H3Y C33 C34
BOND C34 H4X C34 H4Y C34 C35
BOND C35 H5X C35 H5Y C35 C36
BOND C36 H6X C36 H6Y C36 C37
BOND C37 H7X C37 H7Y C37 C38
BOND C38 H8X C38 H8Y C38 C39
BOND C39 H9X C39 H9Y C39 C310
BOND C310 H10X C310 H10Y C310 C311
BOND C311 H11X C311 H11Y C311 C312
BOND C312 H12X C312 H12Y C312 H12Z
IMPR C31 O31 C32 O32
! Polar head (angle names from Sundaralingam)
IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1
IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2
IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0
IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0
IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3
IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0
IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0
IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4
IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0
IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0
IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5
IC C11 C12 N C13 0.0 0.0 180.0 0.0 0.0 !alpha6
IC C12 C13 *N C14 0.0 0.0 120.0 0.0 0.0
IC C12 C13 *N C15 0.0 0.0 240.0 0.0 0.0
! Glycerol
IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1
IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3
! Chain 3
IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1
IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2
IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3
IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0
IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4
IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5
IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6
IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7
IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8
IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9
IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10
IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11
IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12
RESI ETAM 1.00 ! ethanolamine
GROUP !
ATOM N NH3L -0.30 ! HN2
ATOM HN1 HCL 0.33 ! |
ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3
ATOM HN3 HCL 0.33 ! |
ATOM C1 CTL2 0.13 ! |
ATOM H11 HAL2 0.09 ! H12---C1---H11
ATOM H12 HAL2 0.09 ! |
GROUP ! |
ATOM C5 CTL2 0.05 ! |
ATOM H51 HAL2 0.09 ! H52---C5---H51
ATOM H52 HAL2 0.09 ! |
ATOM OH1 OHL -0.66 ! OH1---HO1
ATOM HO1 HOL 0.43 !
BOND N HN1 N HN2 N HN3 N C1
BOND C1 H11 C1 H12 C1 C5
BOND C5 H51 C5 H52
BOND C5 OH1 OH1 HO1
! HF/6-31G* OPTIMIZED STRUCTURE:
IC N C1 C5 OH1 1.5084 107.86 48.44 104.92 1.3987
IC C1 C5 OH1 HO1 1.5191 104.92 173.19 111.99 0.9495
IC HN1 N C1 C5 1.0145 108.35 -49.03 107.86 1.5191
IC HN2 N C1 C5 1.0107 112.05 69.23 107.86 1.5191
IC HN3 N C1 C5 1.0102 112.39 -169.37 107.86 1.5191
IC N C5 *C1 H11 0.0000 000.00 120.00 000.00 0.0000
IC N C5 *C1 H12 0.0000 000.00 -120.00 000.00 0.0000
IC OH1 C1 *C5 H51 0.0000 000.00 120.00 000.00 0.0000
IC OH1 C1 *C5 H52 0.0000 000.00 -120.00 000.00 0.0000
RESI GPE 0.00 ! L-alpha-glycerylphosphorylethanolamine
!
GROUP !
ATOM N NH3L -0.30 ! HN2
ATOM HN1 HCL 0.33 ! |
ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3
ATOM HN3 HCL 0.33 ! |
ATOM C12 CTL2 0.13 ! |
ATOM H12A HAL2 0.09 ! H12A--C12---H12B
ATOM H12B HAL2 0.09 ! |
GROUP ! | alpha5
ATOM C11 CTL2 -0.08 ! |
ATOM H11A HAL2 0.09 ! H11A--C11---H11B
ATOM H11B HAL2 0.09 ! | alpha4
ATOM P PL 1.50 ! (-) O13 O12
ATOM O13 O2L -0.78 ! \ / alpha3
ATOM O14 O2L -0.78 ! P (+)
ATOM O11 OSL -0.57 ! / \ alpha2
ATOM O12 OSL -0.57 ! (-) O14 O11
ATOM C1 CTL2 -0.08 ! | alpha1
ATOM HA HAL2 0.09 ! HA---C1---HB
ATOM HB HAL2 0.09 ! | theta1
GROUP ! |
ATOM C2 CTL1 0.14 ! |
ATOM HS HAL1 0.09 ! HS-C2-OH2-HO2
ATOM OH2 OHL -0.66 ! |
ATOM HO2 HOL 0.43 ! |
GROUP ! |
ATOM C3 CTL2 0.05 ! |
ATOM HX HAL2 0.09 ! HX-C3-OH3-HO3
ATOM HY HAL2 0.09 ! |
ATOM OH3 OHL -0.66 ! HY
ATOM HO3 HOL 0.43 !
! Polar Head
BOND N HN1 N HN2 N HN3 N C12
BOND C12 H12A C12 H12B C12 C11
BOND C11 H11A C11 H11B C11 O12
BOND O12 P P O11 P O13 P O14
! Glycerol Backbone
BOND C1 HA C1 HB C1 C2 C1 O11
BOND C2 HS C2 C3 C2 OH2
BOND C3 HX C3 HY C3 OH3
BOND OH2 HO2
BOND OH3 HO3
!
! Polar head (angle names from Sundaralingam)
IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1
IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2
IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0
IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0
IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3
IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0
IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0
IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4
IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0
IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0
IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5
IC C11 C12 N HN1 0.0 0.0 180.0 0.0 0.0 !alpha6
IC C12 HN1 *N HN2 0.0 0.0 120.0 0.0 0.0
IC C12 HN1 *N HN3 0.0 0.0 240.0 0.0 0.0
! Glycerol
IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1
IC C1 C2 C3 OH3 0.0 0.0 180.0 0.0 0.0 !theta3
IC C1 C3 *C2 OH2 0.0 0.0 -120.0 0.0 0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0
IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0
IC OH2 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0
IC OH3 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0
IC OH3 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0
IC C1 C2 OH2 HO2 0.0 0.0 180.0 0.0 0.0 !beta1
IC C2 C3 OH3 HO3 0.0 0.0 -120.0 0.0 0.0 !gamma1
RESI DLPE 0.00 ! 1,2 dilauroyl-DL-Phosphatidylethanolamine
!
! R1 - CH2
! | (angles and atom names from Sundaralingam)
! R2 - CH
! |
! CH2 - PO4 - CH2 - CH2 - NH3
!
! Polar Head and glycerol backbone
GROUP !
ATOM N NH3L -0.30 ! HN2
ATOM HN1 HCL 0.33 ! |
ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3
ATOM HN3 HCL 0.33 ! |
ATOM C12 CTL2 0.13 ! |
ATOM H12A HAL2 0.09 ! H12A--C12---H12B
ATOM H12B HAL2 0.09 ! |
GROUP ! | alpha5
ATOM C11 CTL2 -0.08 ! |
ATOM H11A HAL2 0.09 ! H11A--C11---H11B
ATOM H11B HAL2 0.09 ! | alpha4
ATOM P PL 1.50 ! (-) O13 O12
ATOM O13 O2L -0.78 ! \ / alpha3
ATOM O14 O2L -0.78 ! P (+)
ATOM O11 OSL -0.57 ! / \ alpha2
ATOM O12 OSL -0.57 ! (-) O14 O11
ATOM C1 CTL2 -0.08 ! | alpha1
ATOM HA HAL2 0.09 ! H1A---C1---H1B
ATOM HB HAL2 0.09 ! | theta1
GROUP ! |
ATOM C2 CTL1 0.04 ! HS---C2- - - - - - -
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.34 ! O22 O21 theta3
ATOM C21 CL 0.63 ! \\ / beta2 |
ATOM O22 OBL -0.52 ! C21
ATOM C22 CTL2 -0.08 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S
ATOM H2S HAL2 0.09 ! | |
GROUP ! beta4
ATOM C3 CTL2 -0.05 ! | |
ATOM HX HAL2 0.09 ! HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.34 ! O32 O31
ATOM C31 CL 0.63 ! | \\ / gamma2
ATOM O32 OBL -0.52 ! C31
ATOM C32 CTL2 -0.08 ! | | gamma3
ATOM H2X HAL2 0.09 ! H2X---C32---H2Y
ATOM H2Y HAL2 0.09 ! | |
GROUP ! gamma4
ATOM C23 CTL2 -0.18 ! | |
ATOM H3R HAL2 0.09 ! H3R ---C23---H3S
ATOM H3S HAL2 0.09 ! | |
GROUP !
ATOM C24 CTL2 -0.18 ! |
ATOM H4R HAL2 0.09 ! H4R ---C24---H4S |
ATOM H4S HAL2 0.09 ! |
GROUP !
ATOM C25 CTL2 -0.18 ! | |
ATOM H5R HAL2 0.09 ! H5R ---C25---H5S
ATOM H5S HAL2 0.09 ! | |
GROUP !
ATOM C26 CTL2 -0.18 ! |
ATOM H6R HAL2 0.09 ! H6R ---C26---H6S |
ATOM H6S HAL2 0.09 ! |
GROUP !
ATOM C27 CTL2 -0.18 ! | |
ATOM H7R HAL2 0.09 ! H7R ---C27---H7S
ATOM H7S HAL2 0.09 ! | |
GROUP !
ATOM C28 CTL2 -0.18 ! |
ATOM H8R HAL2 0.09 ! H8R ---C28---H8S |
ATOM H8S HAL2 0.09 ! |
GROUP !
ATOM C29 CTL2 -0.18 ! | |
ATOM H9R HAL2 0.09 ! H9R ---C29---H9S
ATOM H9S HAL2 0.09 ! | |
GROUP !
ATOM C210 CTL2 -0.18 ! |
ATOM H10R HAL2 0.09 ! H10R---C210--H10S |
ATOM H10S HAL2 0.09 ! |
GROUP !
ATOM C211 CTL2 -0.18 ! | |
ATOM H11R HAL2 0.09 ! H11R---C211--H11S
ATOM H11S HAL2 0.09 ! | |
GROUP !
ATOM C212 CTL3 -0.27 ! |
ATOM H12R HAL3 0.09 ! H12R---C212--H12S |
ATOM H12S HAL3 0.09 ! |
ATOM H12T HAL3 0.09 ! H12T |
GROUP !
ATOM C33 CTL2 -0.18 ! |
ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y
ATOM H3Y HAL2 0.09 ! |
GROUP !
ATOM C34 CTL2 -0.18 ! |
ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y
ATOM H4Y HAL2 0.09 ! |
GROUP !
ATOM C35 CTL2 -0.18 ! |
ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y
ATOM H5Y HAL2 0.09 ! |
GROUP !
ATOM C36 CTL2 -0.18 ! |
ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y
ATOM H6Y HAL2 0.09 ! |
GROUP !
ATOM C37 CTL2 -0.18 ! |
ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y
ATOM H7Y HAL2 0.09 ! |
GROUP !
ATOM C38 CTL2 -0.18 ! |
ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y
ATOM H8Y HAL2 0.09 ! |
GROUP !
ATOM C39 CTL2 -0.18 ! |
ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y
ATOM H9Y HAL2 0.09 ! |
GROUP !
ATOM C310 CTL2 -0.18 ! |
ATOM H10X HAL2 0.09 ! H10X---C310--H10Y
ATOM H10Y HAL2 0.09 ! |
GROUP !
ATOM C311 CTL2 -0.18 ! |
ATOM H11X HAL2 0.09 ! H11X---C311--H11Y
ATOM H11Y HAL2 0.09 ! |
GROUP !
ATOM C312 CTL3 -0.27 ! |
ATOM H12X HAL3 0.09 ! H12X---C312--H12Y
ATOM H12Y HAL3 0.09 ! |
ATOM H12Z HAL3 0.09 ! H12Z
! Polar Head
BOND N HN1 N HN2 N HN3 N C12
BOND C12 H12A C12 H12B C12 C11
BOND C11 H11A C11 H11B C11 O12
BOND O12 P P O11 P O13 P O14
! Glycerol Backbone
BOND C1 HA C1 HB C1 C2 C1 O11
BOND C2 HS C2 C3 C2 O21
BOND C3 HX C3 HY C3 O31
! Chain #2
BOND O21 C21
BOND C21 C22
DOUBLE C21 O22
BOND C22 H2R C22 H2S C22 C23
BOND C23 H3R C23 H3S C23 C24
BOND C24 H4R C24 H4S C24 C25
BOND C25 H5R C25 H5S C25 C26
BOND C26 H6R C26 H6S C26 C27
BOND C27 H7R C27 H7S C27 C28
BOND C28 H8R C28 H8S C28 C29
BOND C29 H9R C29 H9S C29 C210
BOND C210 H10R C210 H10S C210 C211
BOND C211 H11R C211 H11S C211 C212
BOND C212 H12R C212 H12S C212 H12T
! Chain #3
BOND O31 C31
BOND C31 C32
DOUBLE C31 O32
BOND C32 H2X C32 H2Y C32 C33
BOND C33 H3X C33 H3Y C33 C34
BOND C34 H4X C34 H4Y C34 C35
BOND C35 H5X C35 H5Y C35 C36
BOND C36 H6X C36 H6Y C36 C37
BOND C37 H7X C37 H7Y C37 C38
BOND C38 H8X C38 H8Y C38 C39
BOND C39 H9X C39 H9Y C39 C310
BOND C310 H10X C310 H10Y C310 C311
BOND C311 H11X C311 H11Y C311 C312
BOND C312 H12X C312 H12Y C312 H12Z
IMPR C21 O21 C22 O22 C31 O31 C32 O32
! Polar head (angle names from Sundaralingam)
IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1
IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2
IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0
IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0
IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3
IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0
IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0
IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4
IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0
IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0
IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5
IC C11 C12 N HN1 0.0 0.0 180.0 0.0 0.0 !alpha6
IC C12 HN1 *N HN2 0.0 0.0 120.0 0.0 0.0
IC C12 HN1 *N HN3 0.0 0.0 240.0 0.0 0.0
! Glycerol
IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1
IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3
IC C1 C3 *C2 O21 0.0 0.0 -120.0 0.0 0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0
IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0
IC O21 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0
IC O31 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0
IC O31 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0
! Chain 1
IC C1 C2 O21 C21 0.0 0.0 180.0 0.0 0.0 !beta1
IC C2 O21 C21 C22 0.0 0.0 120.0 0.0 0.0 !beta2
IC O21 C21 C22 C23 0.0 0.0 180.0 0.0 0.0 !beta3
IC C22 O21 *C21 O22 0.0 0.0 180.0 0.0 0.0
IC C21 C22 C23 C24 0.0 0.0 180.0 0.0 0.0 !beta4
IC C22 C23 C24 C25 0.0 0.0 180.0 0.0 0.0 !beta5
IC C23 C24 C25 C26 0.0 0.0 180.0 0.0 0.0 !beta6
IC C24 C25 C26 C27 0.0 0.0 180.0 0.0 0.0 !beta7
IC C25 C26 C27 C28 0.0 0.0 180.0 0.0 0.0 !beta8
IC C26 C27 C28 C29 0.0 0.0 180.0 0.0 0.0 !beta9
IC C27 C28 C29 C210 0.0 0.0 180.0 0.0 0.0 !beta10
IC C28 C29 C210 C211 0.0 0.0 180.0 0.0 0.0 !beta11
IC C29 C210 C211 C212 0.0 0.0 180.0 0.0 0.0 !beta12
! Chain 2
IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1
IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2
IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3
IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0
IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4
IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5
IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6
IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7
IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8
IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9
IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10
IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11
IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12
RESI DMPC 0.00 ! 1,2 dimiristoyl-SN-glycero-3-Phosphorylcholine
!
