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top_all36_cgenff.rtf
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top_all36_cgenff.rtf
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* \\\\\\\ CHARMM36 All-Hydrogen Lipid Topology File ///////
* All comments and questions should be submitted to the
* parameter forum at the CHARMM website: www.charmm.org
*
36 1
!updated 2016/8. see toppar_all.history.
!NOTE: Reordering of atoms in the choline region of the PC lipids as
!requried for the domain decomposition code in CHARMM. This will not
!change the energies/forces, but PSFs generated with the previous
!lipid toppar files may not work. To overcome this a toppar stream
!file, toppar_all36_lipid_orig_pc_atom_order.str, has been created
!which contains the original atom ordering. August 2012
!
!references
!
!Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph
!W. O'Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor
!Vorobyov, Alexander D. MacKerell, Jr. and Richard W. Pastor "Update of
!the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six
!Lipid Types" J. Phys. Chem. B 2010, 114, 7830-7843
!
! PUFA Modifications
!Jeffery B. Klauda, Viviana Monje, Taehoon Kim, and Wonpil Im. "Improving
!the CHARMM Force Field for Polyunsaturated Fatty Acid Chains" J. Phys. Chem. B.
!2012 ASAP http://dx.doi.org/10.1021/jp304056p
!Atom nomenclature is based on that of Sundaralingan, M.,
!Ann. N.Y. Acad. Sci. USA, 195:324-355, 1972
!see lipid_convert.tgz for information on nomenclature conversion
!Renaming of atom types by Rick Venable due to switching to the
!nomenclature of Sundaralingan, M., Ann. N.Y. Acad. Sci. USA,
!195:324-355, 1972
!
!1) toppar_all36_lipid_oldxopc.str
!2) convert_lipid_c27_c36_xopc.str
!
!The above stream files have 1) the old definitions of DOPC
!and POPC, which replace the new definitions when used. The second
!stream file does a RENAME conversion, which allows old coord sets to
!be updated to the new "all36_lipid" convention.
MASS -1 HL 1.00800 H ! polar H (equivalent to protein H)
MASS -1 HCL 1.00800 H ! charged H for PE (equivalent to protein HC)
MASS -1 HOL 1.00800 H ! Nucleic acid phosphate hydroxyl proton
MASS -1 HAL1 1.00800 H ! alphatic proton
MASS -1 HAL2 1.00800 H ! alphatic proton
MASS -1 HAL3 1.00800 H ! alphatic proton
MASS -1 HEL1 1.00800 H ! for alkene; RHC=CR
MASS -1 HEL2 1.00800 H ! for alkene; H2C=CR. Currently unused.
MASS -1 HBL 1.00800 H ! POPS SER backbone H
MASS -1 CL 12.01100 C ! carbonyl C (acetic acid/methyl acetate)
MASS -1 CTL1 12.01100 C ! sp3 carbon with 1 H (-CH1-)
MASS -1 CTL2 12.01100 C ! carbon of methylene group (-CH2-)
MASS -1 CTL3 12.01100 C ! carbon of methyl group (-CH3)
MASS -1 CTL5 12.01100 C ! carbon of methyl group (-CH3) for tetramethylammonium
MASS -1 CEL1 12.01100 C ! for alkene; RHC=CR
MASS -1 CEL2 12.01100 C ! for alkene; H2C=CR. Currently unused.
