# peptide_def.par  -- This file Defines the Atoms and Residue of a ALL
#			Amino Acids Used by a variety of programs
#	Line begining with a # is a Comment line and ignored
#	Blank lines Separate one Record or List from the next
#	Spaces and Tabs separate entries within a record

ATOM_NAMES
	N         ND1       HZ1       HN        ND2       HZ2  
	C         HD1       HZ3       O         HD2       OH   
	CA        HD21      HH        HA        HD22      HH2  
	CB        HD1#      HH11      HB1       CE        HH12 
	HB2       CE1       HH21      HB#       CE2       HH22 
	CG        CE3       NH1       CG1       OE1       NH2  
	CG2       OE2       CH2       OG        NE        HE21 
	OG1       NE1       HE22      SG        NE2       HA1  
	HG        HE        HA2       HG1       HE1       HD   
	HG2       HE2       HB        HG1#      HE3       HG2# 
	CD        CZ        HD2#      CD1       CZ2       HG11 
	CD2       CZ3       HG12      OD1       NZ        HE#  
	OD2       HZ        HA#       HG#       HD#       HZ#
	HH1#      HH2#      HE2#      HT#       HB3       HG21
	HG22      HG23      HD11      HD12      HD13      HT1
	HT2       HT3       HD23      HG13      OT1       OT2
	SD        HG*       HD*       HAR
   	HAR1      HAR2      HAR3      HAR4      HAR5      HAR6
    HAR7      HAR8      HAR9      HAR10     HAR11     HAR12
    HAR13     HAR14     HAR15     HAR16     HAR17     HAR18 
    HAR19     HAR20     HAR21     HAR22     HAR23     HAR24 
    HAR25 


RESIDUE_NAMES
	BLNK  GLY   ALA   VAL   ILE   LEU   PHE   PRO   MET   TRP   CYS   
	SER   THR   ASN   GLN   TYR   HIS   HIH   ASP   GLU   LYS   ARG   
	RES   ARO


AA_DEFINITIONS
	AMINO_ACID  BLNK   
		CHAR_CODE	0   
		VALID_ATOMS	
		EXCHANGEABLE	
		SIDE_CHAIN
		BOND_ATOMS


	AMINO_ACID  GLY   
		CHAR_CODE	G   
		VALID_ATOMS	N  HN  CA  HA1  HA2  HA#  C  O
		EXCHANGEABLE	HN
		SIDE_CHAIN
		BOND_ATOMS	N HN   N CA  C O  CA HA1   CA HA2   CA HA#
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HA#	FAST	HA1  HA2


	AMINO_ACID  ALA   
		CHAR_CODE	A
		VALID_ATOMS	N  HN  CA  HA  CB  HB#  HB1 HB2 HB3 C  O
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB# HB1 HB2 HB3
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB HB# -
				CB HB1  CB HB2  CB HB3
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1  HB2 HB3


	AMINO_ACID  VAL   
		CHAR_CODE	V
		VALID_ATOMS	N  HN  CA  HA  CB  HB  CG1  HG1#  -
				CG2  HG2#  C  O  HG11  HG12  HG13  -
				HG21  HG22  HG23  HG# 
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB  CG1  HG1#  CG2  HG2# HG11  HG12  HG13  -
				HG21  HG22  HG23 HG#
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB HB -
				CB CG1  CB CG2  CG1 HG1#  CG2 HG2# -
				CG1 HG11  CG1 HG12  CG1 HG13 -
				CG2 HG21  CG2 HG22  CG2 HG23
		AVRG_ATOM_TBL
		   AVRG_ATOM    Type    True Names
			HG1#	FAST	HG11 HG12 HG13
			HG2#	FAST	HG21 HG22 HG23
			HG# 	SLOW	HG2# HG1#


	AMINO_ACID  ILE   
		CHAR_CODE	I
		VALID_ATOMS	N  HN  CA  HA  CB  HB  CG1  HG11  -
				HG12  HG1# CG2  HG2#  CD  HD#  CD1  HD1#  C  O -
				HG21 HG22 HG23 HD11 HD12 HD13
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB  CG1  HG11  HG12  HG1# CG2  -
				HG2#  CD  HD#  CD1  HD1# -
				HG21 HG22 HG23 HD11 HD12 HD13
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB HB -
				CB CG1  CB CG2  CG1 HG11  CG1 HG12  CG1 HG1#-
				CG2 HG2#  CG1 CD  CD HD#  CG1 CD1  CD1 HD1# -
				CG HG21  CG HG22  CG HG23  -
				CD HD11  CD HD12  CD HD13
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HG1#	FAST	HG11 HG12
			HD1#    ALIAS   HD#
			HD#     ALIAS   HD1#
			HG2#	FAST	HG21 HG22 HG23
			HD1#	FAST	HD11 HD12 HD13
#	IUPAC name is HD1# but this atom has previously been called HD#


