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smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt
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smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt
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# SMIRNOFF (SMIRKS Native Open Force Field) hybrid with parm99.dat and parm@Frosst to capture their chemistry
# Date: Tue Aug 25 2016
# Author: C. I. Bayly, OpenEye Scientific Software
#
DATE
# Updated: Many times during Fall 2016 - Winter 2017, small change with ethers Fri. March 3, 2017
# Significant updates added in early spring 2017
# Date: April 4, 2017
# Date: April 26, 2017
# Date: May 25, 2017
# Date: Aug. 3, 2017
Date: Feb. 27, 2018
# Author: please make sure all authors are on one line, only last line will be used
AUTHOR
C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine
NONBON
# hydrogen
[#1:1] 0.6000 0.0157 parm99 generic by analogy with H,HS assuming electroneg bond partner
[#1:1]-[#6X4] 1.4870 0.0157 parm99 HC OPLS
[#1:1]-[#6X4]-[#7,#8,#9,#16,#17,#35] 1.3870 0.0157 parm99 H1 Veenstra et al JCC,8,(1992),963
[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35] 1.2870 0.0157 parm99 H2 Veenstra et al JCC,8,(1992),963
[#1:1]-[#6X4](-[#7,#8,#9,#16,#17,#35])(-[#7,#8,#9,#16,#17,#35])-[#7,#8,#9,#16,#17,#35] 1.1870 0.0157 parm99 H3 Veenstra et al JCC,8,(1992),963
[#1:1]-[#6X4]~[*;+1;+2] 1.1000 0.0157 parm99 HP Veenstra et al JCC,8,(1992),963
[#1:1]-[#6X3] 1.4590 0.0150 parm99 HA Spellmeyer
[#1:1]-[#6X3]~[#7,#8,#9,#16,#17,#35] 1.4090 0.0150 parm99 H4 Spellmeyer, one electrowithdr. neighbor
[#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35] 1.3590 0.0150 parm99 H5 Spellmeyer, two electrowithdr. neighbor
[#1:1]-[#6X2] 1.4590 0.0150 parm99 HZ H bonded to sp C (Howard et al JCC 16)
[#1:1]-[#7] 0.6000 0.0157 parm99 H
[#1:1]-[#8] 0.0000 0.0000 parm99 HO OPLS Jorgensen, JACS,110,(1988),1657
[#1:1]-[#16] 0.6000 0.0157 parm99 HS
# carbon
[#6:1] 1.9080 0.0860 parm99 generic Spellmeyer
[#6X2:1] 1.9080 0.2100 parm99 Mobley JCTCv5p350-358(2009)
[#6X4:1] 1.9080 0.1094 parm99 CT Spellmeyer
# oxygen
[#8:1] 1.6612 0.2100 parm99 generic O,O2 OPLS
[#8X2H0+0:1] 1.6837 0.1700 parm99 OS OPLS ether
[#8X2H1+0:1] 1.7210 0.2104 parm99 OH OPLS
# nitrogen
[#7:1] 1.8240 0.1700 parm99 generic OPLS
# sulfur
[#16:1] 2.0000 0.2500 parm99 generic
# phosphorus
[#15:1] 2.1000 0.2000 parm99 P JCC,7,(1986),230;
# halogens
[#9:1] 1.75 0.061 parm99 F Gough et al. JCC 13,(1992),963.
[#17:1] 1.948 0.265 parm99 Cl Fox, JPCB,102,8070,(98),flex.mdl CHCl3
[#35:1] 2.22 0.320 parm99 Br Junmei(?)
[#53:1] 2.35 0.40 parm99 I JCC,7,(1986),230;
# Monovalent ions from parm99
[#3+1:1] 1.025 0.0279896 Joung/Cheatham TIP3P
[#11+1:1] 1.369 0.0874393 Joung/Cheatham TIP3P
[#19+1:1] 1.705 0.1936829 Joung/Cheatham TIP3P
[#37+1:1] 1.813 0.3278219 Joung/Cheatham TIP3P
[#55+1:1] 1.976 0.4065394 Joung/Cheatham TIP3P
[#9X0-1:1] 2.303 0.0033640 Joung/Cheatham TIP3P
[#17X0-1:1] 2.513 0.0355910 Joung/Cheatham TIP3P
[#35X0-1:1] 2.608 0.0586554 Joung/Cheatham TIP3P
[#53X0-1:1] 2.860 0.0536816 Joung/Cheatham TIP3P
BOND
# Csp3-Csp3
[#6X4:1]-[#6X4:2] 310.0 1.526 parm99 CT-CT
# Csp3-Csp2
[#6X4:1]-[#6X3:2] 317.0 1.51 parm99 generic
[#6X4:1]-[#6X3:2]=[#8X1+0] 317.0 1.522 parm99 C_-CT peptide backbone CO-Csp3
# Csp2-Csp2 here is where we have conjugation and fractional bond order matters
[#6X3:1]-[#6X3:2] 410. 1.45 parm99 generic
[#6X3:1]:[#6X3:2] 469.0 1.40 parm99 generic
[#6X3:1]=[#6X3:2] 549.0 1.35 parm99 generic
# Csp2-N(trivalent) here is where we have conjugation and fractional bond order matters
[#6:1]-[#7:2] 367.0 1.47 smirnoff generic C-N is like Csp3-ammonium
[#6X3:1]-[#7X3:2] 427.0 1.38 parm99 generic conjugated Csp2-Nsp2
[#6X4:1]-[#7X3:2]-[#6X3]=[#8X1+0] 337.0 1.449 parm99 CT-N peptide backbone N-Csp3
[#6X3:1](=[#8X1+0])-[#7X3:2] 490.0 1.335 parm99 peptide C_-N amide C-N
# Csp2-N(divalent) here is where we have conjugation and fractional bond order matters
[#6X3:1]-[#7X2:2] 410. 1.39 parm99 generic
[#6X3:1]:[#7X2,#7X3+1:2] 480. 1.34 parm99 generic
[#6X3:1]=[#7X2,#7X3+1:2] 530. 1.30 parm99 generic