MASS -1 CCL 12.01100 C ! for POPS
MASS -1 NTL 14.00700 N ! ammonium nitrogen
MASS -1 NH3L 14.00700 N ! nitrogen phosphatidylethanolamine
MASS -1 OBL 15.99940 O ! acetic acid carboxyl oxygen (e. to protein OB)
MASS -1 OCL 15.99940 O ! acetate oxygen
MASS -1 OSL 15.99940 O ! ester oxygen
MASS -1 O2L 15.99940 O ! Nucleic acid =O in phosphate or sulfate
MASS -1 OHL 15.99940 O ! Nucleic acid phosphate hydroxyl oxygen
MASS -1 OSLP 15.99940 O ! Phosphate oxygen, to avoid conflict with methylacetate type O
MASS -1 PL 30.97400 P ! phosphorus
MASS -1 SL 32.06000 S ! Sulfate sulfur
MASS -1 CRL1 12.01100 C ! sp3 carbon with 1 H on a ring (-CH1-) for sterols
MASS -1 CRL2 12.01100 C ! carbon of methylene group on a ring (-CH2-) for sterols
DEFA FIRS none LAST none
AUTOGENERATE ANGLES DIHEDRALS PATCH
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 OSLP -0.57 ! / \ alpha2
ATOM O12 OSLP -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 0.08 ! HX---C3---HY
ATOM HX HAL2 0.09 ! |
ATOM HY HAL2 0.09 ! | gamma1
ATOM O31 OSL -0.49 ! O32 O31
ATOM C31 CL 0.90 ! \\ / gamma2
ATOM O32 OBL -0.63 ! C31
ATOM C32 CTL2 -0.22 ! | 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
!IC table from IC generated, minimized geometry
IC C13 N C12 C11 1.5007 109.16 60.77 118.01 1.5532
IC C13 C12 *N C14 1.5007 109.16 118.95 109.93 1.4962
IC C13 C12 *N C15 1.5007 109.16 -118.66 109.79 1.4970
IC C12 N C13 H13A 1.5283 109.16 -176.25 113.90 1.0739
IC H13A N *C13 H13B 1.0739 113.90 -125.02 111.72 1.0902
IC H13A N *C13 H13C 1.0739 113.90 122.64 109.30 1.0955
IC C12 N C14 H14A 1.5283 109.93 -59.08 109.81 1.0869
IC H14A N *C14 H14B 1.0869 109.81 -118.79 110.87 1.0821
IC H14A N *C14 H14C 1.0869 109.81 119.79 111.30 1.0813
IC C12 N C15 H15A 1.5283 109.79 177.61 111.54 1.0806
IC H15A N *C15 H15B 1.0806 111.54 -118.99 108.75 1.0881
IC H15A N *C15 H15C 1.0806 111.54 122.56 111.42 1.0805
IC C13 N C12 C11 1.5007 109.16 60.77 118.01 1.5532
IC C11 N *C12 H12A 1.5532 118.01 -118.57 109.22 1.0958
IC H12A N *C12 H12B 1.0958 109.22 -116.61 110.32 1.0792
IC N C12 C11 O12 1.5283 118.01 -64.38 111.82 1.4242
IC O12 C12 *C11 H11A 1.4242 111.82 -122.02 109.25 1.1168
IC H11A C12 *C11 H11B 1.1168 109.25 -116.56 110.01 1.1107
IC C12 C11 O12 P 1.5532 111.82 -63.93 119.44 1.5956
IC C11 O12 P O11 1.4242 119.44 -108.05 103.40 1.5764
IC O11 O12 *P O13 1.5764 103.40 -117.37 105.77 1.4773
IC O11 O12 *P O14 1.5764 103.40 117.10 108.18 1.4806
IC O12 P O11 C1 1.5956 103.40 -60.59 122.33 1.4218
IC P O11 C1 C2 1.5764 122.33 128.18 108.48 1.5345