! R1 - CH2
! | (angles and atom names from Sundaralingam)
! R2 - CH
! |
! CH2 - PO4 - CH2 - CH2 - N(CH3)3
!
! Polar Head and glycerol backbone
GROUP ! H15B
ATOM N NTL -0.60 ! |
ATOM C13 CTL5 -0.35 ! H15A-C15-H15C
ATOM H13A HL 0.25 ! |
ATOM H13B HL 0.25 ! H13B | H14A
ATOM H13C HL 0.25 ! | | |
ATOM C14 CTL5 -0.35 !H13A-C13----N----C14-H14B (+)
ATOM H14A HL 0.25 ! | | |
ATOM H14B HL 0.25 ! H13C | H14C
ATOM H14C HL 0.25 ! |
ATOM C15 CTL5 -0.35 ! |
ATOM H15A HL 0.25 ! | alpha6
ATOM H15B HL 0.25 ! |
ATOM H15C HL 0.25 ! |
ATOM C12 CTL2 -0.10 ! H12A--C12---H12B
ATOM H12A HL 0.25 ! |
ATOM H12B HL 0.25 ! |
GROUP ! alpha5
ATOM C11 CTL2 -0.08 ! |
ATOM H11A HAL2 0.09 ! H11A--C11---H11B
ATOM H11B HAL2 0.09 ! | alpha4
ATOM P PL 1.50 ! (-) O13 O12
ATOM O13 O2L -0.78 ! \ / alpha3
ATOM O14 O2L -0.78 ! P (+)
ATOM O11 OSL -0.57 ! / \ alpha2
ATOM O12 OSL -0.57 ! (-) O14 O11
ATOM C1 CTL2 -0.08 ! | alpha1
ATOM HA HAL2 0.09 ! HA---C1---HB
ATOM HB HAL2 0.09 ! | theta1
GROUP ! |
ATOM C2 CTL1 0.04 ! HS---C2- - - - - - -
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.34 ! O22 O21 theta3
ATOM C21 CL 0.63 ! \\ / beta2 |
ATOM O22 OBL -0.52 ! C21
ATOM C22 CTL2 -0.08 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S
ATOM H2S HAL2 0.09 ! | |
GROUP ! beta4
ATOM C3 CTL2 -0.05 ! | |
ATOM HX HAL2 0.09 ! HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.34 ! O32 O31
ATOM C31 CL 0.63 ! | \\ / gamma2
ATOM O32 OBL -0.52 ! C31
ATOM C32 CTL2 -0.08 ! | | gamma3
ATOM H2X HAL2 0.09 ! H2X---C32---H2Y
ATOM H2Y HAL2 0.09 ! | |
GROUP ! gamma4
ATOM C23 CTL2 -0.18 ! | |
ATOM H3R HAL2 0.09 ! H3R ---C23---H3S
ATOM H3S HAL2 0.09 ! | |
GROUP !
ATOM C24 CTL2 -0.18 ! |
ATOM H4R HAL2 0.09 ! H4R ---C24---H4S |
ATOM H4S HAL2 0.09 ! |
GROUP !
ATOM C25 CTL2 -0.18 ! | |
ATOM H5R HAL2 0.09 ! H5R ---C25---H5S
ATOM H5S HAL2 0.09 ! | |
GROUP !
ATOM C26 CTL2 -0.18 ! |
ATOM H6R HAL2 0.09 ! H6R ---C26---H6S |
ATOM H6S HAL2 0.09 ! |
GROUP !
ATOM C27 CTL2 -0.18 ! | |
ATOM H7R HAL2 0.09 ! H7R ---C27---H7S
ATOM H7S HAL2 0.09 ! | |
GROUP !
ATOM C28 CTL2 -0.18 ! |
ATOM H8R HAL2 0.09 ! H8R ---C28---H8S |
ATOM H8S HAL2 0.09 ! |
GROUP !
ATOM C29 CTL2 -0.18 ! | |
ATOM H9R HAL2 0.09 ! H9R ---C29---H9S
ATOM H9S HAL2 0.09 ! | |
GROUP !
ATOM C210 CTL2 -0.18 ! |
ATOM H10R HAL2 0.09 ! H10R---C210--H10S |
ATOM H10S HAL2 0.09 ! |
GROUP !
ATOM C211 CTL2 -0.18 ! | |
ATOM H11R HAL2 0.09 ! H11R---C211--H11S
ATOM H11S HAL2 0.09 ! | |
GROUP !
ATOM C212 CTL2 -0.18 ! |
ATOM H12R HAL2 0.09 ! H12R---C212--H12S |
ATOM H12S HAL2 0.09 ! |
GROUP !
ATOM C213 CTL2 -0.18 ! | |
ATOM H13R HAL2 0.09 ! H13R---C213--H13S
ATOM H13S HAL2 0.09 ! | |
GROUP !
ATOM C214 CTL3 -0.27 ! |
ATOM H14R HAL3 0.09 ! H14R---C214--H14S |
ATOM H14S HAL3 0.09 ! |
ATOM H14T HAL3 0.09 ! H14T |
GROUP !
ATOM C33 CTL2 -0.18 ! |
ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y
ATOM H3Y HAL2 0.09 ! |
GROUP !
ATOM C34 CTL2 -0.18 ! |
ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y
ATOM H4Y HAL2 0.09 ! |
GROUP !
ATOM C35 CTL2 -0.18 ! |
ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y
ATOM H5Y HAL2 0.09 ! |
GROUP !
ATOM C36 CTL2 -0.18 ! |
ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y
ATOM H6Y HAL2 0.09 ! |
GROUP !
ATOM C37 CTL2 -0.18 ! |
ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y
ATOM H7Y HAL2 0.09 ! |
GROUP !
ATOM C38 CTL2 -0.18 ! |
ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y
ATOM H8Y HAL2 0.09 ! |
GROUP !
ATOM C39 CTL2 -0.18 ! |
ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y
ATOM H9Y HAL2 0.09 ! |
GROUP !
ATOM C310 CTL2 -0.18 ! |
ATOM H10X HAL2 0.09 ! H10X---C310--H10Y
ATOM H10Y HAL2 0.09 ! |
GROUP !
ATOM C311 CTL2 -0.18 ! |
ATOM H11X HAL2 0.09 ! H11X---C311--H11Y
ATOM H11Y HAL2 0.09 ! |
GROUP !
ATOM C312 CTL2 -0.18 ! |
ATOM H12X HAL2 0.09 ! H12X---C312--H12Y
ATOM H12Y HAL2 0.09 ! |
GROUP !
ATOM C313 CTL2 -0.18 ! |
ATOM H13X HAL2 0.09 ! H13X---C313--H13Y
ATOM H13Y HAL2 0.09 ! |
GROUP !
ATOM C314 CTL3 -0.27 ! |
ATOM H14X HAL3 0.09 ! H14X---C314--H14Y
ATOM H14Y HAL3 0.09 ! |
ATOM H14Z HAL3 0.09 ! H14Z
! Polar Head
BOND N C13 N C14 N C15
BOND C13 H13A C13 H13B C13 H13C
BOND C14 H14A C14 H14B C14 H14C
BOND C15 H15A C15 H15B C15 H15C
BOND N C12
BOND C12 H12A C12 H12B C12 C11
BOND C11 H11A C11 H11B C11 O12
BOND O12 P P O11 P O13 P O14
! Glycerol Backbone
BOND C1 HA C1 HB C1 C2 C1 O11
BOND C2 HS C2 C3 C2 O21
BOND C3 HX C3 HY C3 O31
! Chain #2
BOND O21 C21
BOND C21 C22
DOUBLE C21 O22
BOND C22 H2R C22 H2S C22 C23
BOND C23 H3R C23 H3S C23 C24
BOND C24 H4R C24 H4S C24 C25
BOND C25 H5R C25 H5S C25 C26
BOND C26 H6R C26 H6S C26 C27
BOND C27 H7R C27 H7S C27 C28
BOND C28 H8R C28 H8S C28 C29
BOND C29 H9R C29 H9S C29 C210
BOND C210 H10R C210 H10S C210 C211
BOND C211 H11R C211 H11S C211 C212
BOND C212 H12R C212 H12S C212 C213
BOND C213 H13R C213 H13S C213 C214
BOND C214 H14R C214 H14S C214 H14T
! Chain #3
BOND O31 C31
BOND C31 C32
DOUBLE C31 O32
BOND C32 H2X C32 H2Y C32 C33
BOND C33 H3X C33 H3Y C33 C34
BOND C34 H4X C34 H4Y C34 C35
BOND C35 H5X C35 H5Y C35 C36
BOND C36 H6X C36 H6Y C36 C37
BOND C37 H7X C37 H7Y C37 C38
BOND C38 H8X C38 H8Y C38 C39
BOND C39 H9X C39 H9Y C39 C310
BOND C310 H10X C310 H10Y C310 C311
BOND C311 H11X C311 H11Y C311 C312
BOND C312 H12X C312 H12Y C312 C313
BOND C313 H13X C313 H13Y C313 C314
BOND C314 H14X C314 H14Y C314 H14Z
IMPR C21 O21 C22 O22 C31 O31 C32 O32
! Polar head (angle names from Sundaralingam)
IC C2 C1 O11 P 0.0 0.0 180.0 0.0 0.0 !alpha1
IC C1 O11 P O12 0.0 0.0 180.0 0.0 0.0 !alpha2
IC O11 O12 *P O13 0.0 0.0 120.0 0.0 0.0
IC O11 O12 *P O14 0.0 0.0 240.0 0.0 0.0
IC O11 P O12 C11 0.0 0.0 180.0 0.0 0.0 !alpha3
IC O12 C12 *C11 H11A 0.0 0.0 120.0 0.0 0.0
IC O12 C12 *C11 H11B 0.0 0.0 240.0 0.0 0.0
IC P O12 C11 C12 0.0 0.0 180.0 0.0 0.0 !alpha4
IC N C11 *C12 H12A 0.0 0.0 120.0 0.0 0.0
IC N C11 *C12 H12B 0.0 0.0 240.0 0.0 0.0
IC O12 C11 C12 N 0.0 0.0 180.0 0.0 0.0 !alpha5
IC C11 C12 N C13 0.0 0.0 180.0 0.0 0.0 !alpha6
IC C12 C13 *N C14 0.0 0.0 120.0 0.0 0.0
IC C12 C13 *N C15 0.0 0.0 240.0 0.0 0.0
! Glycerol
IC O11 C1 C2 C3 0.0 0.0 120.0 0.0 0.0 !theta1
IC C1 C2 C3 O31 0.0 0.0 180.0 0.0 0.0 !theta3
IC C1 C3 *C2 O21 0.0 0.0 -120.0 0.0 0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
IC O11 C2 *C1 HA 0.0 0.0 +120.0 0.0 0.0
IC O11 C2 *C1 HB 0.0 0.0 -120.0 0.0 0.0
IC O21 C1 *C2 HS 0.0 0.0 +120.0 0.0 0.0
IC O31 C2 *C3 HX 0.0 0.0 +120.0 0.0 0.0
IC O31 C2 *C3 HY 0.0 0.0 -120.0 0.0 0.0
! Chain 1
IC C1 C2 O21 C21 0.0 0.0 180.0 0.0 0.0 !beta1
IC C2 O21 C21 C22 0.0 0.0 120.0 0.0 0.0 !beta2
IC O21 C21 C22 C23 0.0 0.0 180.0 0.0 0.0 !beta3
IC C22 O21 *C21 O22 0.0 0.0 180.0 0.0 0.0
IC C21 C22 C23 C24 0.0 0.0 180.0 0.0 0.0 !beta4
IC C22 C23 C24 C25 0.0 0.0 180.0 0.0 0.0 !beta5
IC C23 C24 C25 C26 0.0 0.0 180.0 0.0 0.0 !beta6
IC C24 C25 C26 C27 0.0 0.0 180.0 0.0 0.0 !beta7
IC C25 C26 C27 C28 0.0 0.0 180.0 0.0 0.0 !beta8
IC C26 C27 C28 C29 0.0 0.0 180.0 0.0 0.0 !beta9
IC C27 C28 C29 C210 0.0 0.0 180.0 0.0 0.0 !beta10
IC C28 C29 C210 C211 0.0 0.0 180.0 0.0 0.0 !beta11
IC C29 C210 C211 C212 0.0 0.0 180.0 0.0 0.0 !beta12
IC C210 C211 C212 C213 0.0 0.0 180.0 0.0 0.0 !beta13
IC C211 C212 C213 C214 0.0 0.0 180.0 0.0 0.0 !beta14
! Chain 2
IC C2 C3 O31 C31 0.0 0.0 -120.0 0.0 0.0 !gamma1
IC C3 O31 C31 C32 0.0 0.0 180.0 0.0 0.0 !gamma2
IC O31 C31 C32 C33 0.0 0.0 180.0 0.0 0.0 !gamma3
IC C32 O31 *C31 O32 0.0 0.0 180.0 0.0 0.0
IC C31 C32 C33 C34 0.0 0.0 180.0 0.0 0.0 !gamma4
IC C32 C33 C34 C35 0.0 0.0 180.0 0.0 0.0 !gamma5
IC C33 C34 C35 C36 0.0 0.0 180.0 0.0 0.0 !gamma6
IC C34 C35 C36 C37 0.0 0.0 180.0 0.0 0.0 !gamma7
IC C35 C36 C37 C38 0.0 0.0 180.0 0.0 0.0 !gamma8
IC C36 C37 C38 C39 0.0 0.0 180.0 0.0 0.0 !gamma9
IC C37 C38 C39 C310 0.0 0.0 180.0 0.0 0.0 !gamma10
IC C38 C39 C310 C311 0.0 0.0 180.0 0.0 0.0 !gamma11
IC C39 C310 C311 C312 0.0 0.0 180.0 0.0 0.0 !gamma12
IC C310 C311 C312 C313 0.0 0.0 180.0 0.0 0.0 !gamma13
IC C311 C312 C313 C314 0.0 0.0 180.0 0.0 0.0 !gamma14
RESI SDS -1.00 ! Dodecylsulphate
! based on methylsulfate
GROUP
ATOM S SL 1.33 ! OS2(-1)
ATOM OS1 OSL -0.28 ! |
ATOM OS2 O2L -0.65 ! (-) OS2--S(+2)--OS4 (-)
ATOM OS3 O2L -0.65 ! |
ATOM OS4 O2L -0.65 ! OS1
ATOM C1 CTL2 -0.28 ! \
ATOM H11 HAL2 0.09 ! H11-C1-H12
ATOM H12 HAL2 0.09 ! |
GROUP ! |
ATOM C2 CTL2 -0.18 ! H21-C2-H22
ATOM H21 HAL2 0.09 ! |
ATOM H22 HAL2 0.09 ! |
GROUP ! |
ATOM C3 CTL2 -0.18 ! H31-C3-H32
ATOM H31 HAL2 0.09 ! |
ATOM H32 HAL2 0.09 ! |
GROUP ! |
ATOM C4 CTL2 -0.18 ! H41-C4-H42
ATOM H41 HAL2 0.09 ! |
ATOM H42 HAL2 0.09 ! |
GROUP ! |
ATOM C5 CTL2 -0.18 ! H51-C5-H52
ATOM H51 HAL2 0.09 ! |
ATOM H52 HAL2 0.09 ! |
GROUP ! |
ATOM C6 CTL2 -0.18 ! H61-C6-H62
ATOM H61 HAL2 0.09 ! |
ATOM H62 HAL2 0.09 ! |
GROUP ! |
ATOM C7 CTL2 -0.18 ! H71-C7-H72
ATOM H71 HAL2 0.09 ! |
ATOM H72 HAL2 0.09 ! |
GROUP ! |
ATOM C8 CTL2 -0.18 ! H81-C8-H82
ATOM H81 HAL2 0.09 ! |
ATOM H82 HAL2 0.09 ! |
GROUP ! |
ATOM C9 CTL2 -0.18 ! H91-C9-H92
ATOM H91 HAL2 0.09 ! |
ATOM H92 HAL2 0.09 ! |
GROUP ! |
ATOM C10 CTL2 -0.18 ! H101-C10-H102
ATOM H101 HAL2 0.09 ! |
ATOM H102 HAL2 0.09 ! |
GROUP ! |
ATOM C11 CTL2 -0.18 ! H111-C11-H112
ATOM H111 HAL2 0.09 ! |
ATOM H112 HAL2 0.09 ! |
GROUP ! |
ATOM C12 CTL3 -0.27 ! H121-C12-H123
ATOM H121 HAL3 0.09 ! |
ATOM H122 HAL3 0.09 ! H122
ATOM H123 HAL3 0.09 !