# C~O bonds
[#6X4:1]-[#8X2:2] 320.0 1.410 parm99 aliphatic carbon-oxygen Csp3-O
[#6X4:1]-[#8X2H0:2] 320.0 1.370 Frosst Csp3-ether oxygen in AlkEthOH; R0 xray
[#6X3:1]-[#8X2:2] 350. 1.326 Frosst generic
[#6X3:1]-[#8X2H1:2] 450.0 1.364 parm99 phenol C-OH
[#6X3a:1]-[#8X2H0:2] 450.0 1.323 parm99 aromatic ether aroC-O-nonH
[#6X3:1](=[#8X1])-[#8X2H0:2] 320.0 1.340 Frosst C_-OS force ff94 CT-OS ; R0 xray; SMIRKS updated by DLM to not match C_-OH
[#6X3:1](~[#8X1])~[#8X1:2] 656.0 1.250 parm99 carboxylate C~O
[#6X3:1]=[#8X1+0,#8X2+1:2] 570.0 1.229 parm99 carbonyl oxygen
[#6X3:1]:[#8X2+1:2] 570.0 1.28 parm99 aromatice oxonium guess
# bonds to Csp (alkynes, nitriles, allenes)
[#6X2:1]-[#6:2] 350.0 1.440 Frosst generic
[#6X2:1]-[#6X4:2] 350.0 1.468 Frosst C2-CT RHF/6-31G(d,p) opt estimated force constant
[#6X2:1]=[#6X3:2] 549.0 1.35 smirnoff generic allene is a regular double bond
[#6X2:1]#[#7X1:2] 350.0 1.188 Frosst C2-NL from C2-C2
[#6X2:1]#[#6X2:2] 350.0 1.188 Frosst C2-C2 RHF/6-31G(d,p) opt estimated force constant
[#6X2:1]-[#8X2:2] 350. 1.326 smirnoff generic estimated from trivalentC-Odivalent
[#6X2:1]-[#7:2] 427.0 1.38 smirnoff generic estimated from trivalentC-Ntrivalent
[#6X2:1]=[#7:2] 427.0 1.17 smirnoff R0 from -N=C=S CanJChem_v50p1315(1976)
[#6X2:1]=[#16:2] 427.0 1.54 smirnoff R0 from -N=C=S CanJChem_v50p1315(1976)
# N-N bonds
[#7X3:1]-[#7X3:2] 380. 1.40 Frosst generic
[#7X3:1]-[#7X2:2] 340. 1.33 Frosst generic
[#7X2:1]-[#7X2:2] 340. 1.33 Frosst generic
[#7:1]:[#7:2] 340. 1.33 Frosst generic
[#7:1]=[#7:2] 340. 1.30 Frosst generic
[#7:1]#[#7:2] 380. 1.27 Frosst generic
# N-O bonds
[#7:1]-[#8X2:2] 300. 1.40 Frosst generic
[#7:1]~[#8X1:2] 350. 1.30 Frosst generic
# O-O peroxide
[#8X2:1]-[#8X2:2] 300. 1.46 smirnoff generic bond length from JACSv106p6146-6149(1984)
# bonds to divalent S
[#16:1]-[#6X4:2] 237.0 1.810 parm99 CT-SH
[#16X2:1]-[#1:2] 274.0 1.336 parm99 SH-HS
[#16:1]-[#16:2] 166.0 2.038 parm99 S_-S
[#16X2,#16X1-1,#16X3+1:1]-[#6X4:2] 237.0 1.81 Frosst generic by analogy with parm99 CT-SH
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2] 300.0 1.74 Frosst generic
[#16X2:1]-[#7:2] 300.0 1.69 Frosst generic
[#16X2:1]-[#8X2:2] 300.0 1.60 smirnoff generic by analogy with hypervalent_S-O_divalent
[#16X2:1]=[#8X1,#7X2:2] 300.0 1.44 smirnoff generic by analogy with hypervalent_S-O_monovalent
# bonds to hypervalent S
[#16X4,#16X3+0:1]-[#6:2] 227.0 1.750 Frosst generic
[#16X4,#16X3+0:1]~[#7:2] 265. 1.71 Frosst generic
[#16X4,#16X3+0:1]-[#8X2:2] 300.0 1.596 Frosst OS-SO
[#16X4,#16X3+0:1]~[#8X1:2] 300. 1.44 Frosst generic
# bonds to P (implied hypervalent)
[#15:1]~[#6:2] 160. 1.90 Frosst generic
[#15:1]-[#7:2] 300.0 1.65 smirnoff generic from Appl.Spec.,v57p970(2006)
[#15:1]=[#7:2] 400.0 1.5 smirnoff generic guess
[#15:1]~[#8X2:2] 230.0 1.610 parm99 OS,OH-P
[#15:1]~[#8X1:2] 525.0 1.480 parm99 O2-P
[#15:1]~[#9:2] 300.0 1.639 Frosst F_-P calc: B3LYP/6-311G(d,p) Jan 13 2006
[#15:1]=[#16X1:2] 230.0 1.98 Frosst P-SD RHF/6-31G(d,p) Sept 9 2009 Force constant Taken from OS-P_-> JCC,7,(1986),230
# bonds to halogen
[#6X4:1]-[#9:2] 367.0 1.380 parm99
[#6X3:1]-[#9:2] 386.0 1.359 parm99
[#6X4:1]-[#17:2] 232.0 1.766 parm99
[#6X3:1]-[#17:2] 193.0 1.727 parm99
[#6X4:1]-[#35:2] 159.0 1.944 parm99 Br-CT
[#6X3:1]-[#35:2] 172.0 1.890 parm99 Br-CA
[#6X4:1]-[#53:2] 148.0 2.166 parm99 I_-CT
[#6X3:1]-[#53:2] 171.0 2.075 parm99 I_-CA
# bonds to hydrogen
[#6X4:1]-[#1:2] 340.0 1.090 parm99 aliphatic CH
[#6X3:1]-[#1:2] 367.0 1.080 parm99 vinylic CH
[#6X2:1]-[#1:2] 340.0 1.090 parm99 CZ-HZ alkyne #C-H
[#7:1]-[#1:2] 434.0 1.010 parm99 any NH
[#8:1]-[#1:2] 553.0 0.960 parm99 any OH
ANGL
# begin section from parm99
# Csp3 general
[*:1]~[#6X4:2]-[*:3] 50. 109.5 parm99 generic Csp3
[#1:1]-[#6X4:2]-[#1:3] 35. 109.5 parm99 generic Csp3
[#6X4:1]-[#6X4:2]-[#6X4:3] 40. 109.5 AlkEthOH/parm99
[#8X2:1]-[#6X4:2]-[#8X2:3] 70 109.5 Frosst AlkEthOH OH-CT-OS
# Any atom in 3-membered ring
[*;r3:1]1~;@[*;r3:2]~;@[*;r3:3]1 350. 60. Frosst generic any atom within the 3-membered ring
[*;r3:1]~;@[*;r3:2]~;!@[*:3] 100. 118. Frosst generic 3ringAtom-3ringAtom-substit
[*:1]~;!@[*;r3:2]~;!@[*:3] 100. 113. Frosst generic substit-3ringAtom-nonHsubstit
