Mercurial > repos > marcel > caddsuite_linux_x86_64
diff CADDSuite-1.6/data/OpenBabel/torlib.txt @ 17:25a03362403c draft
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| author | marcel |
|---|---|
| date | Sat, 15 Dec 2012 13:10:41 -0500 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite-1.6/data/OpenBabel/torlib.txt Sat Dec 15 13:10:41 2012 -0500 @@ -0,0 +1,224 @@ +############################################################################## +# # +# Open Babel file: torlib.txt # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# First three lines represent: (used by rotor.cpp::OBRotorRules # +# Hybridization pair (atom types around a rotatable bond) # +# followed by a list of default bond rotation angles (in degrees) # +# # +# Later lines should specify: # +# * A SMARTS pattern for the rotor rule # +# * A set of 4 "reference atoms" (as integers, numbered from 1 # +# in the specified SMARTS pattern # +# * At least one torsion value (in degrees) # +# * Optionally ending with "Delta" and a delta value # +# (i.e., the resolution of a dihedral step # +# # +# SMARTS rules will be attempted first, then hybridization # +# # +############################################################################## + +SP3-SP3 60.0 -60.0 180.0 +SP2-SP2 0.0 180.0 -30.0 30.0 150.0 -150.0 +SP3-SP2 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0 + +# Many of these rules came from the Supporting Information +# from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801 + +#polysaccaride bridges +O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0 +O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0 + +#acids +[OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0 +[a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0 +[OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0 + +#sulfonamides +NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0 +c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0 +O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0 +O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0 +[c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0 +*=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0 +O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0 +[aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0 +[aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0 +[aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0 +[aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0 +[a]cS(=O)(=O)[C,N] 1 2 3 6 60.0 -60.0 90.0 -90.0 120.0 -120.0 0.0 180.0 +aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0 +aaNS(=O)(=O) 1 2 3 4 90.0 -90.0 + +#sulfone +O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0 + +#hydrazides +[O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0 +[O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0 + +#cyclopropyl-ketones +O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0 +O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0 +O=CC1([*])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 120.0 -120.0 90.0 -90.0 30.0 -30.0 + +#epoxy-ketone +O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0 + +#opposite end of tert amide +O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0 +O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 +O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0 + +#misc +[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0 +[cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.0 -110.0 +c[CD2][ND3](C)c 1 2 3 4 90.0 -90.0 60.0 -60.0 120.0 -120.0 + +#carbonyls +O=CC=O 1 2 3 4 180.0 0.0 120.0 -120.0 90.0 -90.0 +C=CC=O 1 2 3 4 0.0 180.0 20.0 -20.0 160.0 -160.0 +O=C[CD2][ND2] 1 2 3 4 0.0 -30.0 30.0 150.0 -150.0 180.0 +O=C[CD2]C=O 1 2 3 4 0.0 -30.0 30.0 60.0 -60.0 130.0 -130.0 +O=C(c)[ND2][CD3][#1] 2 4 5 6 0.0 -30.0 30.0 +O=C[ND2][CD3]* 2 3 4 5 20.0 -20.0 120 -120.0 60.0 -60.0 0.0 +O=CN[CD2]* 2 3 4 5 180.0 150.0 -150.0 -120.0 120.0 0.0 30.0 -30.0 +O=Ccc[OD1] 1 2 3 4 0.0 180.0 90.0 -90.0 30.0 -30.0 +O=C[CD4][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 +O=C[CD3][OD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 +O=C[CD2][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0 +O=C[CD3][#1] 1 2 3 4 0.0 30.0 -30.0 180.0 +#O=C[CD3]* 1 2 3 4 0.0 90.0 -90.0 30.0 -30.0 -120.0 120.0 60.0 -60.0 + +#amidene and guanidine +[aD3]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0 +[a]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0 +*[ND2]~C(~[ND1])~[ND1] 1 2 3 4 0.0 30.0 +[CD2][CD2][ND2]~C(~[ND1])~[ND1] 1 2 3 4 -70.0 70.0 90.0 -90.0 110.0 -110.0 + +#ether +aCO[CD2] 1 2 3 4 180.0 100.0 -100.0 + +#isoprene +C=C[CX4D2]* 1 2 3 4 0.0 180.0 90.0 -90.0 60.0 -60.0 30.0 -30.0 +C=Cc[a] 1 2 3 4 0.0 90.0 -90.0 180.0 30.0 -30.0 150.0 -150.0 + +#aryl secondary amines +[aD2]c([aD2])[ND2][CD2] 1 2 4 5 0.0 180.0 +[aD2]c([aD3])[ND2][CD2] 1 2 4 5 