IC C2 O11 *C1 HA 1.5345 108.48 -121.51 113.56 1.1178
IC HA O11 *C1 HB 1.1178 113.56 -119.54 108.81 1.1133
IC O11 C1 C2 C3 1.4218 108.48 -69.15 113.12 1.5322
IC C3 C1 *C2 HS 1.5322 113.12 -121.29 109.24 1.1115
IC HS C1 *C2 HR 1.1115 109.24 -117.52 108.27 1.1121
IC C1 C2 C3 O31 1.5345 113.12 -65.92 107.84 1.4362
IC O31 C2 *C3 HX 1.4362 107.84 -120.29 109.69 1.1138
IC HX C2 *C3 HY 1.1138 109.69 -118.31 108.07 1.1170
IC C2 C3 O31 C31 1.5322 107.84 166.14 114.22 1.3189
IC C3 O31 C31 C32 1.4362 114.22 -174.70 108.67 1.5288
IC C32 O31 *C31 O32 1.5288 108.67 -179.80 126.24 1.2203
IC O31 C31 C32 C33 1.3189 108.67 -167.94 112.47 1.5443
IC C33 C31 *C32 H2X 1.5443 112.47 -121.71 107.41 1.1092
IC H2X C31 *C32 H2Y 1.1092 107.41 -116.85 107.91 1.1098
IC C31 C32 C33 C34 1.5288 112.47 179.46 112.33 1.5340
IC C34 C32 *C33 H3X 1.5340 112.33 -120.43 109.16 1.1152
IC H3X C32 *C33 H3Y 1.1152 109.16 -117.67 110.02 1.1133
IC C32 C33 C34 C35 1.5443 112.33 -176.69 112.31 1.5344
IC C35 C33 *C34 H4X 1.5344 112.31 -122.05 109.68 1.1126
IC H4X C33 *C34 H4Y 1.1126 109.68 -117.48 108.87 1.1140
IC C33 C34 C35 C36 1.5340 112.31 175.27 112.83 1.5344
IC C36 C34 *C35 H5X 1.5344 112.83 -120.53 108.69 1.1140
IC H5X C34 *C35 H5Y 1.1140 108.69 -117.22 109.46 1.1123
IC C34 C35 C36 C37 1.5344 112.83 -177.21 112.46 1.5347
IC C37 C35 *C36 H6X 1.5347 112.46 -121.92 109.58 1.1126
IC H6X C35 *C36 H6Y 1.1126 109.58 -117.43 108.81 1.1138
IC C35 C36 C37 C38 1.5344 112.46 176.32 112.59 1.5343
IC C38 C36 *C37 H7X 1.5343 112.59 -120.81 108.90 1.1137
IC H7X C36 *C37 H7Y 1.1137 108.90 -117.41 109.31 1.1128
IC C36 C37 C38 C39 1.5347 112.59 -178.70 112.72 1.5347
IC C39 C37 *C38 H8X 1.5347 112.72 -121.68 109.25 1.1130
IC H8X C37 *C38 H8Y 1.1130 109.25 -117.35 108.93 1.1136
IC C37 C38 C39 C310 1.5343 112.72 179.00 112.44 1.5346
IC C310 C38 *C39 H9X 1.5346 112.44 -121.08 109.08 1.1133
IC H9X C38 *C39 H9Y 1.1133 109.08 -117.47 109.24 1.1129
IC C38 C39 C310 C311 1.5347 112.44 -179.02 112.83 1.5338
IC C311 C39 *C310 H10X 1.5338 112.83 -121.47 109.09 1.1131
IC H10X C39 *C310 H10Y 1.1131 109.09 -117.30 109.04 1.1134
IC C39 C310 C311 C312 1.5346 112.83 -179.46 113.19 1.5308
IC C312 C310 *C311 H11X 1.5308 113.19 -121.59 108.75 1.1142
IC H11X C310 *C311 H11Y 1.1142 108.75 -116.77 108.84 1.1140
IC C310 C311 C312 H12X 1.5338 113.19 60.40 110.44 1.1113
IC H12X C311 *C312 H12Y 1.1113 110.44 -119.80 110.43 1.1114
IC H12X C311 *C312 H12Z 1.1113 110.44 120.09 110.66 1.1113
RESI DLPC 0.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylcholine
!