[#1:1]-[*;r3:2]~;!@[*:3] 50. 113. Frosst generic substit-3ringAtom-Hsubstit
# generic Csp2 120.
[*:1]~[#6X3:2]~[*:3] 70. 120. parm99 generic Csp2
[#1:1]-[#6X3:2]~[*:3] 50. 120. parm99 generic Csp2
[#1:1]-[#6X3:2]-[#1:3] 35. 120. parm99 generic Csp2
# fused het6-het5 bridgehead outer angle
[*;r6:1]~;@[*;r5:2]~;@[*;r5;R2:3] 70.0 130. parm99 generic fused het6-het5 bridgehead outer angle
# het5 outer angle
[*:1]~;!@[*;r5:2]~;@[*;r5:3] 70.0 125. Frosst generic het5 substituent outer angle
# carboxylic acid, ester, carboxylate
[#8X1:1]~[#6X3:2]~[#8:3] 80.0 126.00 parm99 generic
# Csp
[*:1]~[#6X2:2]~[*:3] 80. 180.0 parm99 generic smirnoff only sp carbons are linear
# Nsp3 trivalent and divalent: aliphatic N, ie not attached to Csp2 or Csp
# note aliphatic trivalent Nsp3 must be defined before conjugated trivalent Nsp2
[*:1]-[#7X4,#7X3,#7X2-1:2]-[*:3] 70. 109.5 parm99 generic Nsp3 tetravalent
[#1:1]-[#7X4,#7X3,#7X2-1:2]-[*:3] 50. 109.5 parm99 generic Nsp3 tetravalent
# divalent and trivalent conjugated Nsp2
# note this has to follow the trivalent Nsp3 specification
[*:1]~[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]~[*:3] 70. 120. Frosst generic trivalent conjugated Nsp2
[#1:1]-[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]-[*:3] 50. 120. Frosst generic trivalent conjugated Nsp2
[*:1]~[#7X2+0:2]~[*:3] 70. 120. Frosst generic divalent conjugated Nsp2
[#1:1]-[#7X2+0:2]~[*:3] 50. 120. Frosst generic divalent conjugated Nsp2
# nitro group
[#6:1]-[#7X3:2](~[#8X1])~[#8X1:3] 70.000 117.700 Frosst CA-N2-O2 from fit to rhf/6-31G* from T.Halgren 1/26/99
[#8X1:1]~[#7X3:2]~[#8X1:3] 70.000 124.500 Frosst O2-N2-O2 from fit to rhf/6-31G* from T.Halgren 1/26/99
# Nsp
[*:1]~[#7X2:2]~[#7X1:3] 70.0 180.0 Frosst generic smirnoff only sp carbons are linear
# oxygen including endocyclic het5 (a la furan)
[*:1]-[#8:2]-[*:3] 50. 113. Frosst generic divalent oxygen including endocyclic het5
[#6X4:1]-[#8X2:2]-[#1:3] 55. 108.5 parm99 CT-OH-HO AlkEthOH
[#6X4:1]-[#8X2:2]-[#6X4:3] 60. 109.5 parm99 CT-OS-CT AlkEthOH
# Osp2 divalent conjugated in a ring
[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3] 70. 120. Frosst generic Osp2 divalent conjugated in a ring
[*:1]-[#8X2+1:2]=[*:3] 50. 120. Frosst generic divalent oxonium guess
# hypervalent sulfur
[*:1]~[#16X4:2]~[*:3] 70. 109.5 Frosst generic diverse ANG0 (low confidence)
[*:1]-[#16X4,#16X3+0:2]-[*:3] 60. 109.5 parm99 generic hypervalent sulfur
[*:1]~[#16X3$(*~[#8X1,#7X2]):2]~[*:3] 70. 109.5 Frosst generic sulfinyl guess
[*:1]=[#16X2:2]=[*:3] 70. 180. Frosst generic divalent hypervalent e.g. isothiocyanate
# divalent sulfur, both aliphatic and endocyclic in het5 (a la thiophene)
[*:1]-[#16X2,#16X3+1:2]-[*:3] 60. 98. parm99 generic divalent sulfur
[#6X3:1]-[#16X2:2]-[#6X3:3] 60. 95. Frosst generic
[#6X3:1]-[#16X2:2]-[#6X4:3] 60. 100. Frosst generic
[#6X3:1]-[#16X2:2]-[#1:3] 43. 96. Frosst CA-SH-HS by analogy with parm94 CT-SH-HS
# Phosphorus (implied hypervalent)
[*:1]~[#15:2]~[*:3] 70. 109.5 parm99 generic diverse range of angles (low confidence)
DIHE
# C-C bonds
# Csp3-Csp3
[*:1]-[#6X4:2]-[#6X4:3]-[*:4] 9 1.40 0.0 3.0 parm99 X_-CT-CT-X JCC,7,(1986),230
[#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4] 1 0.180 0.0 -3.0 parm99 CT-CT-CT-CT Junmei et al, 1999
[#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4] 1 0.250 180.0 -2.0 parm99 CT-CT-CT-CT Junmei et al, 1999
[#6X4:1]-[#6X4:2]-[#6X4:3]-[#6X4:4] 1 0.200 180.0 1.0 parm99 CT-CT-CT-CT Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3]-[#1:4] 1 0.150 0.0 3.0 parm99 HC-CT-CT-HC Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3]-[#6X4:4] 1 0.160 0.0 3.0 parm99 HC-CT-CT-CT Junmei et al, 1999
[#8X2:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] 1 0.144 0.0 -3.0 parm99 OH-CT-CT-OH parm98, TC,PC,PAK
[#8X2:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] 1 1.175 0.0 2.0 parm99 OH-CT-CT-OH parm98, TC,PC,PAK
[#9:1]-[#6X4:2]-[#6X4:3]-[#9:4] 1 0.000 0.0 -3.0 parm99 F_-CT-CT-F JCC,7,(1986),230
[#9:1]-[#6X4:2]-[#6X4:3]-[#9:4] 1 1.200 180.0 1.0 parm99 F_-CT-CT-F Junmei et al, 1999
[#17:1]-[#6X4:2]-[#6X4:3]-[#17:4] 1 0.000 0.0 -3.0 parm99 Cl-CT-CT-Cl JCC,7,(1986),230
[#17:1]-[#6X4:2]-[#6X4:3]-[#17:4] 1 0.450 180.0 1.0 parm99 Cl-CT-CT-Cl Junmei et al, 1999
[#35:1]-[#6X4:2]-[#6X4:3]-[#35:4] 1 0.000 0.0 -3.0 parm99 Br-CT-CT-Br JCC,7,(1986),230