BOND S OS1 S OS2 S OS3 S OS4
BOND OS1 C1 C1 H11 C1 H12
BOND C1 C2 C2 H21 C2 H22
BOND C2 C3 C3 H31 C3 H32
BOND C3 C4 C4 H41 C4 H42
BOND C4 C5 C5 H51 C5 H52
BOND C5 C6 C6 H61 C6 H62
BOND C6 C7 C7 H71 C7 H72
BOND C7 C8 C8 H81 C8 H82
BOND C8 C9 C9 H91 C9 H92
BOND C9 C10 C10 H101 C10 H102
BOND C10 C11 C11 H111 C11 H112
BOND C11 C12 C12 H121 C12 H122 C12 H123
ACCE OS1
ACCE OS2
ACCE OS3
ACCE OS4
IC C2 OS1 OS2 S 2.56 179.99 0.0 40.1 0.00
IC OS1 OS2 *S OS3 2.37 40.1 120.0 0.00 0.00
IC OS1 OS2 *S OS4 2.37 40.1 -120.0 0.00 0.00
IC OS2 S OS1 C1 0.00 0.00 180.0 0.00 0.00
IC OS4 S OS2 OS1 1.4530 113.50 -113.75 40.11 2.3733
IC OS2 S OS2 OS3 1.4522 0.00 0.00 33.26 2.4296
IC OS3 S OS1 OS4 1.4530 105.51 121.17 35.54 2.4088
IC OS1 S OS3 OS2 1.5716 105.51 112.45 33.24 2.4296
IC C1 OS1 S OS2 1.4263 114.59 -180.00 103.34 1.4522
IC S OS1 C1 OS3 1.5716 114.59 -30.52 56.05 2.8947
IC OS1 S OS4 OS2 1.5716 105.51 -112.45 33.24 2.4296
IC OS1 S OS2 OS3 1.5716 103.34 -113.75 33.26 2.4296
IC OS1 S OS3 OS2 1.5716 105.51 112.45 33.24 2.4296
IC OS4 S OS2 OS1 1.4530 113.50 -113.75 40.11 2.3733
IC OS4 S OS3 OS1 1.4530 114.15 115.37 38.95 2.4088
IC OS3 S OS2 OS1 1.4530 113.50 113.75 40.11 2.3733
IC OS4 S OS1 C1 1.4530 105.51 -60.58 114.59 1.4263
IC OS2 S OS1 C1 1.4522 103.34 -180.00 114.59 1.4263
IC OS3 S OS1 C1 1.4530 105.51 60.58 114.59 1.4263
! REMAINDER IS ALL TRANS
IC S OS1 C1 C2 0.0 0.00 180.00 0.0 0.0
IC OS1 C1 C2 C3 0.0 0.00 180.00 0.0 0.0
IC C1 C2 C3 C4 0.0 0.00 180.00 0.0 0.0
IC C2 C3 C4 C5 0.0 0.00 180.00 0.0 0.0
IC C3 C4 C5 C6 0.0 0.00 180.00 0.0 0.0
IC C4 C5 C6 C7 0.0 0.00 180.00 0.0 0.0
IC C5 C6 C7 C8 0.0 0.00 180.00 0.0 0.0
IC C6 C7 C8 C9 0.0 0.00 180.00 0.0 0.0
IC C7 C8 C9 C10 0.0 0.00 180.00 0.0 0.0
IC C8 C9 C10 C11 0.0 0.00 180.00 0.0 0.0
IC C9 C10 C11 C12 0.0 0.00 180.00 0.0 0.0
IC OS1 C2 *C1 H11 0.0 0.00 120.00 0.0 0.0
IC OS1 C2 *C1 H12 0.0 0.00 -120.00 0.0 0.0
IC C1 C3 *C2 H21 0.0 0.00 120.00 0.0 0.0
IC C1 C3 *C2 H22 0.0 0.00 -120.00 0.0 0.0
IC C2 C4 *C3 H31 0.0 0.00 120.00 0.0 0.0
IC C2 C4 *C3 H32 0.0 0.00 -120.00 0.0 0.0
IC C3 C5 *C4 H41 0.0 0.00 120.00 0.0 0.0
IC C3 C5 *C4 H42 0.0 0.00 -120.00 0.0 0.0
IC C4 C6 *C5 H51 0.0 0.00 120.00 0.0 0.0
IC C4 C6 *C5 H52 0.0 0.00 -120.00 0.0 0.0
IC C5 C7 *C6 H61 0.0 0.00 120.00 0.0 0.0
IC C5 C7 *C6 H62 0.0 0.00 -120.00 0.0 0.0
IC C6 C8 *C7 H71 0.0 0.00 120.00 0.0 0.0
IC C6 C8 *C7 H72 0.0 0.00 -120.00 0.0 0.0
IC C7 C9 *C8 H81 0.0 0.00 120.00 0.0 0.0
IC C7 C9 *C8 H82 0.0 0.00 -120.00 0.0 0.0
IC C8 C10 *C9 H91 0.0 0.00 120.00 0.0 0.0
IC C8 C10 *C9 H92 0.0 0.00 -120.00 0.0 0.0
IC C9 C11 *C10 H101 0.0 0.00 120.00 0.0 0.0
IC C9 C11 *C10 H102 0.0 0.00 -120.00 0.0 0.0
IC C10 C12 *C11 H111 0.0 0.00 120.00 0.0 0.0
IC C10 C12 *C11 H112 0.0 0.00 -120.00 0.0 0.0
IC C10 C11 C12 H121 0.0 0.00 180.00 0.0 0.0
IC C11 H121 *C12 H122 0.0 0.00 120.00 0.0 0.0
IC C11 H121 *C12 H123 0.0 0.00 -120.00 0.0 0.0
RESI POPC 0.00 ! 1-palmytoil-2-oleoyl-sn-glycero-
! 3-Phosphatidylcholine
!
! (May 14, 1999 Carlos F. Lopez)
! No IC's (read in coordinates from file)
!
! Palmytoil - CH2
! |
! Oleyl - CH
! | (-) (+)
! CH2 - PO4 - CH2 - CH2 - N-(CH3)3
!
! Polar Head and glycerol backbone
GROUP ! H31
ATOM N NTL -0.60 ! |
ATOM C11 CTL2 -0.10 ! H33-C13-H32
ATOM C12 CTL5 -0.35 ! |
ATOM C13 CTL5 -0.35 ! H21 | H43
ATOM C14 CTL5 -0.35 ! | | |
ATOM H11 HL 0.25 ! H22-C12---N---C14-H42 (+)
ATOM H12 HL 0.25 ! | | |
ATOM H21 HL 0.25 ! H23 | H41
ATOM H22 HL 0.25 ! |
ATOM H23 HL 0.25 ! |
ATOM H31 HL 0.25 ! |
ATOM H32 HL 0.25 ! H11-C11-H12
ATOM H33 HL 0.25 ! |
ATOM H41 HL 0.25 ! |
ATOM H42 HL 0.25 ! |
ATOM H43 HL 0.25 ! |
GROUP ! |
ATOM C15 CTL2 -0.08 ! |
ATOM H51 HAL2 0.09 ! H51---C15---H52
ATOM H52 HAL2 0.09 ! |
GROUP ! |
ATOM P1 PL 1.50 ! (-) O3 O1
ATOM O3 O2L -0.78 ! \ /
ATOM O4 O2L -0.78 ! P1 (+)
ATOM O1 OSL -0.57 ! / \
ATOM O2 OSL -0.57 ! (-) O4 O2
GROUP ! |
ATOM C1 CTL2 -0.08 ! | alpha1
ATOM HA HAL2 0.09 ! HA---C1---HB
ATOM HB HAL2 0.09 ! | theta1
GROUP ! |
ATOM C2 CTL1 0.04 ! HS---C2--------------
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.34 ! O22 O21 theta3
ATOM C21 CL 0.63 ! \\ / beta2 |
ATOM O22 OBL -0.52 ! C21 |
ATOM C22 CTL2 -0.08 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S |
ATOM H2S HAL2 0.09 ! | |
GROUP ! | beta4 |
ATOM C3 CTL2 -0.05 ! | |
ATOM HX HAL2 0.09 ! | HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.34 ! | O32 O31
ATOM C31 CL 0.63 ! | \\ / gamma2
ATOM O32 OBL -0.52 ! | C31
ATOM C32 CTL2 -0.08 ! | | gamma3
ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y
ATOM H2Y HAL2 0.09 ! | |
GROUP ! | | gamma4
ATOM C23 CTL2 -0.18 ! | |
ATOM H3R HAL2 0.09 ! H3R ---C23---H3S |
ATOM H3S HAL2 0.09 ! | |
GROUP ! | |
ATOM C24 CTL2 -0.18 ! | |
ATOM H4R HAL2 0.09 ! H4R ---C24---H4S |
ATOM H4S HAL2 0.09 ! | |
GROUP ! | |
ATOM C25 CTL2 -0.18 ! | |
ATOM H5R HAL2 0.09 ! H5R ---C25---H5S |
ATOM H5S HAL2 0.09 ! | |
GROUP ! | |
ATOM C26 CTL2 -0.18 ! | |
ATOM H6R HAL2 0.09 ! H6R ---C26---H6S |
ATOM H6S HAL2 0.09 ! | |
GROUP ! | |
ATOM C27 CTL2 -0.18 ! | |
ATOM H7R HAL2 0.09 ! H7R ---C27---H7S |
ATOM H7S HAL2 0.09 ! | |
GROUP ! | |
ATOM C28 CTL2 -0.18 ! | |
ATOM H8R HAL2 0.09 ! H8R ---C28---H8S |
ATOM H8S HAL2 0.09 ! | |
GROUP ! | |
ATOM C29 CEL1 -0.15 ! | |
ATOM H91 HEL1 0.15 ! H91 ---C29 |
GROUP ! || (CIS) |
ATOM C210 CEL1 -0.15 ! || |
ATOM H101 HEL1 0.15 ! H101---C210 |
GROUP ! | |
ATOM C211 CTL2 -0.18 ! | |
ATOM H11R HAL2 0.09 ! H11R---C211--H11S |
ATOM H11S HAL2 0.09 ! | |
GROUP ! | |
ATOM C212 CTL2 -0.18 ! | |
ATOM H12R HAL2 0.09 ! H12R---C212--H12S |
ATOM H12S HAL2 0.09 ! | |
GROUP ! | |
ATOM C213 CTL2 -0.18 ! | |
ATOM H13R HAL2 0.09 ! H13R---C213--H13S |
ATOM H13S HAL2 0.09 ! | |
GROUP ! | |
ATOM C214 CTL2 -0.18 ! | |
ATOM H14R HAL2 0.09 ! H14R---C214--H14S |
ATOM H14S HAL2 0.09 ! | |
GROUP ! | |
ATOM C215 CTL2 -0.18 ! | |
ATOM H15R HAL2 0.09 ! H15R---C215--H15S |
ATOM H15S HAL2 0.09 ! | |
GROUP ! | |
ATOM C216 CTL2 -0.18 ! | |
ATOM H16R HAL2 0.09 ! H16R---C216--H16S |
ATOM H16S HAL2 0.09 ! | |
GROUP ! | |
ATOM C217 CTL2 -0.18 ! | |
ATOM H17R HAL2 0.09 ! H17R---C217--H17S |
ATOM H17S HAL2 0.09 ! | |
GROUP ! | |
ATOM C218 CTL3 -0.27 ! | |
ATOM H18R HAL3 0.09 ! H18R---C218--H18S |
ATOM H18S HAL3 0.09 ! | |
ATOM H18T HAL3 0.09 ! H18T |
GROUP ! |
ATOM C33 CTL2 -0.18 ! |
ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y
ATOM H3Y HAL2 0.09 ! |
GROUP ! |
ATOM C34 CTL2 -0.18 ! |
ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y
ATOM H4Y HAL2 0.09 ! |
GROUP ! |
ATOM C35 CTL2 -0.18 ! |
ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y
ATOM H5Y HAL2 0.09 ! |
GROUP ! |
ATOM C36 CTL2 -0.18 ! |
ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y
ATOM H6Y HAL2 0.09 ! |
GROUP ! |
ATOM C37 CTL2 -0.18 ! |
ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y
ATOM H7Y HAL2 0.09 ! |
GROUP ! |
ATOM C38 CTL2 -0.18 ! |
ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y
ATOM H8Y HAL2 0.09 ! |
GROUP ! |
ATOM C39 CTL2 -0.18 ! |
ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y
ATOM H9Y HAL2 0.09 ! |
GROUP ! |
ATOM C310 CTL2 -0.18 ! |
ATOM H10X HAL2 0.09 ! H10X---C310--H10Y
ATOM H10Y HAL2 0.09 ! |
GROUP ! |
ATOM C311 CTL2 -0.18 ! |
ATOM H11X HAL2 0.09 ! H11X---C311--H11Y
ATOM H11Y HAL2 0.09 ! |
GROUP ! |
ATOM C312 CTL2 -0.18 ! |
ATOM H12X HAL2 0.09 ! H12X---C312--H12Y
ATOM H12Y HAL2 0.09 ! |
GROUP ! |
ATOM C313 CTL2 -0.18 ! |
ATOM H13X HAL2 0.09 ! H13X---C313--H13Y
ATOM H13Y HAL2 0.09 ! |
GROUP ! |
ATOM C314 CTL2 -0.18 ! |
ATOM H14X HAL2 0.09 ! H14X---C314--H14Y
ATOM H14Y HAL2 0.09 ! |
GROUP ! |
ATOM C315 CTL2 -0.18 ! |
ATOM H15X HAL2 0.09 ! H15X---C315--H15Y
ATOM H15Y HAL2 0.09 ! |
GROUP ! |
ATOM C316 CTL3 -0.27 ! |
ATOM H16X HAL3 0.09 ! H16X---C316--H16Y
ATOM H16Y HAL3 0.09 ! |
ATOM H16Z HAL3 0.09 ! H16Z
!BONDING FROM PC
BOND N C11 N C12 N C13 N C14
BOND C11 H11 C11 H12 C11 C15
BOND C12 H21 C12 H22 C12 H23
BOND C13 H31 C13 H32 C13 H33
BOND C14 H41 C14 H42 C14 H43
BOND C15 H51 C15 H52
BOND P1 O1 P1 O2 P1 O3 P1 O4
BOND O1 C15 O2 C1
! Glycerol Backbone
BOND C1 HA C1 HB C1 C2
BOND C2 HS C2 C3 C2 O21
BOND C3 HX C3 HY C3 O31
! Chain from C2
BOND O21 C21
BOND C21 C22
DOUBLE C21 O22
BOND C22 H2R C22 H2S C22 C23
BOND C23 H3R C23 H3S C23 C24
BOND C24 H4R C24 H4S C24 C25
BOND C25 H5R C25 H5S C25 C26
BOND C26 H6R C26 H6S C26 C27
BOND C27 H7R C27 H7S C27 C28
BOND C28 H8R C28 H8S C28 C29
BOND C29 H91
DOUBLE C29 C210