! 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 OSLP -0.57 ! / \ alpha2
ATOM O12 OSLP -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 0.17 ! HS---C2- - - - - - -
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.49 ! O22 O21 theta3
ATOM C21 CL 0.90 ! \\ / beta2 |
ATOM O22 OBL -0.63 ! C21
ATOM C22 CTL2 -0.22 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S
ATOM H2S HAL2 0.09 ! | |
GROUP ! beta4
ATOM C3 CTL2 0.08 ! | |
ATOM HX HAL2 0.09 ! HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.49 ! O32 O31
ATOM C31 CL 0.90 ! | \\ / gamma2
ATOM O32 OBL -0.63 ! C31
ATOM C32 CTL2 -0.22 ! | | 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 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 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
!IC table from IC generate, minimized geometry
IC C13 N C12 C11 1.4966 111.24 166.28 118.98 1.5540
IC C13 C12 *N C14 1.4966 111.24 -121.31 109.70 1.5014
IC C13 C12 *N C15 1.4966 111.24 120.39 109.59 1.5032
IC C12 N C13 H13A 1.5282 111.24 -61.73 111.02 1.0824
IC H13A N *C13 H13B 1.0824 111.02 -119.31 110.03 1.0843
IC H13A N *C13 H13C 1.0824 111.02 121.33 110.99 1.0825
IC C12 N C14 H14A 1.5282 109.70 -175.08 112.24 1.0791
IC H14A N *C14 H14B 1.0791 112.24 -124.93 112.61 1.0781
IC H14A N *C14 H14C 1.0791 112.24 117.38 109.50 1.0986
IC C12 N C15 H15A 1.5282 109.59 -61.54 112.73 1.0781
IC H15A N *C15 H15B 1.0781 112.73 -124.99 112.40 1.0795
IC H15A N *C15 H15C 1.0781 112.73 117.76 109.79 1.0975
IC C11 N *C12 H12A 1.5540 118.98 -122.28 108.97 1.0812
IC H12A N *C12 H12B 1.0812 108.97 -117.10 108.29 1.0835
IC N C12 C11 O12 1.5282 118.98 60.04 111.29 1.4211
IC O12 C12 *C11 H11A 1.4211 111.29 -126.93 110.16 1.1157
IC H11A C12 *C11 H11B 1.1157 110.16 -114.93 108.04 1.1136
IC C12 C11 O12 P 1.5540 111.29 -112.41 123.03 1.5867
IC C11 O12 P O11 1.4211 123.03 -112.11 102.86 1.5750
IC O11 O12 *P O13 1.5750 102.86 -117.06 105.38 1.4772
IC O11 O12 *P O14 1.5750 102.86 117.53 108.43 1.4796
IC O12 P O11 C1 1.5867 102.86 -56.61 121.12 1.4309
IC P O11 C1 C2 1.5750 121.12 -83.15 112.71 1.5564
IC C2 O11 *C1 HA 1.5564 112.71 -117.95 107.87 1.1127
IC HA O11 *C1 HB 1.1127 107.87 -117.85 112.30 1.1145
IC O11 C1 C2 C3 1.4309 112.71 -172.05 111.41 1.5541
IC C3 C1 *C2 O21 1.5541 111.41 122.05 108.04 1.4389
IC C3 C1 *C2 HS 1.5541 111.41 -118.42 106.92 1.1167
IC C1 C2 O21 C21 1.5564 108.04 158.54 115.01 1.3183
IC C2 O21 C21 C22 1.4389 115.01 -173.62 109.25 1.5301
IC C22 O21 *C21 O22 1.5301 109.25 -179.40 126.05 1.2181
IC O21 C21 C22 C23 1.3183 109.25 -117.90 111.70 1.5446
IC C23 C21 *C22 H2R 1.5446 111.70 -120.98 107.48 1.1089
IC H2R C21 *C22 H2S 1.1089 107.48 -117.26 108.89 1.1098
IC C1 C2 C3 O31 1.5564 111.41 -53.99 110.37 1.4448
IC O31 C2 *C3 HX 1.4448 110.37 -121.24 109.56 1.1120