	AMINO_ACID  LEU   
		CHAR_CODE	L
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG -
				HG  CD1  HD1#  CD2  HD2#  HD#  C  O -
				HD11  HD12  HD13  HD21  HD22 HD23
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG  CD1  HD1# -
				CD2  HD2# HD11  HD12  HD13  HD21  HD22 HD23 HD#
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CB CG  CG CD1  -
				CG CD2  CG HG  CD1 HD1#  CD2 HD2# -
				CD1 HD11  CD1 HD12  CD1 HD13  -
				CD2 HD21  CD2 HD22 CD2 HD23
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	    FAST	HB1 HB2
			HD1#	FAST	HD11 HD12 HD13
			HD2#	FAST	HD21 HD22 HD23
			HD# 	SLOW	HD1# HD2#


	AMINO_ACID  PHE   
		CHAR_CODE	F
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				CD1  HD1  CD2  HD2  CE1  HE1  CE2 -
				HD#  HE#  HE2  CZ  HZ  C  O
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  CD1  HD1  CD2  -
				HD2  CE1  HE1  CE2  HE2  CZ  HZ HD# HE#
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB CG -
				CB HB1  CB HB2  CB HB#  CG CD1  CG CD2 -
				CD1 CE1  CD2 CE2  CD1 HD1  CD2 HD2 -
				CE1 CZ  CE2 CZ  CE1 HE1  CE2 HE2  CZ HZ
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HD#	SLOW	HD1 HD2
			HE#	SLOW	HE1 HE2


	AMINO_ACID  PRO   
		CHAR_CODE	P
		VALID_ATOMS	N  CA  HA  CB  HB1  HB2  HB#  CG  HG1  -
				HG2  HG#  CD  HD1  HD2  HD#  C  O
		EXCHANGEABLE	
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG1  HG2  CD  -
				HD1  HD2  HD#
		BOND_ATOMS	N CD  N CA  C O  CA HA   CA CB   CB CG -
				CB HB1  CB HB2  CB HB#  CG CD  CG HG1 -
				CG HG2  CG HG#  CD HD1 CD HD2  CD HD#
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG#	FAST	HG1 HG2
			HD#	FAST	HD1 HD2


	AMINO_ACID  MET   
		CHAR_CODE	M
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				HG1  HG2  HG#  CE  HE#  C  O SD HE1 HE2 HE3
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG1  HG2  HG#  -
				CE  HE# SD HE1 HE2 HE3
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB   CB CG -
				CB HB1  CB HB2  CG HG1  CG HG2  CG HG# -
				CB HB#  CE HE#  CE HE1  CE HE2  CE HE3
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG#	FAST	HG1 HG2
			HE#	FAST	HE1 HE2 HE3


	AMINO_ACID  TRP   
		CHAR_CODE	W
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG -
				CD1  HD1  CD2  NE1  HE1  CE2  CE3  HE3-
				CZ2  HZ2  CZ3  HZ3  CH2  HH2  C  O
		EXCHANGEABLE	HN  HE1
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  CD1  HD1  CD2 -
				NE1  HE1  CE2  CE3  HE3  CZ2  HZ2   -
				CZ3  HZ3  CH2  HH2
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG CD1  CG CD2 -
				CD1 NE1  CD2 CE2  CD2 CE3  CD1 HD1 -
				NE1 CE2  CE2 CZ2  CE3 CZ3  CE3 HE3 -
				NE1 HE1  CZ2 CH2  CZ3 CH2  CZ2 HZ2 -
				CZ3 HZ3  CH2 HH2
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2


	AMINO_ACID  CYS   
		CHAR_CODE	C
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  SG HG C  O
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB# HG
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB HB1 -
				CB HB2  CB HB#  SG HG
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2