BOND C210 H101 C210 C211
BOND C211 H11R C211 H11S C211 C212
BOND C212 H12R C212 H12S C212 C213
BOND C213 H13R C213 H13S C213 C214
BOND C214 H14R C214 H14S C214 C215
BOND C215 H15R C215 H15S C215 C216
BOND C216 H16R C216 H16S C216 C217
BOND C217 H17R C217 H17S C217 C218
BOND C218 H18R C218 H18S C218 H18T
! Chain From C3
BOND O31 C31
BOND C31 C32
DOUBLE C31 O32
BOND C32 H2X C32 H2Y C32 C33
BOND C33 H3X C33 H3Y C33 C34
BOND C34 H4X C34 H4Y C34 C35
BOND C35 H5X C35 H5Y C35 C36
BOND C36 H6X C36 H6Y C36 C37
BOND C37 H7X C37 H7Y C37 C38
BOND C38 H8X C38 H8Y C38 C39
BOND C39 H9X C39 H9Y C39 C310
BOND C310 H10X C310 H10Y C310 C311
BOND C311 H11X C311 H11Y C311 C312
BOND C312 H12X C312 H12Y C312 C313
BOND C313 H13X C313 H13Y C313 C314
BOND C314 H14X C314 H14Y C314 C315
BOND C315 H15X C315 H15Y C315 C316
BOND C316 H16X C316 H16Y C316 H16Z
IMPR C21 O21 C22 O22 C31 O31 C32 O32
!IC table from IC generate, geometry is guessed
IC C12 C11 *N C13 1.4999 109.15 122.15 111.71 1.4949
IC C12 C11 *N C14 1.4999 109.15 -116.51 109.19 1.5011
IC C12 N C11 C15 1.4999 109.15 43.57 118.04 1.5524
IC C15 N *C11 H11 1.5524 118.04 -121.93 109.13 1.0811
IC H11 N *C11 H12 1.0811 109.13 -117.56 108.83 1.0835
IC C11 N C12 H21 1.5284 109.15 -59.57 108.41 1.0953
IC H21 N *C12 H22 1.0953 108.41 -116.60 113.14 1.0854
IC H21 N *C12 H23 1.0953 108.41 118.64 112.84 1.0777
IC C11 N C13 H31 1.5284 111.71 -61.34 110.98 1.0826
IC H31 N *C13 H32 1.0826 110.98 121.24 110.98 1.0826
IC H31 N *C13 H33 1.0826 110.98 -119.19 110.09 1.0845
IC C11 N C14 H41 1.5284 109.19 173.62 112.23 1.0785
IC H41 N *C14 H42 1.0785 112.23 125.69 112.79 1.0778
IC H41 N *C14 H43 1.0785 112.23 -117.12 108.08 1.0983
IC N C11 C15 O1 1.5284 118.04 63.61 111.07 1.4249
IC O1 C11 *C15 H51 1.4249 111.07 -126.47 109.40 1.1165
IC H51 C11 *C15 H52 1.1165 109.40 -115.09 108.53 1.1137
IC C11 C15 O1 P1 1.5524 111.07 -132.50 121.66 1.5873
IC C15 O1 P1 O2 1.4249 121.66 95.32 99.37 1.5870
IC O2 O1 *P1 O3 1.5870 99.37 -113.40 108.96 1.4773
IC O2 O1 *P1 O4 1.5870 99.37 114.27 109.52 1.4735
IC O1 P1 O2 C1 1.5873 99.37 -136.11 119.34 1.4276
IC P1 O2 C1 C2 1.5870 119.34 -174.88 109.28 1.5468
IC C2 O2 *C1 HA 1.5468 109.28 119.70 111.34 1.1169
IC HA O2 *C1 HB 1.1169 111.34 119.72 110.33 1.1141
IC O2 C1 C2 O21 1.4276 109.28 -167.70 109.50 1.4378
IC O21 C1 *C2 C3 1.4378 109.50 -121.42 111.45 1.5543
IC C3 C1 *C2 HS 1.5543 111.45 -117.17 108.32 1.1156
IC C1 C2 O21 C21 1.5468 109.50 90.28 116.64 1.3217
IC C2 O21 C21 C22 1.4378 116.64 174.47 109.18 1.5303
IC C22 O21 *C21 O22 1.5303 109.18 -178.13 126.27 1.2213
IC O21 C21 C22 C23 1.3217 109.18 -78.33 110.83 1.5447
IC C23 C21 *C22 H2R 1.5447 110.83 121.63 109.32 1.1103
IC H2R C21 *C22 H2S 1.1103 109.32 117.81 107.94 1.1092
IC C1 C2 C3 O31 1.5468 111.45 -172.66 111.94 1.4454
IC O31 C2 *C3 HX 1.4454 111.94 -126.15 109.39 1.1150
IC HX C2 *C3 HY 1.1150 109.39 -114.93 107.39 1.1133
IC C2 C3 O31 C31 1.5543 111.94 -96.66 116.55 1.3325
IC C3 O31 C31 C32 1.4454 116.55 177.97 109.29 1.5306
IC C32 O31 *C31 O32 1.5306 109.29 -179.43 126.40 1.2162
IC O31 C31 C32 C33 1.3325 109.29 -177.61 111.07 1.5445
IC C33 C31 *C32 H2X 1.5445 111.07 120.97 108.77 1.1094
IC H2X C31 *C32 H2Y 1.1094 108.77 118.39 108.38 1.1099
IC C21 C22 C23 C24 1.5303 110.83 177.84 113.15 1.5345
IC C24 C22 *C23 H3R 1.5345 113.15 -120.52 109.51 1.1149
IC H3R C22 *C23 H3S 1.1149 109.51 -117.98 109.32 1.1137
IC C22 C23 C24 C25 1.5447 113.15 174.44 112.06 1.5345
IC C25 C23 *C24 H4R 1.5345 112.06 121.05 109.09 1.1140
IC H4R C23 *C24 H4S 1.1140 109.09 117.86 109.72 1.1131
IC C23 C24 C25 C26 1.5345 112.06 175.38 112.95 1.5340
IC C26 C24 *C25 H5R 1.5340 112.95 -121.08 109.34 1.1131
IC H5R C24 *C25 H5S 1.1131 109.34 -117.43 108.99 1.1132
IC C24 C25 C26 C27 1.5345 112.95 174.94 112.21 1.5351
IC C27 C25 *C26 H6R 1.5351 112.21 121.27 109.00 1.1134
IC H6R C25 *C26 H6S 1.1134 109.00 117.60 109.50 1.1130
IC C25 C26 C27 C28 1.5340 112.21 175.67 112.60 1.5394
IC C28 C26 *C27 H7R 1.5394 112.60 -121.40 108.58 1.1142
IC H7R C26 *C27 H7S 1.1142 108.58 -116.93 108.44 1.1140
IC C26 C27 C28 C29 1.5351 112.60 178.25 111.01 1.5083
IC C29 C27 *C28 H8R 1.5083 111.01 119.62 107.18 1.1139
IC H8R C27 *C28 H8S 1.1139 107.18 115.86 109.35 1.1118
IC C27 C28 C29 C210 1.5391 111.34 -141.40 127.31 1.3462
IC C210 C28 *C29 H91 1.3462 127.31 -176.71 114.35 1.1001
IC C28 C29 C210 C211 1.5073 127.31 1.24 127.43 1.5089
IC C211 C29 *C21 H101 1.5089 127.43 179.21 118.33 1.1011
IC C29 C210 C211 C212 1.3462 127.43 -120.91 110.88 1.5393
IC C212 C210 *C21 H11R 1.5393 110.88 121.06 112.51 1.1124
IC H11R C210 *C21 H11S 1.1124 112.51 119.00 109.81 1.1127
IC C210 C211 C212 C213 1.5089 110.88 -176.36 112.76 1.5347
IC C213 C211 *C21 H12R 1.5347 112.76 -120.93 109.33 1.1142
IC H12R C211 *C21 H12S 1.1142 109.33 -118.17 109.94 1.1138
IC C211 C212 C213 C214 1.5393 112.76 -179.47 112.21 1.5338
IC C214 C212 *C21 H13R 1.5338 112.21 121.29 109.31 1.1130
IC H13R C212 *C21 H13S 1.1130 109.31 117.74 109.05 1.1131
IC C212 C213 C214 C215 1.5347 112.21 -178.99 112.92 1.5339
IC C215 C213 *C21 H14R 1.5339 112.92 -121.37 109.00 1.1134
IC H14R C213 *C21 H14S 1.1134 109.00 -117.34 109.08 1.1132
IC C213 C214 C215 C216 1.5338 112.92 179.95 112.20 1.5339
IC C216 C214 *C21 H15R 1.5339 112.20 121.17 109.14 1.1131
IC H15R C214 *C21 H15S 1.1131 109.14 117.63 109.22 1.1132
IC C214 C215 C216 C217 1.5339 112.20 179.53 112.96 1.5328
IC C217 C215 *C21 H16R 1.5328 112.96 -121.41 109.07 1.1135
IC H16R C215 *C21 H16S 1.1135 109.07 -117.43 109.05 1.1130
IC C215 C216 C217 C218 1.5339 112.96 -179.21 113.03 1.5305
IC C218 C216 *C21 H17R 1.5305 113.03 121.55 108.80 1.1140
IC H17R C216 *C21 H17S 1.1140 108.80 116.88 108.83 1.1142
IC C216 C217 C218 H18R 1.5328 113.03 60.41 110.37 1.1113
IC H18R C217 *C21 H18S 1.1113 110.37 -119.78 110.49 1.1115
IC H18R C217 *C21 H18T 1.1113 110.37 120.07 110.59 1.1111
IC C31 C32 C33 C34 1.5333 111.40 179.66 112.54 1.5345
IC C34 C32 *C33 H3X 1.5345 112.54 -121.73 109.66 1.1133
IC H3X C32 *C33 H3Y 1.1133 109.66 -117.45 109.37 1.1151
IC C32 C33 C34 C35 1.5440 112.54 178.40 112.54 1.5346
IC C35 C33 *C34 H4X 1.5346 112.54 121.75 110.03 1.1131
IC H4X C33 *C34 H4Y 1.1131 110.03 117.75 108.84 1.1139
IC C33 C34 C35 C36 1.5345 112.54 -175.14 112.09 1.5349
IC C36 C34 *C35 H5X 1.5349 112.09 -122.26 109.27 1.1127
IC H5X C34 *C35 H5Y 1.1127 109.27 -117.42 109.08 1.1138
IC C34 C35 C36 C37 1.5346 112.09 174.19 113.84 1.5368
IC C37 C35 *C36 H6X 1.5368 113.84 122.38 109.13 1.1124
IC H6X C35 *C36 H6Y 1.1124 109.13 117.02 108.50 1.1143
IC C35 C36 C37 C38 1.5349 113.84 65.26 113.87 1.5343
IC C38 C36 *C37 H7X 1.5343 113.87 120.83 108.55 1.1137
IC H7X C36 *C37 H7Y 1.1137 108.55 116.91 109.10 1.1132
IC C36 C37 C38 C39 1.5368 113.87 178.14 112.45 1.5354
IC C39 C37 *C38 H8X 1.5354 112.45 121.43 109.97 1.1123
IC H8X C37 *C38 H8Y 1.1123 109.97 117.71 108.91 1.1127
IC C37 C38 C39 C310 1.5343 112.45 -176.66 111.96 1.5320
IC C310 C38 *C39 H9X 1.5320 111.96 120.68 109.20 1.1133
IC H9X C38 *C39 H9Y 1.1133 109.20 117.81 109.34 1.1127
IC C38 C39 C310 C311 1.5354 111.96 178.35 113.81 1.5336
IC C311 C39 *C31 H10X 1.5336 113.81 -120.14 108.22 1.1126
IC H10X C39 *C31 H10Y 1.1126 108.22 -117.07 109.45 1.1132
IC C39 C310 C311 C312 1.5320 113.81 -175.46 111.16 1.5334
IC C312 C310 *C31 H11X 1.5334 111.16 120.27 109.12 1.1138
IC H11X C310 *C31 H11Y 1.1138 109.12 118.20 110.02 1.1119
IC C310 C311 C312 C313 1.5336 111.16 173.60 113.47 1.5330
IC C313 C311 *C31 H12X 1.5330 113.47 -120.74 108.01 1.1140
IC H12X C311 *C31 H12Y 1.1140 108.01 -116.85 109.45 1.1130
IC C311 C312 C313 C314 1.5334 113.47 -174.75 111.86 1.5335
IC C314 C312 *C31 H13X 1.5335 111.86 120.28 108.66 1.1135
IC H13X C312 *C31 H13Y 1.1135 108.66 118.03 110.08 1.1125
IC C312 C313 C314 C315 1.5330 111.86 175.21 113.05 1.5325
IC C315 C313 *C31 H14X 1.5325 113.05 -120.81 108.37 1.1133
IC H14X C313 *C31 H14Y 1.1133 108.37 -117.18 109.40 1.1131
IC C313 C314 C315 C316 1.5335 113.05 -177.76 112.89 1.5300
IC C316 C314 *C31 H15X 1.5300 112.89 121.41 108.55 1.1149
IC H15X C314 *C31 H15Y 1.1149 108.55 117.05 109.21 1.1136
IC C314 C315 C316 H16X 1.5325 112.89 57.15 110.07 1.1113
IC H16X C315 *C31 H16Y 1.1113 110.07 -119.27 110.55 1.1106
IC H16X C315 *C31 H16Z 1.1113 110.07 120.81 110.70 1.1116
RESI POPE 0.00 ! 1-palmytoil-2-oleoyl-sn-glycero-
! 3-Phosphatidylethanolamine
!