IC HX C2 *C3 HY 1.1120 109.56 -116.88 106.08 1.1171
IC C2 C3 O31 C31 1.5541 110.37 157.10 114.49 1.3276
IC C3 O31 C31 C32 1.4448 114.49 -179.05 109.34 1.5276
IC C32 O31 *C31 O32 1.5276 109.34 178.85 125.77 1.2163
IC O31 C31 C32 C33 1.3276 109.34 -71.25 112.33 1.5453
IC C33 C31 *C32 H2X 1.5453 112.33 -121.91 107.83 1.1087
IC H2X C31 *C32 H2Y 1.1087 107.83 -117.09 107.48 1.1098
IC C21 C22 C23 C24 1.5301 111.70 174.22 112.39 1.5364
IC C24 C22 *C23 H3R 1.5364 112.39 -120.52 108.74 1.1143
IC H3R C22 *C23 H3S 1.1143 108.74 -117.72 109.66 1.1144
IC C22 C23 C24 C25 1.5446 112.39 176.17 113.71 1.5389
IC C25 C23 *C24 H4R 1.5389 113.71 -121.29 108.85 1.1139
IC H4R C23 *C24 H4S 1.1139 108.85 -117.02 108.83 1.1137
IC C23 C24 C25 C26 1.5364 113.71 58.19 113.57 1.5361
IC C26 C24 *C25 H5R 1.5361 113.57 -121.29 108.91 1.1134
IC H5R C24 *C25 H5S 1.1134 108.91 -117.11 108.87 1.1132
IC C24 C25 C26 C27 1.5389 113.57 178.62 113.16 1.5366
IC C27 C25 *C26 H6R 1.5366 113.16 -122.19 109.43 1.1127
IC H6R C25 *C26 H6S 1.1127 109.43 -117.10 108.68 1.1096
IC C25 C26 C27 C28 1.5361 113.16 174.50 113.47 1.5400
IC C28 C26 *C27 H7R 1.5400 113.47 -122.95 110.10 1.1120
IC H7R C26 *C27 H7S 1.1120 110.10 -116.75 107.49 1.1142
IC C26 C27 C28 C29 1.5366 113.47 -95.83 114.71 1.5424
IC C29 C27 *C28 H8R 1.5424 114.71 -118.57 107.61 1.1152
IC H8R C27 *C28 H8S 1.1152 107.61 -116.24 109.93 1.1111
IC C27 C28 C29 C210 1.5400 114.71 63.13 115.93 1.5407
IC C210 C28 *C29 H9R 1.5407 115.93 -121.53 108.05 1.1138
IC H9R C28 *C29 H9S 1.1138 108.05 -115.66 108.55 1.1127
IC C28 C29 C210 C211 1.5424 115.93 62.76 115.20 1.5388
IC C211 C29 *C21 H10R 6.0255 16.54 100.54 10.30 5.9276
IC H10R C29 *C21 H10S 5.9276 10.30 -42.25 16.19 7.2059
IC C29 C210 C211 C212 1.5407 115.20 64.60 114.34 1.5319
IC C212 C210 *C21 H11R 7.2454 20.82 -38.90 18.34 5.6305
IC H11R C210 *C21 H11S 5.6305 18.34 64.37 16.79 5.3167
IC C210 C211 C212 H12R 1.5388 114.34 -64.54 110.77 1.1107
IC H12R C211 *C21 H12S 7.9945 7.88 89.82 10.46 7.8159
IC H12R C211 *C21 H12T 7.9945 7.88 40.24 16.78 7.0865
IC C31 C32 C33 C34 1.5276 112.33 -71.63 112.59 1.5348
IC C34 C32 *C33 H3X 1.5348 112.59 -119.64 108.68 1.1142
IC H3X C32 *C33 H3Y 1.1142 108.68 -117.31 110.23 1.1138
IC C32 C33 C34 C35 1.5453 112.59 178.52 112.65 1.5353
IC C35 C33 *C34 H4X 1.5353 112.65 -120.91 109.18 1.1129
IC H4X C33 *C34 H4Y 1.1129 109.18 -117.55 109.26 1.1133
IC C33 C34 C35 C36 1.5348 112.65 173.82 114.44 1.5403
IC C36 C34 *C35 H5X 1.5403 114.44 -121.24 108.76 1.1138
IC H5X C34 *C35 H5Y 1.1138 108.76 -116.91 108.64 1.1138
IC C34 C35 C36 C37 1.5353 114.44 58.04 114.79 1.5396
IC C37 C35 *C36 H6X 1.5396 114.79 -123.72 109.93 1.1120
IC H6X C35 *C36 H6Y 1.1120 109.93 -116.21 107.23 1.1147
IC C35 C36 C37 C38 1.5403 114.79 -96.72 113.37 1.5384