[#35:1]-[#6X4:2]-[#6X4:3]-[#35:4] 1 0.000 180.0 1.0 parm99 Br-CT-CT-Br Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] 1 0.000 0.0 -3.0 parm99 HC-CT-CT-OS JCC,7,(1986),230
[#1:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] 1 0.250 0.0 1.0 parm99 HC-CT-CT-OS Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3]-[#9:4] 1 0.000 0.0 -3.0 parm99 HC-CT-CT-F JCC,7,(1986),230
[#1:1]-[#6X4:2]-[#6X4:3]-[#9:4] 1 0.190 0.0 1.0 parm99 HC-CT-CT-F Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3]-[#17:4] 1 0.000 0.0 -3.0 parm99 HC-CT-CT-Cl JCC,7,(1986),230
[#1:1]-[#6X4:2]-[#6X4:3]-[#17:4] 1 0.250 0.0 1.0 parm99 HC-CT-CT-Cl Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3]-[#35:4] 1 0.000 0.0 -3.0 parm99 HC-CT-CT-Br JCC,7,(1986),230
[#1:1]-[#6X4:2]-[#6X4:3]-[#35:4] 1 0.550 0.0 1.0 parm99 HC-CT-CT-Br Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X4:3](-[#8])-[#1:4] 9 1.40 0.0 -3.0 parm99 bug X-CT-CT-X for H*-CT-CT-H* except HC-CT-HC per AlkEthOH
[#1:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] 1 0.0 0.0 -3.0 HC,H1-CT-CT-OH,OS AlkEthOH
[#1:1]-[#6X4:2]-[#6X4:3]-[#8X2:4] 1 0.25 0.0 1.0 HC,H1-CT-CT-OH,OS AlkEthOH
[#8X2:1]-[#6X4:2]-[#6X4:3]-[#1:4] 1 0.0 0.0 -3.0 H_-CT-CT-O_ AlkEthOH
[#8X2:1]-[#6X4:2]-[#6X4:3]-[#1:4] 1 0.25 0.0 1.0 H_-CT-CT-O_ AlkEthOH
[#1:1]-[#6X4:2](-[#8])-[#6X4:3]-[#6X4:4] 9 1.40 0.0 -3.0 X-CT-CT-X for H*-CT-CT-CT torsions AlkEthOH
[#1:1]-[#6X4:2](-[#8])(-[#8])-[#6X4:3]-[OX2:4] 9 1.40 0.0 -3 H2,H3-CT-CT-(OH,OS) AlkEthOH
# Csp3-Csp3cyclopropyl
[*:1]-[#6X4:2]-[#6X4;r3:3]-[*:4] 1 0.000 0.0 1 Frosst X_-CT-CJ-X best fit Dec 1 2004
[*:1]-[#6X4:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.0 0.0 3 Frosst generic
[*:1]-[#6X4;r3:2]-@[#6X4;r3:3]-[*:4] 1 0.000 0.0 2 Frosst generic
[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 3.000 0.0 -2 Frosst generic fit to RHF/6-31G(d)
[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 2.700 0.0 1 Frosst CJ-CJ-CJ-X fit to RHF/6-31G(d)
#
# Csp3-Csp2
[*:1]~[#6X3:2]-[#6X4:3]-[*:4] 1 0.000 0.0 3.0 parm99 generic
#
[#1:1]-[#6X4:2]-[#6X3:3]=[#8X1:4] 1 0.800 0.0 -1.0 parm99 HC-CT-C_-O Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X3:3]=[#8X1:4] 1 0.000 0.0 -2.0 parm99 HC-CT-C_-O
[#1:1]-[#6X4:2]-[#6X3:3]=[#8X1:4] 1 0.080 180.0 3.0 parm99 HC-CT-C_-O Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.380 180.0 -3.0 parm99 HC-CT-CM-CM Junmei et al, 1999
[#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 1.150 0.0 1.0 parm99 HC-CT-CM-CM Junmei et al, 1999
# Csp3-Csp2=X
[*:1]-[#6X4:2]-[#6X3:3]=[*:4] 1 0.000 0.0 2 Frosst X_-CT-CR-X his, ff94 X-CC-CT-X
[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.450 0.0 -3 Frosst CM-CT-CM-CM from ab initio mt
[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.250 180.0 2 Frosst CM-CT-CM-CM from ab initio mt
[#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 1.000 180.0 3 Frosst HC-CT-CM-CM from ab initio mt
#
[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 1.700 180.0 -1.0 parm99 N_-CT-C_-N
[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 2.000 180.0 2.0 parm99 N_-CT-C_-N
[#6X4:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 0.100 0.0 -4.0 parm99 CT-CT-C_-N phi,psi,parm94
[#6X4:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 0.070 0.0 2.0 parm99 CT-CT-C_-N phi,psi,parm94
# Csp3-Csp2-Sdivalent
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.260 0.0 -2 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.350 180.0 1 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.988 0.0 -4 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.258 0.0 -3 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.805 0.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 2.059 270.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 1.710 90.0 1 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.285 270.0 -4 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.669 0.0 -3 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.310 180.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.548 270.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.263 270.0 -1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009
[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.222 0.0 1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009
# Csp3cyclopropyl-Csp2
[*:1]-[#6X4;r3:2]-[#6X3:3]~[*:4] 1 0.000 0.0 1 Frosst generic
[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst CT-CJ-CA-CA guess from CA-CA-CJ-CJ
