MOLDY PDPC Topology
The following was constructed using POPC as a base model, substituting DHA for the sn-2 chain.
RESI PDPC 0.00 ! 1-palmytoil-2-oleoyl-sn-glycero-
! 3-Phosphatidylcholine
!
! (March 27, 2007 J.Taylor)
!
! Palmytoil - CH2
! |
! DHA - 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 CEL1 -0.15 ! | |
ATOM H4A HEL1 0.15 ! H4A---C24
GROUP ! ||
ATOM C25 CEL1 -0.15 ! ||
ATOM H5A HEL1 0.15 ! H5A---C25
GROUP ! |
ATOM C26 CTL2 -0.18 ! |
ATOM H6A HAL2 0.09 ! H6A---C26---H6B
ATOM H6B HAL2 0.09 ! |
GROUP ! |
ATOM C27 CEL1 -0.15 ! |
ATOM H7A HEL1 0.15 ! H7A---C27
GROUP ! ||
ATOM C28 CEL1 -0.15 ! ||
ATOM H8A HEL1 0.15 ! H8A---C28
GROUP ! |
ATOM C29 CTL2 -0.18 ! |
ATOM H9A HAL2 0.09 ! H9A---C29---H9B
ATOM H9B HAL2 0.09 ! |
GROUP !
ATOM C210 CEL1 -0.15 ! |
ATOM H10A HEL1 0.15 ! H10A---C210
GROUP ! ||
ATOM C211 CEL1 -0.15 ! ||
ATOM H11A HEL1 0.15 ! H11A---C211
GROUP ! |
ATOM C212 CTL2 -0.18 ! |
ATOM H12A HAL2 0.09 ! H12A---C212--H12B
ATOM H12B HAL2 0.09 ! |
GROUP !
ATOM C213 CEL1 -0.15 ! |
ATOM H13A HEL1 0.15 ! H13A---C213
GROUP ! ||
ATOM C214 CEL1 -0.15 ! ||
ATOM H14A HEL1 0.15 ! H14A---C214
GROUP ! |
ATOM C215 CTL2 -0.18 ! |
ATOM H15A HAL2 0.09 ! H15A---C215--H15B
ATOM H15B HAL2 0.09 ! |
GROUP !
ATOM C216 CEL1 -0.15 ! |
ATOM H16A HEL1 0.15 ! H16A---C216
GROUP ! ||
ATOM C217 CEL1 -0.15 ! ||
ATOM H17A HEL1 0.15 ! H17A---C217
GROUP ! |
ATOM C218 CTL2 -0.18 ! |
ATOM H18A HAL2 0.09 ! H18A---C218--H18B
ATOM H18B HAL2 0.09 ! |
GROUP !
ATOM C219 CEL1 -0.15 ! |
ATOM H19A HEL1 0.15 ! H19A---C219
GROUP ! ||
ATOM C220 CEL1 -0.15 ! ||
ATOM H20A HEL1 0.15 ! H20A---C220
GROUP ! |
ATOM C221 CTL2 -0.18 ! |
ATOM H21A HAL2 0.09 ! H21A---C221--H21B
ATOM H21B HAL2 0.09 ! |
GROUP ! |
ATOM C222 CTL3 -0.27 ! |
ATOM H22A HAL3 0.09 ! H22A---C222--H22B
ATOM H22B HAL3 0.09 ! |
ATOM H22C HAL3 0.09 ! H22C
! ################################################>
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 H4A
DOUBLE C24 C25
BOND C25 H5A C25 C26
BOND C26 H6A C26 H6B C26 C27
BOND C27 H7A
DOUBLE C27 C28
BOND C28 H8A C28 C29 C29 H9A
BOND C29 H9B C29 C210 C210 H10A
DOUBLE C210 C211
BOND C211 H11A C211 C212
BOND C212 H12A C212 H12B C212 C213
BOND C213 H13A
DOUBLE C213 C214
BOND C214 H14A C214 C215
BOND C215 H15A C215 H15B C215 C216
BOND C216 H16A
DOUBLE C216 C217
BOND C217 H17A C217 C218
BOND C218 H18A C218 H18B C218 C219
BOND C219 H19A
DOUBLE C219 C220
BOND C220 H20A C220 C221 C221 H21A
BOND C221 H21B C221 C222 C222 H22A
BOND C222 H22B C222 H22C
! ############################>
! 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 C22 C23 C24 C25 0.0 0.0 180.0 0.0 0.0
IC C23 C24 C25 C26 0.0 0.0 0.0 0.0 0.0
IC C24 C25 C26 C27 0.0 0.0 180.0 0.0 0.0
IC C25 C26 C27 C28 0.0 0.0 180.0 0.0 0.0
IC C26 C27 C28 C29 0.0 0.0 0.0 0.0 0.0
IC C27 C28 C29 C210 0.0 0.0 180.0 0.0 0.0
IC C28 C29 C210 C211 0.0 0.0 180.0 0.0 0.0
IC C29 C210 C211 C212 0.0 0.0 0.0 0.0 0.0
IC C210 C211 C212 C213 0.0 0.0 180.0 0.0 0.0
IC C211 C212 C213 C214 0.0 0.0 180.0 0.0 0.0
IC C212 C213 C214 C215 0.0 0.0 0.0 0.0 0.0
IC C213 C214 C215 C216 0.0 0.0 180.0 0.0 0.0
IC C214 C215 C216 C217 0.0 0.0 180.0 0.0 0.0