IC C38 C36 *C37 H7X 1.5384 113.37 124.26 109.66 1.1114
IC H7X C36 *C37 H7Y 1.1114 109.66 116.90 108.33 1.1150
IC C36 C37 C38 C39 1.5396 113.37 -176.98 113.66 1.5393
IC C39 C37 *C38 H8X 1.5393 113.66 -123.13 110.21 1.1107
IC H8X C37 *C38 H8Y 1.1107 110.21 -116.72 108.12 1.1141
IC C37 C38 C39 C310 1.5384 113.66 -67.32 114.98 1.5412
IC C310 C38 *C39 H9X 1.5412 114.98 121.99 108.65 1.1131
IC H9X C38 *C39 H9Y 1.1131 108.65 116.07 108.54 1.1129
IC C38 C39 C310 C311 1.5393 114.98 -59.10 115.15 1.5391
IC C311 C39 *C31 H10X 4.3520 21.08 -62.16 20.70 5.5478
IC H10X C39 *C31 H10Y 5.5478 20.70 44.35 19.66 6.4331
IC C39 C310 C311 C312 1.5412 115.15 -56.76 114.89 1.5327
IC C312 C310 *C31 H11X 4.8312 27.76 25.46 5.09 3.4146
IC H11X C310 *C31 H11Y 3.4146 5.09 -91.07 21.38 4.4060
IC C310 C311 C312 H12X 1.5391 114.89 -57.58 110.52 1.1109
IC H12X C311 *C31 H12Y 5.8485 18.17 43.95 25.29 5.0871
IC H12X C311 *C31 H12Z 5.8485 18.17 0.07 29.12 4.3175
RESI DLPE 0.00 ! 2,3 dilauroyl-D-glycero-1-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 OSLP -0.57 ! / \ alpha2
ATOM O12 OSLP -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 0.17 ! HS---C2- - - - - - -
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.49 ! O22 O21 theta3
ATOM C21 CL 0.90 ! \\ / beta2 |
ATOM O22 OBL -0.63 ! C21
ATOM C22 CTL2 -0.22 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S
ATOM H2S HAL2 0.09 ! | |
GROUP ! beta4
ATOM C3 CTL2 0.08 ! | |
ATOM HX HAL2 0.09 ! HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.49 ! O32 O31
ATOM C31 CL 0.90 ! | \\ / gamma2
ATOM O32 OBL -0.63 ! C31
ATOM C32 CTL2 -0.22 ! | | 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
!IC table from IC generate, minimized geometry
IC N C12 C11 O12 1.5081 111.59 -73.10 113.26 1.4276
IC C11 N *C12 H12A 1.5457 111.59 -120.62 107.97 1.1100
IC HN1 C12 *N HN2 1.0538 110.27 -125.06 113.96 1.0325
IC HN1 C12 *N HN3 1.0538 110.27 115.83 105.31 1.0629
IC HN1 N C12 C11 1.0538 110.27 -58.43 111.59 1.5457
IC H12A N *C12 H12B 1.1100 107.97 -118.48 107.57 1.1089
IC O12 C12 *C11 H11A 1.4276 113.26 -118.43 107.57 1.1140
IC H11A C12 *C11 H11B 1.1140 107.57 -115.51 110.35 1.1121
IC C12 C11 O12 P 1.5457 113.26 73.21 123.11 1.5821
IC C11 O12 P O11 1.4276 123.11 34.25 100.92 1.5725
IC O11 O12 *P O13 1.5725 100.92 118.29 112.02 1.4695
IC O11 O12 *P O14 1.5725 100.92 -108.59 105.98 1.4820
IC O12 P O11 C1 1.5821 100.92 93.08 123.05 1.4250
IC P O11 C1 C2 1.5725 123.05 -158.55 108.93 1.5522
IC C2 O11 *C1 HA 1.5522 108.93 -118.72 109.36 1.1135
IC HA O11 *C1 HB 1.1135 109.36 -119.33 112.35 1.1156
IC O11 C1 C2 C3 1.4250 108.93 -50.37 110.31 1.5644
IC C3 C1 *C2 O21 1.5644 110.31 122.15 109.56 1.4463 !defines S chirality
IC C3 C1 *C2 HS 1.5644 110.31 -116.40 109.18 1.1165 !defines S chirality