! (May 14, 1999 Carlos F. Lopez)
!
! Palmytoil - CH2
! |
! Oleyl - CH
! |
! CH2 - PO4 - CH2 - CH2 - NH3
!
! Polar Head and glycerol backbone
GROUP !
ATOM N NH3L -0.30 ! HN2
ATOM HN1 HCL 0.33 ! |
ATOM HN2 HCL 0.33 ! (+) HN1---N---HN3
ATOM HN3 HCL 0.33 ! |
ATOM C12 CTL2 0.13 ! |
ATOM H12A HAL2 0.09 ! H12A--C12---H12B
ATOM H12B HAL2 0.09 ! |
GROUP ! | alpha5
ATOM C11 CTL2 -0.08 ! |
ATOM H11A HAL2 0.09 ! H11A--C11---H11B
ATOM H11B HAL2 0.09 ! | alpha4
ATOM P PL 1.50 ! (-) O13 O12
ATOM O13 O2L -0.78 ! \ / alpha3
ATOM O14 O2L -0.78 ! P (+)
ATOM O11 OSL -0.57 ! / \ alpha2
ATOM O12 OSL -0.57 ! (-) O14 O11
ATOM C1 CTL2 -0.08 ! | alpha1
ATOM HA HAL2 0.09 ! HA---C1---HB
ATOM HB HAL2 0.09 ! | theta1
GROUP ! |
ATOM C2 CTL1 0.04 ! HS---C2--------------
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.34 ! O22 O21 theta3
ATOM C21 CL 0.63 ! \\ / beta2 |
ATOM O22 OBL -0.52 ! C21 |
ATOM C22 CTL2 -0.08 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S |
ATOM H2S HAL2 0.09 ! | |
GROUP ! | beta4 |
ATOM C3 CTL2 -0.05 ! | |
ATOM HX HAL2 0.09 ! | HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.34 ! | O32 O31
ATOM C31 CL 0.63 ! | \\ / gamma2
ATOM O32 OBL -0.52 ! | C31
ATOM C32 CTL2 -0.08 ! | | gamma3
ATOM H2X HAL2 0.09 ! | H2X---C32---H2Y
ATOM H2Y HAL2 0.09 ! | |
GROUP ! | | gamma4
ATOM C23 CTL2 -0.18 ! | |
ATOM H3R HAL2 0.09 ! H3R ---C23---H3S |
ATOM H3S HAL2 0.09 ! | |
GROUP ! | |
ATOM C24 CTL2 -0.18 ! | |
ATOM H4R HAL2 0.09 ! H4R ---C24---H4S |
ATOM H4S HAL2 0.09 ! | |
GROUP ! | |
ATOM C25 CTL2 -0.18 ! | |
ATOM H5R HAL2 0.09 ! H5R ---C25---H5S |
ATOM H5S HAL2 0.09 ! | |
GROUP ! | |
ATOM C26 CTL2 -0.18 ! | |
ATOM H6R HAL2 0.09 ! H6R ---C26---H6S |
ATOM H6S HAL2 0.09 ! | |
GROUP ! | |
ATOM C27 CTL2 -0.18 ! | |
ATOM H7R HAL2 0.09 ! H7R ---C27---H7S |
ATOM H7S HAL2 0.09 ! | |
GROUP ! | |
ATOM C28 CTL2 -0.18 ! | |
ATOM H8R HAL2 0.09 ! H8R ---C28---H8S |
ATOM H8S HAL2 0.09 ! | |
GROUP ! | |
ATOM C29 CEL1 -0.15 ! | |
ATOM H91 HEL1 0.15 ! H91 ---C29 |
GROUP ! || (CIS) |
ATOM C210 CEL1 -0.15 ! || |
ATOM H101 HEL1 0.15 ! H101---C210 |
GROUP ! | |
ATOM C211 CTL2 -0.18 ! | |
ATOM H11R HAL2 0.09 ! H11R---C211--H11S |
ATOM H11S HAL2 0.09 ! | |
GROUP ! | |
ATOM C212 CTL2 -0.18 ! | |
ATOM H12R HAL2 0.09 ! H12R---C212--H12S |
ATOM H12S HAL2 0.09 ! | |
GROUP ! | |
ATOM C213 CTL2 -0.18 ! | |
ATOM H13R HAL2 0.09 ! H13R---C213--H13S |
ATOM H13S HAL2 0.09 ! | |
GROUP ! | |
ATOM C214 CTL2 -0.18 ! | |
ATOM H14R HAL2 0.09 ! H14R---C214--H14S |
ATOM H14S HAL2 0.09 ! | |
GROUP ! | |
ATOM C215 CTL2 -0.18 ! | |
ATOM H15R HAL2 0.09 ! H15R---C215--H15S |
ATOM H15S HAL2 0.09 ! | |
GROUP ! | |
ATOM C216 CTL2 -0.18 ! | |
ATOM H16R HAL2 0.09 ! H16R---C216--H16S |
ATOM H16S HAL2 0.09 ! | |
GROUP ! | |
ATOM C217 CTL2 -0.18 ! | |
ATOM H17R HAL2 0.09 ! H17R---C217--H17S |
ATOM H17S HAL2 0.09 ! | |
GROUP ! | |
ATOM C218 CTL3 -0.27 ! | |
ATOM H18R HAL3 0.09 ! H18R---C218--H18S |
ATOM H18S HAL3 0.09 ! | |
ATOM H18T HAL3 0.09 ! H18T |
GROUP ! |
ATOM C33 CTL2 -0.18 ! |
ATOM H3X HAL2 0.09 ! H3X ---C33---H3Y
ATOM H3Y HAL2 0.09 ! |
GROUP ! |
ATOM C34 CTL2 -0.18 ! |
ATOM H4X HAL2 0.09 ! H4X ---C34---H4Y
ATOM H4Y HAL2 0.09 ! |
GROUP ! |
ATOM C35 CTL2 -0.18 ! |
ATOM H5X HAL2 0.09 ! H5X ---C35---H5Y
ATOM H5Y HAL2 0.09 ! |
GROUP ! |
ATOM C36 CTL2 -0.18 ! |
ATOM H6X HAL2 0.09 ! H6X ---C36---H6Y
ATOM H6Y HAL2 0.09 ! |
GROUP ! |
ATOM C37 CTL2 -0.18 ! |
ATOM H7X HAL2 0.09 ! H7X ---C37---H7Y
ATOM H7Y HAL2 0.09 ! |
GROUP ! |
ATOM C38 CTL2 -0.18 ! |
ATOM H8X HAL2 0.09 ! H8X ---C38---H8Y
ATOM H8Y HAL2 0.09 ! |
GROUP ! |
ATOM C39 CTL2 -0.18 ! |
ATOM H9X HAL2 0.09 ! H9X ---C39---H9Y
ATOM H9Y HAL2 0.09 ! |
GROUP ! |
ATOM C310 CTL2 -0.18 ! |
ATOM H10X HAL2 0.09 ! H10X---C310--H10Y
ATOM H10Y HAL2 0.09 ! |
GROUP ! |
ATOM C311 CTL2 -0.18 ! |
ATOM H11X HAL2 0.09 ! H11X---C311--H11Y
ATOM H11Y HAL2 0.09 ! |
GROUP ! |
ATOM C312 CTL2 -0.18 ! |
ATOM H12X HAL2 0.09 ! H12X---C312--H12Y
ATOM H12Y HAL2 0.09 ! |
GROUP ! |
ATOM C313 CTL2 -0.18 ! |
ATOM H13X HAL2 0.09 ! H13X---C313--H13Y
ATOM H13Y HAL2 0.09 ! |
GROUP ! |
ATOM C314 CTL2 -0.18 ! |
ATOM H14X HAL2 0.09 ! H14X---C314--H14Y
ATOM H14Y HAL2 0.09 ! |
GROUP ! |
ATOM C315 CTL2 -0.18 ! |
ATOM H15X HAL2 0.09 ! H15X---C315--H15Y
ATOM H15Y HAL2 0.09 ! |
GROUP ! |
ATOM C316 CTL3 -0.27 ! |
ATOM H16X HAL3 0.09 ! H16X---C316--H16Y
ATOM H16Y HAL3 0.09 ! |
ATOM H16Z HAL3 0.09 ! H16Z
! Polar Head
BOND N HN1 N HN2 N HN3 N C12
BOND C12 H12A C12 H12B C12 C11
BOND C11 H11A C11 H11B C11 O12
BOND O12 P P O11 P O13 P O14
! Glycerol Backbone
BOND C1 HA C1 HB C1 C2 C1 O11
BOND C2 HS C2 C3 C2 O21
BOND C3 HX C3 HY C3 O31
! Chain from C2
BOND O21 C21
BOND C21 C22
DOUBLE C21 O22
BOND C22 H2R C22 H2S C22 C23
BOND C23 H3R C23 H3S C23 C24
BOND C24 H4R C24 H4S C24 C25
BOND C25 H5R C25 H5S C25 C26
BOND C26 H6R C26 H6S C26 C27
BOND C27 H7R C27 H7S C27 C28
BOND C28 H8R C28 H8S C28 C29
BOND C29 H91
DOUBLE C29 C210
BOND C210 H101 C210 C211
BOND C211 H11R C211 H11S C211 C212
BOND C212 H12R C212 H12S C212 C213
BOND C213 H13R C213 H13S C213 C214
BOND C214 H14R C214 H14S C214 C215
BOND C215 H15R C215 H15S C215 C216
BOND C216 H16R C216 H16S C216 C217
BOND C217 H17R C217 H17S C217 C218
BOND C218 H18R C218 H18S C218 H18T
! Chain From C3
BOND O31 C31
BOND C31 C32
DOUBLE C31 O32
BOND C32 H2X C32 H2Y C32 C33
BOND C33 H3X C33 H3Y C33 C34
BOND C34 H4X C34 H4Y C34 C35
BOND C35 H5X C35 H5Y C35 C36
BOND C36 H6X C36 H6Y C36 C37
BOND C37 H7X C37 H7Y C37 C38
BOND C38 H8X C38 H8Y C38 C39
BOND C39 H9X C39 H9Y C39 C310
BOND C310 H10X C310 H10Y C310 C311
BOND C311 H11X C311 H11Y C311 C312
BOND C312 H12X C312 H12Y C312 C313
BOND C313 H13X C313 H13Y C313 C314
BOND C314 H14X C314 H14Y C314 C315
BOND C315 H15X C315 H15Y C315 C316
BOND C316 H16X C316 H16Y C316 H16Z
IMPR C21 O21 C22 O22 C31 O31 C32 O32
!IC table from IC generate, geometry is guessed
IC HN1 C12 *N HN2 1.0524 110.54 127.93 115.12 1.0338
IC HN1 C12 *N HN3 1.0524 110.54 -112.33 100.76 1.0488
IC HN1 N C12 C11 1.0524 110.54 70.07 107.99 1.5341
IC C11 N *C12 H12A 1.5341 107.99 -122.80 109.40 1.1069
IC H12A N *C12 H12B 1.1069 109.40 -119.69 107.75 1.1114
IC N C12 C11 O12 1.5038 107.99 46.85 109.27 1.4315
IC O12 C12 *C11 H11A 1.4315 109.27 -121.18 109.30 1.1164
IC H11A C12 *C11 H11B 1.1164 109.30 -117.51 109.07 1.1179
IC C12 C11 O12 P 1.5341 109.27 178.59 119.49 1.5904
IC C11 O12 P O11 1.4315 119.49 104.93 100.57 1.5835
IC O11 O12 *P O13 1.5835 100.57 -114.66 107.37 1.4782
IC O11 O12 *P O14 1.5835 100.57 115.52 107.48 1.4694
IC O12 P O11 C1 1.5904 100.57 -68.41 122.45 1.4279
IC P O11 C1 C2 1.5835 122.45 113.33 109.83 1.5458
IC C2 O11 *C1 HA 1.5458 109.83 118.28 108.95 1.1134
IC HA O11 *C1 HB 1.1134 108.95 118.31 112.84 1.1153
IC O11 C1 C2 O21 1.4279 109.83 -169.38 109.43 1.4399
IC O21 C1 *C2 C3 1.4399 109.43 -120.76 111.51 1.5508
IC C3 C1 *C2 HS 1.5508 111.51 -116.85 107.06 1.1136
IC C1 C2 O21 C21 1.5458 109.43 123.06 117.42 1.3213
IC C2 O21 C21 C22 1.4399 117.42 163.64 109.74 1.5303
IC C22 O21 *C21 O22 1.5303 109.74 -176.86 126.01 1.2239
IC O21 C21 C22 C23 1.3213 109.74 -113.72 109.53 1.5428
IC C23 C21 *C22 H2R 1.5428 109.53 120.69 110.65 1.1107
IC H2R C21 *C22 H2S 1.1107 110.65 118.78 108.83 1.1092
IC C1 C2 C3 O31 1.5458 111.51 -171.21 111.32 1.4465
