#	(c) Copyright 1995 by Garry Paul Gippert, All Rights Reserved 
# GAP/TORDEF.LIB
#
# Garry Gippert, The Scripps Research Institute, 1995
# garry@scripps.edu
#
# $Id: tordef.lib,v 1.5 1997/05/21 06:50:33 garry Exp $
# WHEN REPORTING ERRORS, PLEASE INCLUDE THE ENTIRE $Id LINE.
#
# This file contains Torsion Angle Definitions for standard
# (20+) amino-acid and (4) deoxyribo-nucleic-acid residues in
# approximately IUPAC atom nomenclature.
#
# NOTE: Atom nomenclature will vary according to philosophy,
# taste, program anacronisms, etc., therefore this library
# may not suit your needs.  Feel free to create your own copy
# of this library with your own modifications, but PLEASE
# contact the author with corrections, omissions.
#
# A "-" sign or "+" sign suffix to a familiar atom name tells
# the TORVIO program to look in the residue preceeding or
# following the current residue, respectively.
#
# Please do not confuse PDB format with IUPAC nomenclature.
# Contrary to opinion, the "wrapped" proton index is NOT
# "correct". PDB uses, for example, "1HG1" to represent one of
# the HG protons attached to CG1 in a Valine. I'm sorry, pdb,
# but the correct atom name is "HG11". The TORVIO program
# reads either wrapped or unwrapped proton indices, and
# compares the upwrapped name to the strings found here.
#
# NEW ADDITION!
# lines beginning with PSEUDO followed by torsion name (residue
# and torsion angle) and five torsion angle names will generate
# pseudo-rotation phase angles. If the five angles are called
# N0, N1, N2, N3, N4, then P is given by (From Saenger, p 20)
# P = arctan[ ((N4+N1)-(N3+N0))/(2*N2(sin 36deg + sin 72deg)) ].
#
ALA	OMEGA	CA-  C-   N    CA
ALA	PHI	C-   N    CA   C
ALA	PSI	N    CA   C    N+
ALA     CHI1    N    CA   CB   HB1
#
ARG	OMEGA	CA-  C-   N    CA
ARG	PHI	C-   N    CA   C
ARG	PSI	N    CA   C    N+
ARG	CHI1	N    CA   CB   CG
ARG	CHI2	CA   CB   CG   CD
ARG	CHI3	CB   CG   CD   NE
ARG	CHI4	CG   CD   NE   CZ
ARG	CHI5	CD   NE   CZ   NH1
ARG	CHI61	NE   CZ   NH1  HH11
ARG	CHI62	NE   CZ   NH2  HH21
#
ASN	OMEGA	CA-  C-   N    CA
ASN	PHI	C-   N    CA   C
ASN	PSI	N    CA   C    N+
ASN	CHI1	N    CA   CB   CG
ASN	CHI2	CA   CB   CG   OD1
ASN	CIS	OD1  CG   ND2  HD21
#
ASP	OMEGA	CA-  C-   N    CA
ASP	PHI	C-   N    CA   C
ASP	PSI	N    CA   C    N+
ASP	CHI1	N    CA   CB   CG
ASP	CHI2	CA   CB   CG   OD1
#
CYS	OMEGA	CA-  C-   N    CA
CYS	PHI	C-   N    CA   C
CYS	PSI	N    CA   C    N+
CYS	CHI1	N    CA   CB   SG
#
CYM	OMEGA	CA-  C-   N    CA
CYM	PHI	C-   N    CA   C
CYM	PSI	N    CA   C    N+
CYM	CHI1	N    CA   CB   SG
#
GLN	OMEGA	CA-  C-   N    CA
GLN	PHI	C-   N    CA   C
GLN	PSI	N    CA   C    N+
GLN	CHI1	N    CA   CB   CG