[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst CT-CJ-CA-CA Feb 1 2005
[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010
[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 0.0 -3 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010
[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 180.0 2 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 1.392 0.0 -2 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.645 180.0 -1 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.961 180.0 3 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 3.174 180.0 -2 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.277 180.0 -1 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.514 180.0 3 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005
[#6X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.128 180.0 2 Frosst generic
[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004
[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.250 0.0 -3 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.010 180.0 2 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.065 180.0 -4 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.550 180.0 2 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.050 180.0 -4 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.250 0.0 -3 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.010 180.0 2 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]=;@[#6X3;r5:4] 1 0.300 180.0 1 Frosst CJ-CJ-CC-CW RHF/6-31G(d,p) opt Sept 2 2008
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#6X4:4] 1 0.000 0.0 1 Frosst CJ-CJ-C_-CT set to zero for CJ-CJ-C-O
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 2.100 180.0 -2 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.432 180.0 -1 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.620 0.0 3 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.300 0.0 -3 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.950 180.0 -2 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.275 180.0 1 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.065 180.0 -4 Frosst CJ-CJ-C_-OS Taken from CA-CA-CJ-CJ June 29 2007
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.550 180.0 2 Frosst CJ-CJ-C_-OS
[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 2.400 320.0 2 Frosst generic
#
# Csp2-Csp2 : conjugation is everything
[*:1]~[#6X3:2]-[#6X3:3]~[*:4] 1 0.625 180.0 2 Frosst generic
[*:1]~[#6X3:2]:[#6X3:3]~[*:4] 1 3.625 180.0 2.0 parm99 generic Caro-Caro
[*:1]-,:[#6X3:2]=[#6X3:3]-,:[*:4] 1 5.4 180.0 2 Frosst generic
[#6X4:1]-[#6X3:2]=[#6X3:3]-[#6X4:4] 1 6.650 180.0 -2.0 parm99 CT-CM-CM-CT Junmei et al, 1999
[#6X4:1]-[#6X3:2]=[#6X3:3]-[#6X4:4] 1 1.900 180.0 1.0 parm99 CT-CM-CM-CT Junmei et al, 1999
# Csp2-Csp2 specific torsions
[*:1]~[#6X3:2]-[#6X3$(*=[#8,#16,#7]):3]~[*:4] 1 0.250 180.0 2 Frosst generic alpha,beta unsat carbonyl
[#6X3:1]=[#6X3:2]-[#6X3:3]=[#8X1:4] 1 2.175 180.0 -2.0 parm99 CM-CM-C_-O Junmei et al, 1999
[#6X3:1]=[#6X3:2]-[#6X3:3]=[#8X1:4] 1 0.300 0.0 3.0 parm99 CM-CM-C_-O Junmei et al, 1999
# Csp bonds dealt with later
#
# C-N bonds
# note : the following general trivalent Nsp3 means conj N must come after
[*:1]-[#6X4:2]-[#7X4:3]-[*:4] 1 0.156 0.0 3.0 parm99 X_-CT-N3-X JCC,7,(1986),230
[*:1]-[#6X4:2]-[#7X3:3]-[*:4] 1 0.300 0.0 3.0 parm99 X_-CT-NT-X Junmei et al, 1999
[#6X4:1]-[#6X4:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.300 0.0 -3.0 parm99 CT-CT-NT-CT Junmei et al, 1999
[#6X4:1]-[#6X4:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.480 180.0 2.0 parm99 CT-CT-NT-CT Junmei et al, 1999
# trivalent Nsp3-Csp3cyclopropyl
[*:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4] 1 1.000 0.0 3 Frosst CT-N3-CJ-CJ from CT-CT-CJ-CJ
[#1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4] 1 0.000 0.0 1 Frosst generic
[#1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 2.700 0.0 1 Frosst H_-N3-CJ-CJ from CJ-CJ-CJ-HC
[!1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[*:4] 1 0.156 0.0 3 Frosst CT-N3-CJ-CT N3-CT-CJ-CJ
[!#1:1]-[#7X4,#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.000 0.0 3 Frosst SO-N3-CJ-CJ from S-CT-CJ-CJ
#
# conj trivalent Nsp3-Csp2
[*:1]-[#7X4:2]-[#6X3:3]~[*:4] 1 0.000 0.0 1 Frosst generic
# conj trivalent Nsp2-Csp3
[*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 -2.0 parm99 X_-CT-N2,N,N*-X JCC,7,(1986),230