IC O31 C2 *C3 HX 1.4465 111.32 -126.25 108.41 1.1159
IC HX C2 *C3 HY 1.1159 108.41 -114.81 107.61 1.1132
IC C2 C3 O31 C31 1.5508 111.32 -117.52 117.59 1.3317
IC C3 O31 C31 C32 1.4465 117.59 -177.93 109.00 1.5333
IC C32 O31 *C31 O32 1.5333 109.00 -179.19 126.42 1.2107
IC O31 C31 C32 C33 1.3317 109.00 -176.00 111.40 1.5440
IC C33 C31 *C32 H2X 1.5440 111.40 120.79 108.80 1.1093
IC H2X C31 *C32 H2Y 1.1093 108.80 118.57 108.70 1.1101
IC C21 C22 C23 C24 1.5303 109.53 168.08 112.83 1.5322
IC C24 C22 *C23 H3R 1.5322 112.83 -119.08 109.34 1.1146
IC H3R C22 *C23 H3S 1.1146 109.34 -118.17 109.92 1.1133
IC C22 C23 C24 C25 1.5428 112.83 179.85 112.06 1.5333
IC C25 C23 *C24 H4R 1.5333 112.06 120.31 108.77 1.1150
IC H4R C23 *C24 H4S 1.1150 108.77 117.76 110.16 1.1129
IC C23 C24 C25 C26 1.5322 112.06 172.89 112.33 1.5326
IC C26 C24 *C25 H5R 1.5326 112.33 -120.75 109.47 1.1135
IC H5R C24 *C25 H5S 1.1135 109.47 -117.79 109.27 1.1131
IC C24 C25 C26 C27 1.5333 112.33 175.30 112.46 1.5342
IC C27 C25 *C26 H6R 1.5342 112.46 121.40 108.94 1.1138
IC H6R C25 *C26 H6S 1.1138 108.94 117.47 109.32 1.1131
IC C25 C26 C27 C28 1.5326 112.46 176.92 112.22 1.5391
IC C28 C26 *C27 H7R 1.5391 112.22 -121.53 108.81 1.1141
IC H7R C26 *C27 H7S 1.1141 108.81 -117.10 108.50 1.1141
IC C26 C27 C28 C29 1.5342 112.22 177.27 111.34 1.5073
IC C29 C27 *C28 H8R 1.5073 111.34 119.85 107.24 1.1140
IC H8R C27 *C28 H8S 1.1140 107.24 115.81 109.06 1.1117
IC C27 C28 C29 C210 1.5391 111.34 -141.40 127.31 1.3462
IC C210 C28 *C29 H91 1.3462 127.31 -176.71 114.35 1.1001
IC C28 C29 C210 C211 1.5073 127.31 1.24 127.43 1.5089
IC C211 C29 *C21 H101 1.5089 127.43 179.21 118.33 1.1011
IC C29 C210 C211 C212 1.3462 127.43 -120.91 110.88 1.5393
IC C212 C210 *C21 H11R 1.5393 110.88 121.06 112.51 1.1124
IC H11R C210 *C21 H11S 1.1124 112.51 119.00 109.81 1.1127
IC C210 C211 C212 C213 1.5089 110.88 -176.36 112.76 1.5347
IC C213 C211 *C21 H12R 1.5347 112.76 -120.93 109.33 1.1142
IC H12R C211 *C21 H12S 1.1142 109.33 -118.17 109.94 1.1138
IC C211 C212 C213 C214 1.5393 112.76 -179.47 112.21 1.5338
IC C214 C212 *C21 H13R 1.5338 112.21 121.29 109.31 1.1130
IC H13R C212 *C21 H13S 1.1130 109.31 117.74 109.05 1.1131
IC C212 C213 C214 C215 1.5347 112.21 -178.99 112.92 1.5339
IC C215 C213 *C21 H14R 1.5339 112.92 -121.37 109.00 1.1134
IC H14R C213 *C21 H14S 1.1134 109.00 -117.34 109.08 1.1132
IC C213 C214 C215 C216 1.5338 112.92 179.95 112.20 1.5339
IC C216 C214 *C21 H15R 1.5339 112.20 121.17 109.14 1.1131
IC H15R C214 *C21 H15S 1.1131 109.14 117.63 109.22 1.1132
IC C214 C215 C216 C217 1.5339 112.20 179.53 112.96 1.5328
IC C217 C215 *C21 H16R 1.5328 112.96 -121.41 109.07 1.1135
IC H16R C215 *C21 H16S 1.1135 109.07 -117.43 109.05 1.1130
IC C215 C216 C217 C218 1.5339 112.96 -179.21 113.03 1.5305
IC C218 C216 *C21 H17R 1.5305 113.03 121.55 108.80 1.1140
IC H17R C216 *C21 H17S 1.1140 108.80 116.88 108.83 1.1142
IC C216 C217 C218 H18R 1.5328 113.03 60.41 110.37 1.1113
IC H18R C217 *C21 H18S 1.1113 110.37 -119.78 110.49 1.1115
IC H18R C217 *C21 H18T 1.1113 110.37 120.07 110.59 1.1111
IC C31 C32 C33 C34 1.5333 111.40 179.66 112.54 1.5345
IC C34 C32 *C33 H3X 1.5345 112.54 -121.73 109.66 1.1133
IC H3X C32 *C33 H3Y 1.1133 109.66 -117.45 109.37 1.1151
IC C32 C33 C34 C35 1.5440 112.54 178.40 112.54 1.5346
IC C35 C33 *C34 H4X 1.5346 112.54 121.75 110.03 1.1131
IC H4X C33 *C34 H4Y 1.1131 110.03 117.75 108.84 1.1139
IC C33 C34 C35 C36 1.5345 112.54 -175.14 112.09 1.5349
IC C36 C34 *C35 H5X 1.5349 112.09 -122.26 109.27 1.1127
IC H5X C34 *C35 H5Y 1.1127 109.27 -117.42 109.08 1.1138
IC C34 C35 C36 C37 1.5346 112.09 174.19 113.84 1.5368
IC C37 C35 *C36 H6X 1.5368 113.84 122.38 109.13 1.1124
IC H6X C35 *C36 H6Y 1.1124 109.13 117.02 108.50 1.1143
IC C35 C36 C37 C38 1.5349 113.84 65.26 113.87 1.5343
IC C38 C36 *C37 H7X 1.5343 113.87 120.83 108.55 1.1137
IC H7X C36 *C37 H7Y 1.1137 108.55 116.91 109.10 1.1132
IC C36 C37 C38 C39 1.5368 113.87 178.14 112.45 1.5354
IC C39 C37 *C38 H8X 1.5354 112.45 121.43 109.97 1.1123
IC H8X C37 *C38 H8Y 1.1123 109.97 117.71 108.91 1.1127
IC C37 C38 C39 C310 1.5343 112.45 -176.66 111.96 1.5320
IC C310 C38 *C39 H9X 1.5320 111.96 120.68 109.20 1.1133
IC H9X C38 *C39 H9Y 1.1133 109.20 117.81 109.34 1.1127
IC C38 C39 C310 C311 1.5354 111.96 178.35 113.81 1.5336
IC C311 C39 *C31 H10X 1.5336 113.81 -120.14 108.22 1.1126
IC H10X C39 *C31 H10Y 1.1126 108.22 -117.07 109.45 1.1132
IC C39 C310 C311 C312 1.5320 113.81 -175.46 111.16 1.5334
IC C312 C310 *C31 H11X 1.5334 111.16 120.27 109.12 1.1138
IC H11X C310 *C31 H11Y 1.1138 109.12 118.20 110.02 1.1119
IC C310 C311 C312 C313 1.5336 111.16 173.60 113.47 1.5330
IC C313 C311 *C31 H12X 1.5330 113.47 -120.74 108.01 1.1140
IC H12X C311 *C31 H12Y 1.1140 108.01 -116.85 109.45 1.1130
IC C311 C312 C313 C314 1.5334 113.47 -174.75 111.86 1.5335
IC C314 C312 *C31 H13X 1.5335 111.86 120.28 108.66 1.1135
IC H13X C312 *C31 H13Y 1.1135 108.66 118.03 110.08 1.1125
IC C312 C313 C314 C315 1.5330 111.86 175.21 113.05 1.5325
IC C315 C313 *C31 H14X 1.5325 113.05 -120.81 108.37 1.1133
IC H14X C313 *C31 H14Y 1.1133 108.37 -117.18 109.40 1.1131
IC C313 C314 C315 C316 1.5335 113.05 -177.76 112.89 1.5300
IC C316 C314 *C31 H15X 1.5300 112.89 121.41 108.55 1.1149
IC H15X C314 *C31 H15Y 1.1149 108.55 117.05 109.21 1.1136
IC C314 C315 C316 H16X 1.5325 112.89 57.15 110.07 1.1113
IC H16X C315 *C31 H16Y 1.1113 110.07 -119.27 110.55 1.1106
IC H16X C315 *C31 H16Z 1.1113 110.07 120.81 110.70 1.1116
!The following two residues (PALM and PCGL) and the two subsequent
!patches (EST1 and EST2) are a modular way to create DPPC.
!See the comments with EST1 and EST2 for more details. adm jr., Jul 99
RESI PALM -1.00 ! Palmitate
! based on methylsulfate
GROUP O1 O2 (-)
ATOM C1 CL 0.62 ! \\ /
ATOM O1 OCL -0.76 ! C1
ATOM O2 OCL -0.76 ! |
! |
ATOM C2 CTL2 -0.28 ! H2A-C2-H2B
ATOM H2A HAL2 0.09 ! |
ATOM H2B HAL2 0.09 ! |
GROUP ! |
ATOM C3 CTL2 -0.18 ! H3A-C3-H3B
ATOM H3A HAL2 0.09 ! |
ATOM H3B HAL2 0.09 ! |
GROUP ! |
ATOM C4 CTL2 -0.18 ! H4A-C4-H4B
ATOM H4A HAL2 0.09 ! |
ATOM H4B HAL2 0.09 ! |
GROUP ! |
ATOM C5 CTL2 -0.18 ! H5A-C5-H5B
ATOM H5A HAL2 0.09 ! |
ATOM H5B HAL2 0.09 ! |
GROUP ! |
ATOM C6 CTL2 -0.18 ! H6A-C6-H6B
ATOM H6A HAL2 0.09 ! |
ATOM H6B HAL2 0.09 ! |
GROUP ! |
ATOM C7 CTL2 -0.18 ! H7A-C7-H7B
ATOM H7A HAL2 0.09 ! |
ATOM H7B HAL2 0.09 ! |
GROUP ! |
ATOM C8 CTL2 -0.18 ! H8A-C8-H8B
ATOM H8A HAL2 0.09 ! |
ATOM H8B HAL2 0.09 ! |
GROUP ! |
ATOM C9 CTL2 -0.18 ! H9A-C9-H9B
ATOM H9A HAL2 0.09 ! |
ATOM H9B HAL2 0.09 ! |
GROUP ! |
ATOM C10 CTL2 -0.18 ! H10A-C10-H10B
ATOM H10A HAL2 0.09 ! |
ATOM H10B HAL2 0.09 ! |
GROUP ! |
ATOM C11 CTL2 -0.18 ! H11A-C11-H11B
ATOM H11A HAL2 0.09 ! |
ATOM H11B HAL2 0.09 ! |
GROUP ! |
ATOM C12 CTL2 -0.18 ! H12A-C12-H12B
ATOM H12A HAL2 0.09 ! |
ATOM H12B HAL2 0.09 ! |
GROUP ! |
ATOM C13 CTL2 -0.18 ! H13A-C13-H13B
ATOM H13A HAL2 0.09 ! |
ATOM H13B HAL2 0.09 ! |
GROUP ! |
ATOM C14 CTL2 -0.18 ! H14A-C14-H14B
ATOM H14A HAL2 0.09 ! |
ATOM H14B HAL2 0.09 ! |
GROUP ! |
ATOM C15 CTL2 -0.18 ! H15A-C15-H15B
ATOM H15A HAL2 0.09 ! |
ATOM H15B HAL2 0.09 ! |
GROUP ! |
ATOM C16 CTL3 -0.27 ! H16A-C16-H16B
ATOM H16A HAL3 0.09 ! |
ATOM H16B HAL3 0.09 ! H16C
ATOM H16C HAL3 0.09 !