GLN	CHI2	CA   CB   CG   CD
GLN	CHI3	CB   CG   CD   OE1
GLN	CIS	OE1  CD   NE2  HE21
#
GLU	OMEGA	CA-  C-   N    CA
GLU	PHI	C-   N    CA   C
GLU	PSI	N    CA   C    N+
GLU	CHI1	N    CA   CB   CG
GLU	CHI2	CA   CB   CG   CD
GLU	CHI3	CB   CG   CD   OE1
#
GLY	OMEGA	CA-  C-   N    CA
GLY	PHI	C-   N    CA   C
GLY	PSI	N    CA   C    N+
#
HIS	OMEGA	CA-  C-   N    CA
HIS	PHI	C-   N    CA   C
HIS	PSI	N    CA   C    N+
HIS	CHI1	N    CA   CB   CG
HIS	CHI2	CA   CB   CG   ND1
#
HID	OMEGA	CA-  C-   N    CA
HID	PHI	C-   N    CA   C
HID	PSI	N    CA   C    N+
HID	CHI1	N    CA   CB   CG
HID	CHI2	CA   CB   CG   ND1
#
HIE	OMEGA	CA-  C-   N    CA
HIE	PHI	C-   N    CA   C
HIE	PSI	N    CA   C    N+
HIE	CHI1	N    CA   CB   CG
HIE	CHI2	CA   CB   CG   ND1
#
ILE	OMEGA	CA-  C-   N    CA
ILE	PHI	C-   N    CA   C
ILE	PSI	N    CA   C    N+
ILE	CHI1	N    CA   CB   CG1
ILE	CHI21	CA   CB   CG1  CD1
ILE     CHI22   CA   CB   CG2  HG21
ILE     CHI31   CB   CG1  CD1  HD11
#
LEU	OMEGA	CA-  C-   N    CA
LEU	PHI	C-   N    CA   C
LEU	PSI	N    CA   C    N+
LEU	CHI1	N    CA   CB   CG
LEU	CHI2	CA   CB   CG   CD1
LEU     CHI31   CB   CG   CD1  HD11
LEU     CHI32   CB   CG   CD2  HD21
#
LYS	OMEGA	CA-  C-   N    CA
LYS	PHI	C-   N    CA   C
LYS	PSI	N    CA   C    N+
LYS	CHI1	N    CA   CB   CG
LYS	CHI2	CA   CB   CG   CD
LYS	CHI3	CB   CG   CD   CE
LYS	CHI4	CG   CD   CE   NZ
LYS	CHI5	CD   CE   NZ   HZ1
#
MET	OMEGA	CA-  C-   N    CA
MET	PHI	C-   N    CA   C
MET	PSI	N    CA   C    N+
MET	CHI1	N    CA   CB   CG
MET	CHI2	CA   CB   CG   SD
MET	CHI3	CB   CG   SD   CE
MET     CHI4    CG   SD   CE   HE1
#
PHE	OMEGA	CA-  C-   N    CA
PHE	PHI	C-   N    CA   C
PHE	PSI	N    CA   C    N+
PHE	CHI1	N    CA   CB   CG
PHE	CHI2	CA   CB   CG   CD1
#
PRO	OMEGA	CA-  C-   N    CA
PRO	PHI	C-   N    CA   C
PRO	PSI	N    CA   C    N+
PRO	CHI1	N    CA   CB   CG
PRO	CHI2	CA   CB   CG   CD
PRO	CHI3	CB   CG   CD   N
PRO	CHI4	CG   CD   N    CA
PRO	THETA	CD   N    CA   CB
PRO 	CHI0	CD   N    CA   CB	#  aka
PSEUDO	PRO	PPA	CHI0	CHI1	CHI2	CHI3	CHI4
#
# also known as CPRO
CPR 	OMEGA	CA-  C-   N    CA
CPR 	PHI	C-   N    CA   C
CPR 	PSI	N    CA   C    N+
CPR 	CHI1	N    CA   CB   CG
CPR 	CHI2	CA   CB   CG   CD
CPR 	CHI3	CB   CG   CD   N
CPR 	CHI4	CG   CD   N    CA
CPR 	THETA	CD   N    CA   CB
CPR 	CHI0	CD   N    CA   CB	# aka
PSEUDO	CPR	PPA	CHI0	CHI1	CHI2	CHI3	CHI4
#
SER	OMEGA	CA-  C-   N    CA
SER	PHI	C-   N    CA   C
SER	PSI	N    CA   C    N+
SER	CHI1	N    CA   CB   OG
SER	CHI2	CA   CB   OG   HG
#
SEP	OMEGA	CA-  C-   N    CA
SEP	PHI	C-   N    CA   C
SEP	PSI	N    CA   C    N+
SEP	CHI1	N    CA   CB   OG
SEP	CHI2	CA   CB   OG   HG
#
THR	OMEGA	CA-  C-   N    CA
THR	PHI	C-   N    CA   C
THR	PSI	N    CA   C    N+
THR	CHI1	N    CA   CB   OG1