IC C1 C2 O21 C21 1.5522 109.56 79.76 113.36 1.3301
IC C2 O21 C21 C22 1.4463 113.36 -171.78 109.82 1.5286
IC C22 O21 *C21 O22 1.5286 109.82 179.59 125.69 1.2157
IC O21 C21 C22 C23 1.3301 109.82 -96.56 112.64 1.5461
IC C23 C21 *C22 H2R 1.5461 112.64 -119.55 106.22 1.1113
IC H2R C21 *C22 H2S 1.1113 106.22 -116.80 109.41 1.1071
IC C1 C2 C3 O31 1.5522 110.31 153.88 112.56 1.4435
IC O31 C2 *C3 HX 1.4435 112.56 -125.97 110.32 1.1120
IC HX C2 *C3 HY 1.1120 110.32 -114.28 106.98 1.1128
IC C2 C3 O31 C31 1.5644 112.56 -90.79 115.60 1.3262
IC C3 O31 C31 C32 1.4435 115.60 169.19 109.07 1.5269
IC C32 O31 *C31 O32 1.5269 109.07 -178.13 126.32 1.2224
IC O31 C31 C32 C33 1.3262 109.07 105.25 113.97 1.5441
IC C33 C31 *C32 H2X 1.5441 113.97 -122.05 108.45 1.1103
IC H2X C31 *C32 H2Y 1.1103 108.45 -116.70 107.29 1.1094
IC C21 C22 C23 C24 1.5286 112.64 72.21 112.51 1.5338
IC C24 C22 *C23 H3R 1.5338 112.51 -123.50 110.52 1.1136
IC H3R C22 *C23 H3S 1.1136 110.52 -117.13 108.24 1.1150
IC C22 C23 C24 C25 1.5461 112.51 173.89 113.24 1.5353
IC C25 C23 *C24 H4R 1.5353 113.24 -120.86 108.78 1.1132
IC H4R C23 *C24 H4S 1.1132 108.78 -117.56 109.21 1.1134
IC C23 C24 C25 C26 1.5338 113.24 -179.11 112.15 1.5349
IC C26 C24 *C25 H5R 1.5349 112.15 -121.41 109.36 1.1133
IC H5R C24 *C25 H5S 1.1133 109.36 -117.59 109.16 1.1133
IC C24 C25 C26 C27 1.5353 112.15 177.84 113.48 1.5342
IC C27 C25 *C26 H6R 1.5342 113.48 -121.24 108.98 1.1132
IC H6R C25 *C26 H6S 1.1132 108.98 -117.52 109.02 1.1130
IC C25 C26 C27 C28 1.5349 113.48 -179.41 112.03 1.5353
IC C28 C26 *C27 H7R 1.5353 112.03 -121.20 109.25 1.1132
IC H7R C26 *C27 H7S 1.1132 109.25 -117.63 109.28 1.1130
IC C26 C27 C28 C29 1.5342 112.03 -179.77 113.13 1.5342
IC C29 C27 *C28 H8R 1.5342 113.13 -121.43 109.07 1.1131
IC H8R C27 *C28 H8S 1.1131 109.07 -117.27 109.04 1.1132
IC C27 C28 C29 C210 1.5353 113.13 -179.80 112.43 1.5353
IC C210 C28 *C29 H9R 1.5353 112.43 -121.20 109.12 1.1132
IC H9R C28 *C29 H9S 1.1132 109.12 -117.50 109.24 1.1131
IC C28 C29 C210 C211 1.5342 112.43 -179.68 112.77 1.5338
IC C211 C29 *C210 H10R 1.5338 112.77 -121.35 109.16 1.1131
IC H10R C29 *C210 H10S 1.1131 109.16 -117.35 109.14 1.1132
IC C29 C210 C211 C212 1.5353 112.77 -179.85 113.38 1.5309
IC C212 C210 *C211 H11R 1.5309 113.38 -121.68 108.78 1.1141
IC H11R C210 *C211 H11S 1.1141 108.78 -116.64 108.78 1.1140
IC C210 C211 C212 H12R 1.5338 113.38 60.06 110.50 1.1112
IC H12R C211 *C212 H12S 1.1112 110.50 -119.88 110.53 1.1113
IC H12R C211 *C212 H12T 1.1112 110.50 120.06 110.61 1.1113
IC C31 C32 C33 C34 1.5269 113.97 -176.87 110.60 1.5345
IC C34 C32 *C33 H3X 1.5345 110.60 -121.15 110.42 1.1131
IC H3X C32 *C33 H3Y 1.1131 110.42 -119.02 109.90 1.1145
IC C32 C33 C34 C35 1.5441 110.60 178.15 113.68 1.5334