BOND C1 O1 C1 O2
BOND C1 C2 C2 H2A C2 H2B
BOND C2 C3 C3 H3A C3 H3B
BOND C3 C4 C4 H4A C4 H4B
BOND C4 C5 C5 H5A C5 H5B
BOND C5 C6 C6 H6A C6 H6B
BOND C6 C7 C7 H7A C7 H7B
BOND C7 C8 C8 H8A C8 H8B
BOND C8 C9 C9 H9A C9 H9B
BOND C9 C10 C10 H10A C10 H10B
BOND C10 C11 C11 H11A C11 H11B
BOND C11 C12 C12 H12A C12 H12B
BOND C12 C13 C13 H13A C13 H13B
BOND C13 C14 C14 H14A C14 H14B
BOND C14 C15 C15 H15A C15 H15B
BOND C15 C16 C16 H16A C16 H16B C16 H16C
IMPR C1 O1 C2 O2
ACCE O1
ACCE O2
!IC table insufficent to create cartesian coordinates
IC O1 C2 *C1 O2 0.0000 0.00 180.00 0.00 0.0000
IC O1 C1 C2 C3 0.0000 0.00 180.00 0.00 0.0000
IC C3 C1 *C2 H2A 0.0000 0.00 120.00 0.00 0.0000
IC H2A C1 *C2 H2B 0.0000 0.00 -120.00 0.00 0.0000
IC C1 C2 C3 C4 0.0000 0.00 180.00 0.00 0.0000
IC C4 C2 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000
IC H3A C2 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000
IC C2 C3 C4 C5 0.0000 0.00 180.00 0.00 0.0000
IC C5 C3 *C4 H4A 0.0000 0.00 120.00 0.00 0.0000
IC H4A C3 *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000
IC C3 C4 C5 C6 0.0000 0.00 180.00 0.00 0.0000
IC C6 C4 *C5 H5A 0.0000 0.00 120.00 0.00 0.0000
IC H5A C4 *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000
IC C4 C5 C6 C7 0.0000 0.00 180.00 0.00 0.0000
IC C7 C5 *C6 H6A 0.0000 0.00 120.00 0.00 0.0000
IC H6A C5 *C6 H6B 0.0000 0.00 -120.00 0.00 0.0000
IC C5 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000
IC C8 C6 *C7 H7A 0.0000 0.00 120.00 0.00 0.0000
IC H7A C6 *C7 H7B 0.0000 0.00 -120.00 0.00 0.0000
IC C6 C7 C8 C9 0.0000 0.00 180.00 0.00 0.0000
IC C9 C7 *C8 H8A 0.0000 0.00 120.00 0.00 0.0000
IC H8A C7 *C8 H8B 0.0000 0.00 -120.00 0.00 0.0000
IC C7 C8 C9 C10 0.0000 0.00 180.00 0.00 0.0000
IC C10 C8 *C9 H9A 0.0000 0.00 120.00 0.00 0.0000
IC H9A C8 *C9 H9B 0.0000 0.00 -120.00 0.00 0.0000
IC C8 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000
IC C11 C9 *C10 H10A 0.0000 0.00 120.00 0.00 0.0000
IC H10A C9 *C10 H10B 0.0000 0.00 -120.00 0.00 0.0000
IC C9 C10 C11 C12 0.0000 0.00 180.00 0.00 0.0000
IC C12 C10 *C11 H11A 0.0000 0.00 120.00 0.00 0.0000
IC H11A C10 *C11 H11B 0.0000 0.00 -120.00 0.00 0.0000
IC C10 C11 C12 C13 0.0000 0.00 180.00 0.00 0.0000
IC C13 C11 *C12 H12A 0.0000 0.00 120.00 0.00 0.0000
IC H12A C11 *C12 H12B 0.0000 0.00 -120.00 0.00 0.0000
IC C11 C12 C13 C14 0.0000 0.00 180.00 0.00 0.0000
IC C14 C12 *C13 H13A 0.0000 0.00 120.00 0.00 0.0000
IC H13A C12 *C13 H13B 0.0000 0.00 -120.00 0.00 0.0000
IC C12 C13 C14 C15 0.0000 0.00 180.00 0.00 0.0000
IC C15 C13 *C14 H14A 0.0000 0.00 120.00 0.00 0.0000
IC H14A C13 *C14 H14B 0.0000 0.00 -120.00 0.00 0.0000
IC C13 C14 C15 C16 0.0000 0.00 180.00 0.00 0.0000
IC C16 C14 *C15 H15A 0.0000 0.00 120.00 0.00 0.0000
IC H15A C14 *C15 H15B 0.0000 0.00 -120.00 0.00 0.0000
IC C14 C15 C16 H16A 0.0000 0.00 180.00 0.00 0.0000
IC H16A C15 *C16 H16B 0.0000 0.00 120.00 0.00 0.0000
IC H16A C15 *C16 H16C 0.0000 0.00 -120.00 0.00 0.0000
RESI PCGL 0.00 ! glycerolphosphorylcholine
! nomenclature for creation of DPPC
GROUP ! from PALM and PCGL via patches EST1 and EST2
ATOM N NTL -0.60 !
ATOM C5 CTL2 -0.10 ! |
ATOM C6 CTL5 -0.35 ! -C7-
ATOM C7 CTL5 -0.35 ! |
ATOM C8 CTL5 -0.35 ! | | |
ATOM H5A HL 0.25 ! -C6---N---C8- (+)
ATOM H5B HL 0.25 ! | | |
ATOM H6A HL 0.25 ! |
ATOM H6B HL 0.25 ! -C5-
ATOM H6C HL 0.25 ! |
ATOM H7A HL 0.25 ! |
ATOM H7B HL 0.25 ! |
ATOM H7C HL 0.25 ! |
ATOM H8A HL 0.25 ! |
ATOM H8B HL 0.25 ! |
ATOM H8C HL 0.25 ! |
GROUP ! |
ATOM C4 CTL2 -0.08 ! |
ATOM H4A HAL2 0.09 ! H4A---C4---H4B
ATOM H4B HAL2 0.09 ! |
ATOM P PL 1.50 ! (-) OP3 OP2
ATOM OP3 O2L -0.78 ! \ /
ATOM OP4 O2L -0.78 ! P (+)
ATOM OP1 OSL -0.57 ! / \
ATOM OP2 OSL -0.57 ! (-) OP4 OP1
ATOM C3 CTL2 -0.08 ! |
ATOM H3A HAL2 0.09 ! H3A-C3-H3B
ATOM H3B HAL2 0.09 ! |
GROUP ! |
ATOM C2 CTL1 0.14 ! |
ATOM H2A HAL1 0.09 ! H2A-C2-O2-H2
ATOM O2 OHL -0.66 ! |
ATOM H2 HOL 0.43 ! |
GROUP ! |
ATOM C1 CTL2 0.05 ! |
ATOM H1A HAL2 0.09 ! H1A-C1-O1-H1
ATOM H1B HAL2 0.09 ! |
ATOM O1 OHL -0.66 ! H1B
ATOM H1 HOL 0.43 !
BOND N C5 N C6 N C7 N C8
BOND C5 C4 C4 OP2 OP2 P P OP1
BOND P OP3 P OP4
BOND OP1 C3 C3 C2 C2 C1
BOND C2 O2 C1 O1
BOND O1 H1 O2 H2
BOND C1 H1A C1 H1B
BOND C2 H2A
BOND C3 H3A C3 H3B
BOND C4 H4A C4 H4B
BOND C5 H5A C5 H5B
BOND C6 H6A C6 H6B C6 H6C
BOND C7 H7A C7 H7B C7 H7C
BOND C8 H8A C8 H8B C8 H8C
!IC table insufficent to create cartesian coordinates
IC C6 C5 *N C7 0.0000 0.00 120.00 0.00 0.0000
IC C6 C5 *N C8 0.0000 0.00 -120.00 0.00 0.0000
IC C6 N C5 C4 0.0000 0.00 180.00 0.00 0.0000
IC C4 N *C5 H5A 0.0000 0.00 120.00 0.00 0.0000
IC C4 N *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000
IC C5 N C6 H6A 0.0000 0.00 180.00 0.00 0.0000
IC H6A N *C6 H6B 0.0000 0.00 120.00 0.00 0.0000
IC H6A N *C6 H6C 0.0000 0.00 -120.00 0.00 0.0000
IC C5 N C7 H7A 0.0000 0.00 180.00 0.00 0.0000
IC H7A N *C7 H7B 0.0000 0.00 120.00 0.00 0.0000
IC H7A N *C7 H7C 0.0000 0.00 -120.00 0.00 0.0000
IC C5 N C8 H8A 0.0000 0.00 180.00 0.00 0.0000
IC H8A N *C8 H8B 0.0000 0.00 120.00 0.00 0.0000
IC H8A N *C8 H8C 0.0000 0.00 -120.00 0.00 0.0000
IC N C5 C4 OP2 0.0000 0.00 180.00 0.00 0.0000
IC OP2 C5 *C4 H4A 0.0000 0.00 120.00 0.00 0.0000
IC OP2 C5 *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000
IC C5 C4 OP2 P 0.0000 0.00 180.00 0.00 0.0000
IC C4 OP2 P OP1 0.0000 0.00 180.00 0.00 0.0000
IC OP1 OP2 *P OP3 0.0000 0.00 120.00 0.00 0.0000
IC OP1 OP2 *P OP4 0.0000 0.00 -120.00 0.00 0.0000
IC OP2 P OP1 C3 0.0000 0.00 180.00 0.00 0.0000
IC P OP1 C3 C2 0.0000 0.00 180.00 0.00 0.0000
IC C2 OP1 *C3 H3A 0.0000 0.00 120.00 0.00 0.0000
IC C2 OP1 *C3 H3B 0.0000 0.00 -120.00 0.00 0.0000
IC OP1 C3 C2 C1 0.0000 0.00 180.00 0.00 0.0000
IC C1 C3 *C2 O2 0.0000 0.00 120.00 0.00 0.0000
IC C1 C3 *C2 H2A 0.0000 0.00 -120.00 0.00 0.0000
IC C3 C2 O2 H2 0.0000 0.00 180.00 0.00 0.0000
IC C3 C2 C1 O1 0.0000 0.00 180.00 0.00 0.0000
IC O1 C2 *C1 H1A 0.0000 0.00 120.00 0.00 0.0000
IC O1 C2 *C1 H1B 0.0000 0.00 -120.00 0.00 0.0000
IC C2 C1 O1 H1 0.0000 0.00 180.00 0.00 0.0000
RESI DPPC 0.00 ! Palmitate
!
GROUP
ATOM C1 CTL5 -0.35 ! |
ATOM H1C HL 0.25 ! -C1-
ATOM H1A HL 0.25 ! |
ATOM H1B HL 0.25 ! |
! |
ATOM C2 CTL5 -0.35 ! | | |
ATOM H2A HL 0.25 ! -C2---NT---C3-
ATOM H2B HL 0.25 ! | | |
ATOM H2C HL 0.25 ! |
! |
ATOM C3 CTL5 -0.35 ! |
ATOM H3A HL 0.25 ! |
ATOM H3B HL 0.25 ! |
ATOM H3C HL 0.25 ! |
! |
ATOM NT NTL -0.60 ! |
! |
ATOM C4 CTL2 -0.10 ! |
ATOM H4A HL 0.25 ! -H4A---C4---H4B- (+)
ATOM H4B HL 0.25 ! |
! |
GROUP ! |
ATOM C5 CTL2 -0.08 ! |
ATOM H5A HAL2 0.09 ! H5A---C5---H5B
ATOM H5B 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 C6 CTL2 -0.08 ! |
ATOM H6A HAL2 0.09 ! H6A-C6-H6B
ATOM H6B HAL2 0.09 ! |
GROUP ! |
ATOM C7 CTL1 0.04 ! |
ATOM H7A HAL1 0.09 ! H2A-C7-O7-(H2)PALM1
ATOM O7 OSL -0.34 ! |
GROUP ! |
ATOM C8 CTL2 -0.05 ! |
ATOM H8A HAL2 0.09 ! H8A-C8-O8-(H1)PALM2
ATOM H8B HAL2 0.09 ! |
ATOM O8 OSL -0.34 ! H8B
! PALM1
GROUP ! O1 (O7 (-)) PCGL-O7
ATOM C9 CL 0.63 ! \\ /
ATOM O1 OBL -0.52 ! C9
GROUP ! |
ATOM C10 CTL2 -0.08 ! 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 CTL2 -0.18 ! H16A-C16-H16B
ATOM H16A HAL2 0.09 ! |
ATOM H16B HAL2 0.09 ! |
GROUP ! |
ATOM C17 CTL2 -0.18 ! H17A-C17-H17B
ATOM H17A HAL2 0.09 ! |
ATOM H17B HAL2 0.09 ! |
GROUP ! |
ATOM C18 CTL2 -0.18 ! H18A-C18-H18B
ATOM H18A HAL2 0.09 ! |
ATOM H18B HAL2 0.09 ! |
GROUP ! |
ATOM C19 CTL2 -0.18 ! H19A-C19-H19B
ATOM H19A HAL2 0.09 ! |
ATOM H19B HAL2 0.09 ! |
GROUP ! |
ATOM C20 CTL2 -0.18 ! H20A-C20-H20B
ATOM H20A HAL2 0.09 ! |
ATOM H20B HAL2 0.09 ! |
GROUP ! |
ATOM C21 CTL2 -0.18 ! H21A-C21-H21B
ATOM H21A HAL2 0.09 ! |
ATOM H21B HAL2 0.09 ! |
GROUP ! |
ATOM C22 CTL2 -0.18 ! H22A-C22-H22B
ATOM H22A HAL2 0.09 ! |
ATOM H22B HAL2 0.09 ! |
GROUP ! |
ATOM C23 CTL2 -0.18 ! H23A-C23-H23B
ATOM H23A HAL2 0.09 ! |
ATOM H23B HAL2 0.09 ! |
GROUP ! |
ATOM C24 CTL3 -0.27 ! H24A-C24-H24B
ATOM H24A HAL3 0.09 ! |
ATOM H24B HAL3 0.09 ! H24C
ATOM H24C HAL3 0.09 !
!