0.0 +[aD2]c([aD2])[ND2][CD1] 1 2 4 5 0.0 90.0 -90.0 180.0 +ac[ND2][CD2] 1 2 3 4 90.0 -90.0 160.0 -160.0 20.0 -20.0 + +#aromatic subtituents +[aD3]c([aD3])[CD2]C 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0 +[aD2]c([aD2])[ND3]([CD1])[CD2] 1 2 4 5 0.0 180.0 +[aD3][c,n]([aD2])[C^3D3][#1] 1 2 4 5 0.0 -30.0 30.0 60.0 -60.0 160.0 -160.0 +a[CD2X4][ND3^3]* 1 2 3 4 60.0 -60.0 180.0 160.0 -160.0 90.0 -90.0 120.0 -120.0 +an[CD2X4][CD1] 1 2 3 4 90.0 -90.0 +[aD3]c([aD2])C(=O)[C^3] 1 2 4 5 0.0 20.0 -20.0 150.0 -150.0 180.0 +[aD3]c([aD2])O[CD2] 1 2 3 4 180.0 +a[ND2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0 +[ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0 +[aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0 +[a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0 +[a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0 +[a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 +[a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 + +#borderline low-res +[CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0 + +#conjugated substituents +a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0 +C=CC=C 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 60.0 -60.0 120.0 -120.0 +cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0 +C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0 +c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0 +C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0 + +#ureas +[ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0 +[ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0 + +#carbamates +C[ND2]C(=O)O 1 2 3 4 0.0 180.0 +[ND2]C(=O)OC 3 2 4 5 0.0 +OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0 + +#piperidine amide +O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0 + +#amides and esters +[*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 +[OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0 +[O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0 +[O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0 +[O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0 +[O,SD1]=C(C)cn 1 2 4 5 0.0 180.0 +[O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0 +[O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180 +O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0 +O=CNc([aD2,aD3])[aD3] 2 3 4 5 20.0 -20.0 -90.0 90.0 60.0 -60.0 120.0 -120.0 0.0 +O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0 +O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0 +O=C([CD1])O[CD1] 1 2 4 5 0.0 +[O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0 +O=CO[CD2][CD1] 2 3 4 5 0.0 180.0 +O=CO[CD2]* 2 3 4 5 180.0 60.0 0.0 -60.0 90.0 -90.0 +O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0 +O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0 +O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 +O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 +O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0 +O=C[ND3]* 1 2 3 4 0.0 180.0 +CC[ND3](CC)[CD2,CD3]* 2 3 6 7 180.0 60.0 -60.0 120.0 -120.0 0.0 180.0 30.0 -30.0 +[a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0 +[ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0 +[CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0 + +#t-butyl +C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0 +**C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0 + +#propyl +[CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0 + +#highly substituted alkane +#[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 +*[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0 +c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0 +[CD2^3][CD2^3][CD3^3][#1] 1 2 3 4 60.0 -60.0 180.0 30.0 -30.0 0.0 160.0 -160.0 120.0 -120.0 +[*D2][CD2][CRH]([*R])[*R] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 0.0 +[*D2][CD2][CX4D3][*D2] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 +*[CHD3][CH2D2]* 1 2 3 4 150.0 -150.0 60.0 -60.0 180.0 -90.0 90.0 0.0 30.0 -30.0 +[CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0 + +#long unsubstituted alkanes +[CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0 +[CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0 +[CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0 +[*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0 + +#nitro +[aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0 +[a]cN(~[OD1])~[OD1] 1 2 3 4 0.0 + +#trifluoromethyl +**C(F)(F)F 1 2 3 4 0.0 + +#trichloromethyl +[a]cC(Cl)(Cl)Cl 1 2 3 4 0.0 + +#CSD SPECIFIC RULES +a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0 +PPcc 1 2 3 4 60.0 -60.0 + +#phosphorus containing groups +#[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0 +#[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0 +#S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0 +#[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0