IC C215 C216 C217 C218 0.0 0.0 0.0 0.0 0.0
IC C216 C217 C218 C219 0.0 0.0 180.0 0.0 0.0
IC C217 C218 C219 C220 0.0 0.0 180.0 0.0 0.0
IC C218 C219 C220 C221 0.0 0.0 0.0 0.0 0.0
IC C219 C220 C221 C222 0.0 0.0 180.0 0.0 0.0
IC C23 C24 C25 H5A 0.0 0.0 180.0 0.0 0.0
IC C26 C25 C24 H4A 0.0 0.0 180.0 0.0 0.0
IC C26 C27 C28 H8A 0.0 0.0 180.0 0.0 0.0
IC C29 C28 C27 H7A 0.0 0.0 180.0 0.0 0.0
IC C29 C210 C211 H11A 0.0 0.0 180.0 0.0 0.0
IC C212 C211 C210 H10A 0.0 0.0 180.0 0.0 0.0
IC C212 C213 C214 H14A 0.0 0.0 180.0 0.0 0.0
IC C215 C214 C213 H13A 0.0 0.0 180.0 0.0 0.0
IC C215 C216 C217 H17A 0.0 0.0 180.0 0.0 0.0
IC C218 C217 C216 H16A 0.0 0.0 180.0 0.0 0.0
IC C218 C219 C220 H20A 0.0 0.0 180.0 0.0 0.0
IC C221 C220 C219 H19A 0.0 0.0 180.0 0.0 0.0
IC C220 C221 C222 H22A 0.0000 0.00 180.00 0.00 0.0000
IC H6A C25 *C26 C27 0.0000 0.00 120.00 0.00 0.0000
IC H6B C25 *C26 C27 0.0000 0.00 -120.00 0.00 0.0000
IC H9A C28 *C29 C210 0.0000 0.00 120.00 0.00 0.0000
IC H9B C28 *C29 C210 0.0000 0.00 -120.00 0.00 0.0000
IC H12A C211 *C212 C213 0.0000 0.00 120.00 0.00 0.0000
IC H12B C211 *C212 C213 0.0000 0.00 -120.00 0.00 0.0000
IC H15A C214 *C215 C216 0.0000 0.00 120.00 0.00 0.0000
IC H15B C214 *C215 C216 0.0000 0.00 -120.00 0.00 0.0000
IC H18A C217 *C218 C219 0.0000 0.00 120.00 0.00 0.0000
IC H18B C217 *C218 C219 0.0000 0.00 -120.00 0.00 0.0000
IC H21A C220 *C221 C222 0.0000 0.00 120.00 0.00 0.0000
IC H21B C220 *C221 C222 0.0000 0.00 -120.00 0.00 0.0000
IC C220 C221 C222 H22A 0.0000 0.00 180.00 0.00 0.0000
IC H22A C221 *C222 H22B 0.0000 0.00 120.00 0.00 0.0000
IC H22A C221 *C222 H22C 0.0000 0.00 -120.00 0.00 0.0000
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
! ############################################ PALM CHAIN
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 *C310 H10X 1.5336 113.81 -120.14 108.22 1.1126 ! Changed, JT
IC H10X C39 *C310 H10Y 1.1126 108.22 -117.07 109.45 1.1132 ! Changed, JT
IC C39 C310 C311 C312 1.5320 113.81 -175.46 111.16 1.5334
IC C312 C310 *C311 H11X 1.5334 111.16 120.27 109.12 1.1138 ! Changed, JT
IC H11X C310 *C311 H11Y 1.1138 109.12 118.20 110.02 1.1119 ! Changed, JT
IC C310 C311 C312 C313 1.5336 111.16 173.60 113.47 1.5330
IC C313 C311 *C312 H12X 1.5330 113.47 -120.74 108.01 1.1140 ! Changed, JT
IC H12X C311 *C312 H12Y 1.1140 108.01 -116.85 109.45 1.1130 ! Changed, JT
IC C311 C312 C313 C314 1.5334 113.47 -174.75 111.86 1.5335
IC C314 C312 *C313 H13X 1.5335 111.86 120.28 108.66 1.1135 ! Changed, JT
IC H13X C312 *C313 H13Y 1.1135 108.66 118.03 110.08 1.1125 ! Changed, JT
IC C312 C313 C314 C315 1.5330 111.86 175.21 113.05 1.5325
IC C315 C313 *C314 H14X 1.5325 113.05 -120.81 108.37 1.1133 ! Changed, JT
IC H14X C313 *C314 H14Y 1.1133 108.37 -117.18 109.40 1.1131 ! Changed, JT
IC C313 C314 C315 C316 1.5335 113.05 -177.76 112.89 1.5300
IC C316 C314 *C315 H15X 1.5300 112.89 121.41 108.55 1.1149 ! Changed, JT
IC H15X C314 *C315 H15Y 1.1149 108.55 117.05 109.21 1.1136 ! Changed, JT
IC C314 C315 C316 H16X 1.5325 112.89 57.15 110.07 1.1113
IC H16X C315 *C316 H16Y 1.1113 110.07 -119.27 110.55 1.1106 ! Changed, JT
IC H16X C315 *C316 H16Z 1.1113 110.07 120.81 110.70 1.1116 ! Changed, JT