[*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 3.0 parm99 X_-CT-N2,N,N*-X JCC,7,(1986),230
[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.850 180.0 -2.0 parm99 C_-N_-CT-C
[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.800 0.0 1.0 parm99 C_-N_-CT-C
[#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.500 180.0 -4.0 parm99 CT-CT-N_-C phi,psi,parm94
[#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.150 180.0 -3.0 parm99 CT-CT-#7_-C phi,psi,parm94
[#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.000 0.0 -2.0 parm99 CT-CT-N_-C JCC,7,(1986),230
[#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.530 0.0 1.0 parm99 CT-CT-N_-C phi,psi,parm94
[#8X2H0:1]-[#6X4:2]-[#7X3:3]-[#6X3:4] 1 0.000 0.0 -2.0 parm99 OS-CT-N*-CK parm98, TC,PC,PAK
[#8X2H0:1]-[#6X4:2]-[#7X3:3]-[#6X3:4] 1 2.500 0.0 1.0 parm99 OS-CT-N*-CK parm98, TC,PC,PAK
# trivalent Nsp2-Csp3cyclopropyl
[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -3 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008
[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.750 0.0 -2 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008
[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.250 0.0 1 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008
# divalent Nsp2-Csp3
[*:1]~[#7X2:2]-[#6X4:3]-[*:4] 1 0.000 0.0 1 Frosst generic
[#6X3:1]=[#7X2,#7X3+1:2]-[#6X4:3]-[#1:4] 1 0.500 0.0 1 Frosst generic
[#6X3:1]=[#7X2,#7X3+1:2]-[#6X4:3]-[#6X3,#6X4:4] 1 1.000 0.0 1 Frosst generic
#
# trivalent Nsp2-Csp2 : conjugation is important (Nsp2 pyramidalization and torsion barrier)
[*:1]~[#7X3,#7X2-1:2]-[#6X3:3]~[*:4] 1 1. 180.0 2 Frosst generic
#
[*:1]~[#7X3,#7X2-1:2]-!@[#6X3:3]~[*:4] 1 0.625 180.0 2 Frosst generic conjugated exocyclic
[#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] 1 2.500 180.0 -2.0 parm99 H_-N_-C_-O JCC,7,(1986),230
[#1:1]-[#7X3:2]-[#6X3:3]=[#8,#16,#7:4] 1 2.000 0.0 1.0 parm99 H_-N_-C_-O J.C.cistrans-NMA DE
[*:1]-[#7X3;r5:2]-@[#6X3;r5:3]~[*:4] 1 1.40 180.0 2 Frosst generic het5
[#8X1:1]~[#7X3:2]~[#6X3:3]~[*:4] 1 3.600 180.0 2 Frosst O2-N_-CB-CB N-oxide From CA-CA-CA-CA Oct 14 2008
#
# divalent N~Csp2 : conjugation important here but usually endocyclic
# divalent N-Csp2
[*:1]=[#7X2,#7X3+1:2]-[#6X3:3]-[*:4] 1 0.0 180.0 2 Frosst generic
[*:1]=[#7X2,#7X3+1:2]-[#6X3:3]=,:[*:4] 1 1.5 180.0 2 Frosst generic
# divalent Naro-Caro
[*:1]~[#7X2,#7X3$(*~[#8X1]):2]:[#6X3:3]~[*:4] 1 3. 180.0 2 Frosst generic
[#6X3:1]:[#7X2:2]:[#6X3:3]:[#6X3:4] 1 4.800 180.0 2 Frosst generic
# divalent N=Csp2
[*:1]-,:[#6X3:2]=[#7X2:3]-[*:4] 1 5. 180.0 2.0 parm99 generic
[*:1]-[#7X3+1:2]=,:[#6X3:3]-,:[*:4] 1 2.400 180.0 2 Frosst generic Amidine,guanidine
[#16X4,#16X3+0:1]-[#7X2:2]=[#6X3:3]-[#7X3:4] 1 7.500 180.0 2 Frosst SO-NB-C*-N* RHF/6-31G(d) Mar 7 2007
[#16X4,#16X3+0:1]-[#7X2:2]=[#6X3:3]-[#16X2,#16X3+1:4] 1 7.500 180.0 2 Frosst SO-NB-C*-S RHF/6-31G(d) Mar 7 2007
#
# univalent N: corner cases such as azides
[#7X1:1]~[#7X2:2]-[#6X3:3]~[#6X3:4] 1 0.500 180.0 2 Frosst NL-NL-CA-CA guess
[#7X1:1]~[#7X2:2]-[#6X4:3]-[#6X3:4] 1 0.000 0.0 2 Frosst NL-NL-CT-CA guess
[#7X1:1]~[#7X2:2]-[#6X4:3]~[#1:4] 1 0.000 0.0 2 Frosst NL-NL-CT-H1 guess
#
# C-O bonds
# O-Csp3
[*:1]-[#6X4:2]-[#8X2:3]-[#1:4] 3 0.500 0.0 -3.0 parm99 X_-CT-OH-X JCC,7,(1986),230
[#6X4:1]-[#6X4:2]-[#8X2H1:3]-[#1:4] 1 0.160 0.0 -3.0 parm99 HO-OH-CT-CT Junmei et al, 1999
[#6X4:1]-[#6X4:2]-[#8X2H1:3]-[#1:4] 1 0.250 0.0 1.0 parm99 HO-OH-CT-CT Junmei et al, 1999
[a,A:1]-[#6X4:2]-[#8X2:3]-[!#1:4] 3 1.150 0.0 -3.0 Frosst X_-CT-OS-X AlkEthOH
[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-CT
[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.100 180.0 2.0 parm99 CT-CT-OS-CT
[#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X3:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-C Junmei et al, 1999
[#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X3:4] 1 0.800 180.0 1.0 parm99 CT-CT-OS-C Junmei et al, 1999
[#6X4:1]-[#8X2:2]-[#6X4:3]-[#8X2H0:4] 1 0.100 0.0 -3.0 parm99 CT-OS-CT-OS Junmei et al, 1999
[#6X4:1]-[#8X2:2]-[#6X4:3]-[#8X2H0:4] 1 0.850 180.0 2.0 parm99 CT-OS-CT-OS Junmei et al, 1999
[#6X4:1]-[#8X2:2]-[#6X4:3]-[#8X2H0:4] 1 1.350 180.0 1.0 parm99 CT-OS-CT-OS Junmei et al, 1999
[#6X4:1]-[#8X2:2]-[#6X4:3]-[#7X3:4] 1 0.383 0.0 -3.0 parm99 CT-OS-CT-N* parm98.dat, TC,PC,PAK
[#6X4:1]-[#8X2:2]-[#6X4:3]-[#7X3:4] 1 0.650 0.0 2.0 parm99 CT-OS-CT-N* Piotr et al.