IC C35 C33 *C34 H4X 1.5334 113.68 -121.01 108.74 1.1141
IC H4X C33 *C34 H4Y 1.1141 108.74 -116.97 109.36 1.1132
IC C33 C34 C35 C36 1.5345 113.68 -177.06 111.90 1.5350
IC C36 C34 *C35 H5X 1.5350 111.90 -121.43 109.53 1.1127
IC H5X C34 *C35 H5Y 1.1127 109.53 -117.89 109.27 1.1134
IC C34 C35 C36 C37 1.5334 111.90 179.23 112.99 1.5340
IC C37 C35 *C36 H6X 1.5340 112.99 -121.08 108.94 1.1138
IC H6X C35 *C36 H6Y 1.1138 108.94 -117.23 109.34 1.1132
IC C35 C36 C37 C38 1.5350 112.99 -177.88 112.25 1.5344
IC C38 C36 *C37 H7X 1.5344 112.25 -121.43 109.33 1.1129
IC H7X C36 *C37 H7Y 1.1129 109.33 -117.59 109.16 1.1132
IC C36 C37 C38 C39 1.5340 112.25 179.64 112.89 1.5342
IC C39 C37 *C38 H8X 1.5342 112.89 -121.23 109.02 1.1134
IC H8X C37 *C38 H8Y 1.1134 109.02 -117.22 109.17 1.1131
IC C37 C38 C39 C310 1.5344 112.89 -179.25 112.43 1.5347
IC C310 C38 *C39 H9X 1.5347 112.43 -121.34 109.21 1.1130
IC H9X C38 *C39 H9Y 1.1130 109.21 -117.49 109.18 1.1132
IC C38 C39 C310 C311 1.5342 112.43 -179.94 112.73 1.5336
IC C311 C39 *C310 H10X 1.5336 112.73 -121.36 109.09 1.1132
IC H10X C39 *C310 H10Y 1.1132 109.09 -117.30 109.12 1.1130
IC C39 C310 C311 C312 1.5347 112.73 -179.76 113.35 1.5310
IC C312 C310 *C311 H11X 1.5310 113.35 -121.66 108.73 1.1141
IC H11X C310 *C311 H11Y 1.1141 108.73 -116.65 108.75 1.1141
IC C310 C311 C312 H12X 1.5336 113.35 60.17 110.49 1.1114
IC H12X C311 *C312 H12Y 1.1114 110.49 -119.95 110.51 1.1114
IC H12X C311 *C312 H12Z 1.1114 110.49 120.02 110.54 1.1114
RESI DLPS -1.00 ! 2,3 dilauroyl-D-glycero-1-Phosphatidylserine
!
! R1 - CH2
! | (-)
! R2 - CH CO2
! | (-) | (+)
! CH2 - PO4 - CH2 - CH - NH3
!
! Polar Head and glycerol backbone
GROUP !
ATOM N NH3L -0.30 ! HN2
ATOM HN1 HCL 0.33 ! |
ATOM HN2 HCL 0.33 ! |
ATOM HN3 HCL 0.33 ! |
ATOM C12 CTL1 0.21 ! (+) HN1---N---HN3
ATOM H12A HBL 0.10 ! |
GROUP ! | O13A (-)
ATOM C13 CCL 0.34 ! | ||
ATOM O13A OCL -0.67 ! H12A--C12----C13---O13B
ATOM O13B OCL -0.67 ! |
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 O12 OSLP -0.57 ! / \ alpha2
ATOM O11 OSLP -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 0.17 ! HS---C2--------------
ATOM HS HAL1 0.09 ! | beta1 |
ATOM O21 OSL -0.49 ! O22 O21 theta3
ATOM C21 CL 0.90 ! \\ / beta2 |
ATOM O22 OBL -0.63 ! C21 |
ATOM C22 CTL2 -0.22 ! | beta3 |
ATOM H2R HAL2 0.09 ! H2R---C22---H2S |
ATOM H2S HAL2 0.09 ! | |
GROUP ! | beta4 |
ATOM C3 CTL2 0.08 ! | |
ATOM HX HAL2 0.09 ! | HX---C3---HY
ATOM HY HAL2 0.09 ! | | gamma1
ATOM O31 OSL -0.49 ! | O32 O31
ATOM C31 CL 0.90 ! | \\ / gamma2
ATOM O32 OBL -0.63 ! | C31
ATOM C32 CTL2 -0.22 ! | | 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 O13B C13 C13 C12
DOUBLE C13 O13A
BOND C12 H12A C12 C11 C1 O11
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
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