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Copy pathhydrocarbon_topology_CHEMDRAW.dat
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hydrocarbon_topology_CHEMDRAW.dat
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!List of parameters for acyl chains
!
!
!KEY: ELEMENT LINKER CONNECTIVITY RING BRANCH BOND
! ELEMENT: chemical element (C, N, O, ...)
! LINKER: is it linked to the head group? [0, 1]
! CONNECTIVITY: how many atoms are connected
! RING: Does this belong to a ring? [0, 1]
! BRANCH: does tail branch here? [0, 1]
! BOND: what kind of bond
!
! *: any residue or atom
! &: Improper angle
! -: previous atom
! +: following atom
!Thomas Lemmin
!Laboratory for Biomolecular Modeling, EPFL
!2013
!
!RESI CH0 ! triple bond carbon !No Parameters are currently available
! KEY C 0 2 0 0 3:1
! KEY C 0 2 0 0 1:3
! HATOM C CTL0 -0.09
!ISER
RESI CH1 ! double bond CH1 CIS
KEY C 0 2 0 0 2:1
KEY C 0 2 0 0 1:2
KEY C 0 2 0 0 -1:2
HATOM C CEL1 -0.15
ATOM H1 HEL1 0.15
STEREO *:C*+ *:C*- &CH1:C CH1:H1 1.58 110 180 121 1.08
ISER
RESI CH1 ! double bond CH1 TRANS
KEY C 0 2 0 0 2:-1
HATOM C CEL1 -0.15
ATOM H1 HEL1 0.15
STEREO *:C*+ *:C*- &CH1:C CH1:H1 1.58 110 180 121 1.08
ISER
RESI CH2 ! single bond CH2
KEY C 0 2 0 0 1:1
KEY C 0 2 0 0 1:-1
KEY C 0 2 0 0 -1:1
HATOM C CTL2 -0.18
ATOM H1 HAL2 0.09
ATOM H2 HAL2 0.09
STEREO *:C*+ *:C*- &CH2:C CH2:H1 1.53 110 -120 110 1.10
STEREO CH2:H1 *:C*- &CH2:C CH2:H2 1.10 110 -120 110 1.10
ISER
RESI CLH2 ! linker CH2
KEY C 1 1 0 0 1
HATOM C CTL2 -0.22
ATOM H1 HAL2 0.09
ATOM H2 HAL2 0.09
!STEREO *:C-- *:C- &CH2:C CH2:H1 1.53 110 120 110 1.10
!STEREO CH2:H1 *:C- &CH2:C CH2:H2 1.10 110 120 110 1.10
ISER
RESI CLH3 ! linker CH3
KEY C 1 0 0 0 1
HATOM C CTL3 -0.31
ATOM H1 HAL3 0.09
ATOM H2 HAL3 0.09
ATOM H3 HAL3 0.09
!STEREO *:C-- *:C- &CH2:C CH2:H1 1.53 110 120 110 1.10
!STEREO CH2:H1 *:C- &CH2:C CH2:H2 1.10 110 120 110 1.10
ISER
RESI CH3 ! terminal CH3
KEY C 0 1 0 0 1
HATOM C CTL3 -0.27
ATOM H1 HAL3 0.09
ATOM H2 HAL3 0.09
ATOM H3 HAL3 0.09
STEREO *:C*-- *:C*- CH3:C CH3:H1 1.53 110 120 110 1.10
STEREO CH3:H1 *:C*- &CH3:C CH3:H2 1.10 110 120 110 1.10