# O-Csp3cyclopropyl
[#6X3:1]-[#8X2:2]-[#6X4;r3:3]-@[#6X4;r3:4] 1 0.000 0.0 1 Frosst CA-OS-CJ-CJ guess; 26 April 2006
[#6X3:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.000 0.0 1 Frosst CA-OS-CJ-H1 guess; 26 April 2006
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.500 0.0 2 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004
[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004
# O-Csp2
[*:1]~[#6X3:2]-[#8X2:3]-[*:4] 1 1.050 180.0 2.0 parm99 X_-CM-OS-X Junmei et al, 1999
[*:1]~[#6X3:2]-[#8X2:3]-[#1:4] 1 0.900 180.0 2.0 parm99 X_-CA-OH-X Junmei et al, 99
[*:1]~[#6X3:2](=[#8,#16,#7])-[#8X2H0:3]-[*:4] 1 2.700 180.0 2.0 parm99 X_-C_-OS-X Junmei et al, 1999
[*:1]~[#6X3:2](=[#8,#16,#7])-[#8:3]-[#1:4] 1 2.300 180.0 2.0 parm99 X_-C_-OH-X Junmei et al, 1999
[#1:1]-[#8X2:2]-[#6X3:3]=[#8X1:4] 1 2.300 180.0 -2.0 parm99 HO-OH-C_-O Junmei et al, 1999
[#1:1]-[#8X2:2]-[#6X3:3]=[#8X1:4] 1 1.900 0.0 1.0 parm99 HO-OH-C_-O Junmei et al, 1999
[#8,#16,#7:1]=[#6X3:2]-[#8X2H0:3]-[#6X4:4] 1 2.700 180.0 -2.0 parm99 O_-C_-OS-CT Junmei et al, 1999
[#8,#16,#7:1]=[#6X3:2]-[#8X2H0:3]-[#6X4:4] 1 1.400 180.0 1.0 parm99 O_-C_-OS-CT Junmei et al, 1999
[#1:1]-[#8X2H1:2]-@[#6X3:3]~[*:4] 1 2.500 180.0 2 Frosst generic endocyclic
[*:1]-[#8X2+1:2]=[#6X3:3]-[*:4] 1 3. 180.0 2 smirnoff generic oxonium guess
[*:1]=[#8X2+1:2]-[#6:3]~[*:4] 1 0.5 180.0 2 smirnoff generic oxonium guess
#
# S-C bonds
# divalent S-C
[*:1]-[#16X2,#16X3+1:2]-[#6:3]~[*:4] 1 0.333 180.0 2 parm99 X_-CT-S_-X JCC,7,(1986),230
[*:1]-[#16X2,#16X3+1:2]-[#6:3]-[#1:4] 1 0.250 0.0 3 parm99 X_-CT-SH-X JCC,7,(1986),230
[#6X3:1]-@[#16X2,#16X1-1,#16X3+1:2]-@[#6X3,#7X2;r5:3]=@[#6,#7;r5:4] 1 2. 180.0 2 Frosst generic divalent S in het5
# hypervalent S-C
[*:1]~[#16X4,#16X3+0:2]-[#6X4:3]-[*:4] 1 0.000 0.0 3 Frosst X_-SO-CT-X guess
[#6X4:1]-[#16X4,#16X3+0:2]-[#6X4:3]-[#1:4] 1 0.250 0.0 1 Frosst CT-SO-CT-H1 RHF/6-41G(d,p) Dec 12 1997
[#6X4:1]-[#16X4,#16X3+0:2]-[#6X4:3]~[#6X4:4] 1 0.800 0.0 3 Frosst CT-SO-CT-CT RHF/6-41G(d,p) Dec 12 1997
[*:1]~[#16X4,#16X3+0:2]-[#6X3:3]~[*:4] 1 1.750 180.0 2 Frosst X_-SO-CA-X generic guess
[#6:1]-[#16X4,#16X3+0:2]-[#6X3:3]~[*:4] 1 0.750 0.0 1 Frosst generic
#
# P-C bonds : note these are implicitly hypervalent P
[*:1]~[#15:2]-[#6:3]-[*:4] 1 0.000 0.0 1 Frosst X_-P_-CT-X dummy
[*:1]~[#15:2]-[#6X3:3]~[*:4] 1 1.000 0.0 1 Frosst X_-P_-CA-X dummy
#
# O-N bonds
[*:1]~[#8X2:2]-[#7:3]~[*:4] 1 0.000 0.0 1 Frosst generic
[*:1]-[#8X2r5:2]-;@[#7X3r5:3]~[*:4] 1 0.000 0.0 1 Frosst generic het5 endocyclic
[*:1]-[#8X2r5:2]-;@[#7X2r5:3]~[*:4] 1 0.000 0.0 1 Frosst generic het5 endocyclic
#
# N-N bonds
# trivalent Nsp3 - trivalent Nsp3
# note : the following general trivalent Nsp3 means conj N must come after
[*:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[*:4] 1 0. 0.0 3 Frosst generic
[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.125 0.0 -3 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98
[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.875 0.0 -2 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98
[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.750 0.0 1 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98
[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.400 0.0 -3 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98
[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 2.150 0.0 -2 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98
[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.200 0.0 1 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98
[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.375 0.0 -3 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98
[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.125 0.0 -2 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98
[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98
# trivalent Nsp3 - trivalent Nsp2
[*:1]-[#7X4,#7X3:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 1 Frosst generic
# trivalent Nsp2 - trivalent Nsp2
[*:1]-[#7X3$(*-[#6X3,#6X2]):2]-[#7X3$(*-[#6X3,#6X2]):3]-[*:4] 1 0.000 0.0 1 Frosst X_-N2-N_-X June 29 2007
[*:1]-[#7X3$(*-[#6X3,#6X2])r5:2]-@[#7X3$(*-[#6X3,#6X2])r5:3]~[*:4] 1 3.600 180.0 2 Frosst generic het5 endocyclic
# divalent N-N
[*:1]~[#7X2:2]-[#7X3:3]~[*:4] 1 0.625 180.0 1 Frosst generic CIBayly2016sep:barrier seems small