! PALM2
GROUP ! O2 (O1 (-)) PCGL-O1
ATOM C25 CL 0.63 ! \\ /
ATOM O2 OBL -0.52 ! C25
! |
ATOM C26 CTL2 -0.08 ! H26A-C26-H26B
ATOM H26A HAL2 0.09 ! |
ATOM H26B HAL2 0.09 ! |
GROUP ! |
ATOM C27 CTL2 -0.18 ! H27A-C27-H27B
ATOM H27A HAL2 0.09 ! |
ATOM H27B HAL2 0.09 ! |
GROUP ! |
ATOM C28 CTL2 -0.18 ! H28A-C28-H28B
ATOM H28A HAL2 0.09 ! |
ATOM H28B HAL2 0.09 ! |
GROUP ! |
ATOM C29 CTL2 -0.18 ! H29A-C29-H29B
ATOM H29A HAL2 0.09 ! |
ATOM H29B HAL2 0.09 ! |
GROUP ! |
ATOM C30 CTL2 -0.18 ! H30A-C30-H30B
ATOM H30A HAL2 0.09 ! |
ATOM H30B HAL2 0.09 ! |
GROUP ! |
ATOM C31 CTL2 -0.18 ! H31A-C31-H31B
ATOM H31A HAL2 0.09 ! |
ATOM H31B HAL2 0.09 ! |
GROUP ! |
ATOM C32 CTL2 -0.18 ! H32A-C32-H32B
ATOM H32A HAL2 0.09 ! |
ATOM H32B HAL2 0.09 ! |
GROUP ! |
ATOM C33 CTL2 -0.18 ! H33A-C33-H33B
ATOM H33A HAL2 0.09 ! |
ATOM H33B HAL2 0.09 ! |
GROUP ! |
ATOM C34 CTL2 -0.18 ! H34A-C34-H34B
ATOM H34A HAL2 0.09 ! |
ATOM H34B HAL2 0.09 ! |
GROUP ! |
ATOM C35 CTL2 -0.18 ! H35A-C35-H35B
ATOM H35A HAL2 0.09 ! |
ATOM H35B HAL2 0.09 ! |
GROUP ! |
ATOM C36 CTL2 -0.18 ! H36A-C36-H36B
ATOM H36A HAL2 0.09 ! |
ATOM H36B HAL2 0.09 ! |
GROUP ! |
ATOM C37 CTL2 -0.18 ! H37A-C37-H37B
ATOM H37A HAL2 0.09 ! |
ATOM H37B HAL2 0.09 ! |
GROUP ! |
ATOM C38 CTL2 -0.18 ! H38A-C38-H38B
ATOM H38A HAL2 0.09 ! |
ATOM H38B HAL2 0.09 ! |
GROUP ! |
ATOM C39 CTL2 -0.18 ! H39A-C39-H39B
ATOM H39A HAL2 0.09 ! |
ATOM H39B HAL2 0.09 ! |
GROUP ! |
ATOM C40 CTL3 -0.27 ! H40A-C40-H40B
ATOM H40A HAL3 0.09 ! |
ATOM H40B HAL3 0.09 ! H40C
ATOM H40C HAL3 0.09 !
!
!PCGL
BOND NT C1 NT C2 NT C3 NT C4
BOND C4 C5 C5 OP2 OP2 P P OP1
BOND P OP3 P OP4
BOND OP1 C6 C6 C7 C7 C8
BOND C7 O7 C8 O8
BOND C1 H1A C1 H1B C1 H1C
BOND C2 H2A C2 H2B C2 H2C
BOND C3 H3A C3 H3B C3 H3C
BOND C4 H4A C4 H4B
BOND C5 H5A C5 H5B
BOND C6 H6A C6 H6B
BOND C7 H7A
BOND C8 H8A C8 H8B
!PALM 1
DOUBLE C9 O1
BOND C9 C10 C9 O7 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
BOND C16 C17 C17 H17A C17 H17B
BOND C17 C18 C18 H18A C18 H18B
BOND C18 C19 C19 H19A C19 H19B
BOND C19 C20 C20 H20A C20 H20B
BOND C20 C21 C21 H21A C21 H21B
BOND C21 C22 C22 H22A C22 H22B
BOND C22 C23 C23 H23A C23 H23B
BOND C23 C24 C24 H24A C24 H24B C24 H24C
!PALM 2
DOUBLE C25 O2
BOND C25 C26 C25 O8 C26 H26A C26 H26B
BOND C26 C27 C27 H27A C27 H27B
BOND C27 C28 C28 H28A C28 H28B
BOND C28 C29 C29 H29A C29 H29B
BOND C29 C30 C30 H30A C30 H30B
BOND C30 C31 C31 H31A C31 H31B
BOND C31 C32 C32 H32A C32 H32B
BOND C32 C33 C33 H33A C33 H33B
BOND C33 C34 C34 H34A C34 H34B
BOND C34 C35 C35 H35A C35 H35B
BOND C35 C36 C36 H36A C36 H36B
BOND C36 C37 C37 H37A C37 H37B
BOND C37 C38 C38 H38A C38 H38B
BOND C38 C39 C39 H39A C39 H39B
BOND C39 C40 C40 H40A C40 H40B C40 H40C
!PASTE BOTH
IMPR C9 C10 O7 O1 C25 O8 C26 O2
IMPR C7 O7 C8 C6
IMPR P OP1 OP4 OP3
IMPR NT C4 C3 C2
ACCE O1
ACCE O2
END
!PSGL
!IC table insufficent to create cartesian coordinates
IC C2 C5 *NT C1 0.0000 0.00 120.00 0.00 0.0000
IC C2 C5 *NT C3 0.0000 0.00 -120.00 0.00 0.0000
IC C2 NT C4 C5 0.0000 0.00 180.00 0.00 0.0000
IC C5 NT *C4 H4A 0.0000 0.00 120.00 0.00 0.0000
IC C5 NT *C4 H4B 0.0000 0.00 -120.00 0.00 0.0000
IC C4 NT C2 H2A 0.0000 0.00 180.00 0.00 0.0000
IC H2A NT *C2 H2B 0.0000 0.00 120.00 0.00 0.0000
IC H2A NT *C2 H2C 0.0000 0.00 -120.00 0.00 0.0000
IC C4 NT C1 H1A 0.0000 0.00 180.00 0.00 0.0000
IC H1A NT *C1 H1B 0.0000 0.00 120.00 0.00 0.0000
IC H1A NT *C1 H1C 0.0000 0.00 -120.00 0.00 0.0000
IC C4 NT C3 H3A 0.0000 0.00 180.00 0.00 0.0000
IC H3A NT *C3 H3B 0.0000 0.00 120.00 0.00 0.0000
IC H3A NT *C3 H3C 0.0000 0.00 -120.00 0.00 0.0000
IC NT C4 C5 OP2 0.0000 0.00 180.00 0.00 0.0000
IC OP2 C5 *C5 H5A 0.0000 0.00 120.00 0.00 0.0000
IC OP2 C5 *C5 H5B 0.0000 0.00 -120.00 0.00 0.0000
IC C4 C5 OP2 P 0.0000 0.00 180.00 0.00 0.0000
IC C5 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 C6 0.0000 0.00 180.00 0.00 0.0000
IC P OP1 C6 C7 0.0000 0.00 180.00 0.00 0.0000
IC C7 OP1 *C6 H6A 0.0000 0.00 120.00 0.00 0.0000
IC C7 OP1 *C6 H6B 0.0000 0.00 -120.00 0.00 0.0000
IC OP1 C6 C7 C8 0.0000 0.00 180.00 0.00 0.0000
IC C8 C6 *C7 O2 0.0000 0.00 120.00 0.00 0.0000
IC C8 C6 *C7 H7A 0.0000 0.00 -120.00 0.00 0.0000
!IC C6 C7 O7 H2 0.0000 0.00 180.00 0.00 0.0000
IC C6 C7 C8 O7 0.0000 0.00 180.00 0.00 0.0000
IC O8 C7 *C8 H8A 0.0000 0.00 120.00 0.00 0.0000
IC O8 C7 *C8 H8B 0.0000 0.00 -120.00 0.00 0.0000
!IC C2 C1 O7 H1 0.0000 0.00 180.00 0.00 0.0000
!PALM1
!IC table insufficent to create cartesian coordinates
IC O1 C10 *C9 O7 0.0000 0.00 180.00 0.00 0.0000
IC O11 C9 C10 C11 0.0000 0.00 180.00 0.00 0.0000
IC C3 C9 *C10 H10A 0.0000 0.00 120.00 0.00 0.0000
IC H2A 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 C17 0.0000 0.00 180.00 0.00 0.0000
IC C17 C15 *C16 H16A 0.0000 0.00 120.00 0.00 0.0000
IC H16A C15 *C16 H16B 0.0000 0.00 -120.00 0.00 0.0000
IC C15 C16 C17 C18 0.0000 0.00 180.00 0.00 0.0000
IC C18 C16 *C17 H17A 0.0000 0.00 120.00 0.00 0.0000
IC H17A C16 *C17 H17B 0.0000 0.00 -120.00 0.00 0.0000
IC C16 C17 C18 C19 0.0000 0.00 180.00 0.00 0.0000
IC C19 C17 *C18 H18A 0.0000 0.00 120.00 0.00 0.0000
IC H18A C17 *C18 H18B 0.0000 0.00 -120.00 0.00 0.0000
IC C17 C18 C19 C20 0.0000 0.00 180.00 0.00 0.0000
IC C20 C18 *C19 H19A 0.0000 0.00 120.00 0.00 0.0000
IC H19A C18 *C19 H19B 0.0000 0.00 -120.00 0.00 0.0000
IC C18 C19 C20 C21 0.0000 0.00 180.00 0.00 0.0000
IC C21 C19 *C20 H20A 0.0000 0.00 120.00 0.00 0.0000
IC H20A C19 *C20 H20B 0.0000 0.00 -120.00 0.00 0.0000
IC C19 C20 C21 C12 0.0000 0.00 180.00 0.00 0.0000
IC C22 C20 *C21 H21A 0.0000 0.00 120.00 0.00 0.0000
IC H21A C20 *C21 H21B 0.0000 0.00 -120.00 0.00 0.0000
IC C20 C21 C22 C23 0.0000 0.00 180.00 0.00 0.0000
IC C23 C21 *C22 H22A 0.0000 0.00 120.00 0.00 0.0000
IC H22A C21 *C22 H22B 0.0000 0.00 -120.00 0.00 0.0000
IC C21 C22 C23 C24 0.0000 0.00 180.00 0.00 0.0000
IC C24 C22 *C23 H23A 0.0000 0.00 120.00 0.00 0.0000
IC H23A C22 *C23 H23B 0.0000 0.00 -120.00 0.00 0.0000
IC C22 C23 C24 H24A 0.0000 0.00 180.00 0.00 0.0000
IC H24A C23 *C24 H24B 0.0000 0.00 120.00 0.00 0.0000
IC H24A C23 *C24 H24C 0.0000 0.00 -120.00 0.00 0.0000
!PALM2
!IC table insufficent to create cartesian coordinates
IC O2 C26 *C25 O8 0.0000 0.00 180.00 0.00 0.0000
IC O12 C25 C26 C27 0.0000 0.00 180.00 0.00 0.0000
IC C27 C25 *C26 H26A 0.0000 0.00 120.00 0.00 0.0000
IC H26A C25 *C26 H26B 0.0000 0.00 -120.00 0.00 0.0000
IC C25 C26 C27 C28 0.0000 0.00 180.00 0.00 0.0000
IC C28 C26 *C27 H27A 0.0000 0.00 120.00 0.00 0.0000
IC H27A C26 *C27 H27B 0.0000 0.00 -120.00 0.00 0.0000
IC C26 C27 C28 C29 0.0000 0.00 180.00 0.00 0.0000
IC C29 C27 *C28 H28A 0.0000 0.00 120.00 0.00 0.0000
IC H28A C27 *C28 H28B 0.0000 0.00 -120.00 0.00 0.0000
IC C27 C28 C29 C30 0.0000 0.00 180.00 0.00 0.0000
IC C30 C28 *C29 H29A 0.0000 0.00 120.00 0.00 0.0000
IC H29A C28 *C29 H29B 0.0000 0.00 -120.00 0.00 0.0000
IC C28 C29 C30 C31 0.0000 0.00 180.00 0.00 0.0000
IC C31 C29 *C30 H30A 0.0000 0.00 120.00 0.00 0.0000
IC H30A C29 *C30 H30B 0.0000 0.00 -120.00 0.00 0.0000
IC C29 C30 C31 C32 0.0000 0.00 180.00 0.00 0.0000
IC C32 C30 *C31 H31A 0.0000 0.00 120.00 0.00 0.0000
IC H31A C30 *C31 H31B 0.0000 0.00 -120.00 0.00 0.0000
IC C30 C31 C32 C33 0.0000 0.00 180.00 0.00 0.0000
IC C33 C31 *C32 H32A 0.0000 0.00 120.00 0.00 0.0000
IC H32A C31 *C32 H32B 0.0000 0.00 -120.00 0.00 0.0000
IC C31 C32 C33 C34 0.0000 0.00 180.00 0.00 0.0000
IC C34 C32 *C33 H33A 0.0000 0.00 120.00 0.00 0.0000
IC H33A C32 *C33 H33B 0.0000 0.00 -120.00 0.00 0.0000
IC C32 C33 C34 C35 0.0000 0.00 180.00 0.00 0.0000
IC C35 C33 *C34 H34A 0.0000 0.00 120.00 0.00 0.0000
IC H34A C33 *C34 H34B 0.0000 0.00 -120.00 0.00 0.0000
IC C33 C34 C35 C36 0.0000 0.00 180.00 0.00 0.0000
IC C36 C34 *C35 H35A 0.0000 0.00 120.00 0.00 0.0000
IC H35A C34 *C35 H35B 0.0000 0.00 -120.00 0.00 0.0000
IC C34 C35 C36 C37 0.0000 0.00 180.00 0.00 0.0000
IC C37 C35 *C36 H36A 0.0000 0.00 120.00 0.00 0.0000
IC H36A C35 *C36 H36B 0.0000 0.00 -120.00 0.00 0.0000
IC C35 C36 C37 C38 0.0000 0.00 180.00 0.00 0.0000
IC C38 C36 *C37 H37A 0.0000 0.00 120.00 0.00 0.0000
IC H37A C36 *C37 H37B 0.0000 0.00 -120.00 0.00 0.0000
IC C36 C37 C38 C39 0.0000 0.00 180.00 0.00 0.0000
IC C39 C37 *C38 H38A 0.0000 0.00 120.00 0.00 0.0000
IC H38A C37 *C38 H38B 0.0000 0.00 -120.00 0.00 0.0000
IC C37 C38 C39 C40 0.0000 0.00 180.00 0.00 0.0000
IC C40 C38 *C39 H39A 0.0000 0.00 120.00 0.00 0.0000
IC H39A C38 *C39 H39B 0.0000 0.00 -120.00 0.00 0.0000
IC C38 C39 C40 H40A 0.0000 0.00 180.00 0.00 0.0000
IC H40A C39 *C40 H40B 0.0000 0.00 120.00 0.00 0.0000
IC H40A C39 *C40 H40C 0.0000 0.00 -120.00 0.00 0.0000
END
- application/vnd.palm attachment: dppc_alsalas.pdb
- application/vnd.palm attachment: dppc_4.pdb
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