STEREO CH3:H1 *:C*- &CH3:C CH3:H3 1.10 110 -120 110 1.10
ISER
RESI CH2T ! terminal CH2
KEY C 0 1 0 0 2
HATOM C CGT2 -0.42
ATOM H1 HGT2 0.21
ATOM H2 HGT2 0.21
STEREO *:C*-- *:C*- CH2T:C CH2T:H1 1.53 110 120 110 1.10
STEREO CH3:H1 *:C*- &CH2T:C CH2T:H2 1.10 110 120 110 1.10
ISER
RESI CBH1 ! branched CH1
KEY C 0 3 0 1 1:1:1
HATOM C CTL1 -0.09
ATOM H1 HAL1 0.09
!STEREO *:C*-- *:C*- CBH1:C CBH1:H1 1.53 110 -120 110 1.10
ISER
RESI CRH2 ! cycloprane CH2
KEY C 0 2 1 0 1:1
HATOM C CCP2 -0.18
ATOM H1 HCP2 0.09
ATOM H2 HCP2 0.09
STEREO CRH1:C+ CRH1:C- &CRH2:C CRH2:H1 1.53 110 -112.42 110 1.10
STEREO CRH1:C+ CRH1:C- &CRH2:C CRH2:H2 1.53 110 112.42 110 1.10
ISER
RESI CRH1 ! cycloprane CH1
KEY C 0 3 1 0 1:1:1
KEY C 0 3 1 0 -1:1:1
KEY C 0 3 1 0 1:1:-1
HATOM C CCP1 -0.09
ATOM H1 HCP1 0.09
!STEREO *:C*-- CRH1:C- CRH1:C CRH1:H1 1.53 65 -129 115 1.10
STEREO CRH2:C+ *:C*- &CRH1:C CRH1:H1 1.53 115 -145 115 1.10
STEREO CRH1:C+ *:C*- &CRH1:C CRH1:H1 1.53 115 145 115 1.10
ISER
RESI CBRH1 ! cycloprane CH1 branch
KEY C 0 3 1 1 1:1:1
HATOM C CCP1 -0.09
ATOM H1 HCP1 0.09
STEREO *:C*+ CRH1:C- &CBRH1:C CBRH1:H1 1.53 115 -145 115 1.10
ISER
BOND
*:C* *:C* 1.52 ! default value C-C
!single bond
CH2:C CH2:C 1.52
!double bond
CH1:C CH1:C 1.35
! triple bond
CH0:C CH0:C 1.20
!cyclopropane
CRH1:C CRH1:C 2.56
CRH1:C CRH2:C 1.51
CRH2:C CRH1:C 1.51
ANGLE
*:C* *:C* *:C* 116
CH2:C CH2:C CH2:C 116
*:C* CH1:C CH1:C 147
CH1:C CH1:C *:C* 147
*:C* CH0:C CH0:C 180
CH0:C CH0:C *:C* 180
*:C* CH1:C CH2:C 116
CH1:C CH2:C *:C* 116
*:C* CBH1:C *:C* 110
!cyclopropane
CRH2:C CRH1:C CRH1:C 60
CRH1:C CRH2:C CRH1:C 60
CRH1:C CRH1:C CRH2:C 60
*:C* CRH1:C CRH2:C 117
*:C* CRH1:C CRH1:C 117
CRH1:C CRH1:C *:C* 117
CRH2:C CRH1:C *:C* 117
!branched cyclopropane
*:C* CRH1:C CBRH1:C 117
CBRH1:C CRH1:C *:C* 117
CRH1:C CBRH1:C *:C* 117
DIHEDRAL
*:C* *:C* *:C* *:C* 180
*:C* CH2:C CBH1:C *:C* 0 120 240
CRH2:C CRH1:C *:C* *:C* 0
CRH1:C CRH1:C *:C* *:C* 180
!cyclopropane
*:C* *:C* CRH1:C CRH2:C 120.30 -120.36
*:C* CRH1:C CRH1:C *:C* 0
*:C* CRH2:C CRH1:C *:C* 134
CRH1:C CRH2:C CRH1:C *:C* -134
*:C* *:C* CRH1:C CRH1:C 176
CRH1:C CRH1:C *:C* *:C* 176
CRH2:C CRH1:C *:C* *:C* -116
*:C* *:C* CRH1:C CRH2:C 116