[*:1]=[#7X2:2]-[#7X2:3]=[*:4] 1 1.4 180.0 1 Frosst generic guess
[*:1]~[#7X2:2]=,:[#7X2:3]~[*:4] 1 6.000 180.0 1 Frosst X_-NB-NB-X
[*:1]~[#7X3+1:2]=,:[#7X2:3]~[*:4] 1 3.000 180.0 1 Frosst X_-NB-NB-X
# univalent N
[#6:1]-[#7X2:2]~[#7X2:3]~[#7X1:4] 1 0.000 0.0 2 Frosst generic
#
# divalent S-N (or S-notCarbon)
[*:1]-[#16X2,#16X3+1:2]-[!#6:3]~[*:4] 1 0.0 180.0 2 smirnoff placeholder guess
# hypS-N
[*:1]~[#16X4,#16X3+0:2]-[#7:3]~[*:4] 1 0.000 0.0 1 Frosst generic
# hypS-Nsp3 trivalent : assumes N is not conjugated (although it could be on the other substituent on the N)
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.000 0.0 1 Frosst CT-SO-N3-H RHF/6-41G(d,p) Dec 12 1997
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.500 0.0 3 Frosst CA-SO-N3-H RHF/6-41G(d,p) Dec 12 1997
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.500 0.0 -1 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.750 0.0 3 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 1.000 180.0 -1 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.250 0.0 3 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.200 0.0 -3 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.300 180.0 -2 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009
# hypS-Nsp2 trivalent
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CA similar to case with CT instead of CA
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CA similar to case with CT instead of CA
[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CA similar to case with CT instead of CA
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 90.0 -3 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.375 0.0 2 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.750 0.0 1 Frosst O_-SO-N3-CA similar to case with CT instead of CA
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X3:3]-[#7X2:4] 1 0.000 0.0 1 Frosst O_-SO-N3-NB guess
# hypS-Nsp2 divalent
[*:1]~[#16X4,#16X3+0:2]=,:[#7X2:3]-,:[*:4] 1 0. 0.0 1 smirnoff generic TEMPORARY PLACEHOLDER
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.040 0.0 -6 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.407 0.0 -5 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.013 0.0 -4 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.018 0.0 -3 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.329 180.0 -2 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.927 0.0 1 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.071 0.0 -6 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.697 0.0 -5 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.208 180.0 -4 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 3.931 180.0 -2 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.940 180.0 -3 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007
[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 2.448 0.0 1 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007
# hypS-Odivalent
[*:1]~[#16X4,#16X3+0:2]-[#8X2:3]-[*:4] 1 0.000 0.0 1 Frosst generic
#
# S-S bonds
[*:1]-[#16X2,#16X3+1:2]-[#16X2,#16X3+1:3]-[*:4] 1 3.500 0.0 -2 Frosst generic from parm99 CT-S_-S_-CT JCC,7,(1986),230
[*:1]-[#16X2,#16X3+1:2]-[#16X2,#16X3+1:3]-[*:4] 1 0.600 0.0 3 Frosst generic from parm99 CT-S_-S_-CT JCC,7,(1986),230
#
# O-P bonds
[*:1]-[#8X2:2]-[#15:3]~[*:4] 1 0.750 0.0 3.0 parm99 X_-OS-P_-X JCC,7,(1986),230
[#8X2:1]-[#15:2]-[#8X2:3]-[#6X4:4] 1 0.250 0.0 -3.0 parm99 OS-P_-OS-CT JCC,7,(1986),230
[#8X2:1]-[#15:2]-[#8X2:3]-[#6X4:4] 1 1.200 0.0 2.0 parm99 OS-P_-OS-CT gg> ene.631g*/mp2
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# torsions involving linear bonds (acetylene, nitrile, azide) cannot have a real torsion angle
[*:1]-[*:2]#[*:3]-[*:4] 1 0.000 0.0 1 Frosst generic
[*:1]~[*:2]-[*:3]#[*:4] 1 0.000 0.0 1 Frosst generic
[*:1]~[*:2]=[#6,#7,#16,#15;X2:3]=[*:4] 1 0.000 0.0 1 smirnoff generic allene-like or isothiocyanate-like
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IMPR
[*:1]~[#6X3:2](~[*:3])~[*:4] 1.1 180. 2. parm99 generic Csp2
[*:1]~[#6X3:2](~[#8X1:3])~[#8:4] 10.5 180. 2. parm99 generic -COO-H,R,-1
[*:1]~[#7X3$(*~[#6X3]):2](~[*:3])~[*:4] 1.0 180. 2. parm99 generic Nsp2
[*:1]~[#6X3:2](=[#7X2,#7X3+1:3])~[#7:4] 10.5 180. 2. Frosst generic amidinium,guanidinium