THR     CHI22   CA   CB   CG2  HG21
#
THP	OMEGA	CA-  C-   N    CA
THP	PHI	C-   N    CA   C
THP	PSI	N    CA   C    N+
THP	CHI1	N    CA   CB   OG1
THP     CHI22   CA   CB   CG2  HG21
#
TRP	OMEGA	CA-  C-   N    CA
TRP	PHI	C-   N    CA   C
TRP	PSI	N    CA   C    N+
TRP	CHI1	N    CA   CB   CG
TRP	CHI2	CA   CB   CG   CD1
#
TYR	OMEGA	CA-  C-   N    CA
TYR	PHI	C-   N    CA   C
TYR	PSI	N    CA   C    N+
TYR	CHI1	N    CA   CB   CG
TYR	CHI2	CA   CB   CG   CD1
#
TYP	OMEGA	CA-  C-   N    CA
TYP	PHI	C-   N    CA   C
TYP	PSI	N    CA   C    N+
TYP	CHI1	N    CA   CB   CG
TYP	CHI2	CA   CB   CG   CD1
#
VAL	OMEGA	CA-  C-   N    CA
VAL	PHI	C-   N    CA   C
VAL	PSI	N    CA   C    N+
VAL	CHI1	N    CA   CB   CG1
VAL     CHI21   CA   CB   CG1  HG11
VAL     CHI22   CA   CB   CG2  HG21
#
#
# STANDARD NUCLEIC ACIDS
#
# Deoxyribonucleic acids
#
ADE	ALPHA	O3'-	P	O5'	C5'
ADE	BETA	P	O5'	C5'	C4'
ADE	GAMMA	O5'	C5'	C4'	C3'
ADE	DELTA	C5'	C4'	C3'	O3'
ADE	EPSLN	C4'	C3'	O3'	P+
ADE	ZETA	C3'	O3'	P+	O5'+
ADE	NU0	C4'	O4'	C1'	C2'
ADE	NU1	O4'	C1'	C2'	C3'
ADE	NU2	C1'	C2'	C3'	C4'
ADE	NU3	C2'	C3'	C4'	O4'
ADE	NU4	C3'	C4'	O4'	C1'
ADE	CHI	O4'	C1'	N9	C4
# alternative spelling
ADE	EPSILON	C4'	C3'	O3'	P+
ADE	EPSILN	C4'	C3'	O3'	P+
# PSEUDO-ROTATION PHASE defined in terms of the NU angles
PSEUDO	ADE	PPA	NU0	NU1	NU2	NU3	NU4
#
THY	ALPHA	O3'-	P	O5'	C5'
THY	BETA	P	O5'	C5'	C4'
THY	GAMMA	O5'	C5'	C4'	C3'
THY	DELTA	C5'	C4'	C3'	O3'
THY	EPSLN	C4'	C3'	O3'	P+
THY	ZETA	C3'	O3'	P+	O5'+
THY	NU0	C4'	O4'	C1'	C2'
THY	NU1	O4'	C1'	C2'	C3'
THY	NU2	C1'	C2'	C3'	C4'
THY	NU3	C2'	C3'	C4'	O4'
THY	NU4	C3'	C4'	O4'	C1'
THY	CHI	O4'	C1'	N1	C2
# alternative spelling
THY	EPSILON	C4'	C3'	O3'	P+
THY	EPSILN	C4'	C3'	O3'	P+
# PSEUDO-ROTATION PHASE defined in terms of the NU angles
PSEUDO	THY	PPA	NU0	NU1	NU2	NU3	NU4
#
GUA	ALPHA	O3'-	P	O5'	C5'
GUA	BETA	P	O5'	C5'	C4'
GUA	GAMMA	O5'	C5'	C4'	C3'
GUA	DELTA	C5'	C4'	C3'	O3'
GUA	EPSLN	C4'	C3'	O3'	P+
GUA	ZETA	C3'	O3'	P+	O5'+
GUA	NU0	C4'	O4'	C1'	C2'
GUA	NU1	O4'	C1'	C2'	C3'
GUA	NU2	C1'	C2'	C3'	C4'
GUA	NU3	C2'	C3'	C4'	O4'
GUA	NU4	C3'	C4'	O4'	C1'
GUA	CHI	O4'	C1'	N9	C4
# alternative spelling
GUA	EPSILON	C4'	C3'	O3'	P+
GUA	EPSILN	C4'	C3'	O3'	P+
#
# PSEUDO-ROTATION PHASE defined in terms of the NU angles
PSEUDO	GUA	PPA	NU0	NU1	NU2	NU3	NU4
#
CYT	ALPHA	O3'-	P	O5'	C5'
CYT	BETA	P	O5'	C5'	C4'
CYT	GAMMA	O5'	C5'	C4'	C3'
CYT	DELTA	C5'	C4'	C3'	O3'
CYT	EPSLN	C4'	C3'	O3'	P+
CYT	ZETA	C3'	O3'	P+	O5'+
CYT	NU0	C4'	O4'	C1'	C2'
CYT	NU1	O4'	C1'	C2'	C3'
CYT	NU2	C1'	C2'	C3'	C4'
CYT	NU3	C2'	C3'	C4'	O4'
CYT	NU4	C3'	C4'	O4'	C1'
CYT	CHI	O4'	C1'	N1	C2
# alternative spelling
CYT	EPSILON	C4'	C3'	O3'	P+
CYT	EPSILN	C4'	C3'	O3'	P+
#
# PSEUDO-ROTATION PHASE defined in terms of the NU angles
PSEUDO	CYT	PPA	NU0	NU1	NU2	NU3	NU4