	AMINO_ACID  SER   
		CHAR_CODE	S
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  OG -
				HG1  HG  C  O  OT1 OT2
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  OG  HG1 HG  OT1 OT2
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB HB1 -
				CB HB2  CB HB#  CB OG  HG1 OG   HG OG
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG	ALIAS   HG1
			HG1	ALIAS   HG
#	IUPAC name is HG but this atom has previously been called HG1


	AMINO_ACID  THR   
		CHAR_CODE	T
		VALID_ATOMS	N  HN  CA  HA  CB  HB   OG1  HG1  CG2 -
				HG2#  HG21  HG22  HG23  C  O
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB   OG1  HG1 CG2  HG2# HG21  HG22  HG23
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB OG1 -
				CB CG2  CB HB  OG1 HG1  CG2 HG2# -
				CG2 HG21  CG2 HG22  CG2 HG23
		AVRG_ATOM_TBL
		   AVRG_ATOM    Type    True Names
			HG2#	FAST	HG21  HG22  HG23


	AMINO_ACID  RES
		CHAR_CODE	X
		VALID_ATOMS	N  HN  CA  HA  CB  HB   OG1  HG1 HG2 CG2-
				HG1# HG2#  HG21  HG22  HG23  C  O HA1 HA2 HB1 HB2 HB#-
				HG HG# HD1 HD2 HD1# HD2# HD#
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB   OG1  HG1 CG2  HG2# HG21  HG22  HG23
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB OG1 -
				CB CG2  CB HB  OG1 HG1  CG2 HG2# -
				CG2 HG21  CG2 HG22  CG2 HG23
		AVRG_ATOM_TBL
		   AVRG_ATOM    Type    True Names
            HG2#   FAST    HG21  HG22  HG23	


	AMINO_ACID  ARO
		CHAR_CODE	Z
		VALID_ATOMS	HAR1 HAR2 HAR3 HAR4 HAR5 HAR6 HAR7 HAR8 HAR9 HAR10-
                   HAR11 HAR12 HAR13 HAR14 HAR15 HAR16 HAR17 HAR18 HAR19-
                   HAR20 HAR21 HAR22 HAR23 HAR24 HAR25- 
		           N  HN  CA  HA  CB  HB   OG1  HG1 HG2 CG2-
				   HG1# HG2#  HG21  HG22  HG23  C  O HA1 HA2 HB1 HB2 HB#-
				   HG HG# HD1 HD2 HD1# HD2# HD#
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB   OG1  HG1 CG2  HG2# HG21  HG22  HG23
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB OG1 -
				CB CG2  CB HB  OG1 HG1  CG2 HG2# -
				CG2 HG21  CG2 HG22  CG2 HG23 HAR1 HAR2 HAR2 HAR3 -
                                HAR3 HAR4 HAR4 HAR5 HAR5 HAR6 HAR6 HAR7 HAR7 HAR8 -
                                HAR8 HAR9 HAR9 HAR10 HAR10 HAR11 HAR11 HAR12 HAR12 HAR13 -
                                HAR13 HAR14 HAR14 HAR15 HAR15 HAR16 HAR16 HAR17 HAR17 HAR18 -
                                HAR18 HAR19 HAR19 HAR20 HAR20 HAR21 HAR21 HAR22 HAR22 HAR23 -
                                HAR23 HAR24 HAR24 HAR25
		AVRG_ATOM_TBL
		   AVRG_ATOM    Type    True Names
            HG2#   FAST    HG21  HG22  HG23

	
	AMINO_ACID  ASN   
		CHAR_CODE	N
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG -
				OD1  ND2  HD21  HD22  HD2#  C  O
		EXCHANGEABLE	HN  HD21  HD22
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  OD1  ND2  HD21  HD22
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG ND2  CG OD1 -
				ND2 HD21  ND2 HD22  ND2 HD2#
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	SLOW	HB1 HB2
			HD2#	FAST	HD21 HD22


	AMINO_ACID  GLN   
		CHAR_CODE	Q
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				HG1  HG2  HG#  CD  OE1  NE2  HE21  HE22    -
				HE2#  C  O
		EXCHANGEABLE	HN  HE21  HE22  HE2#
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG1  HG2  HG#  CD   -
				OE1  NE2  HE21  HE22  HE2#
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB CG -
				CB HB1  CB HB2  CB HB#  CG CD  CG HG1 -
				CG HG2  CG HG#  CD OE1  CD NE2  NE2 HE21 -
				NE2 HE22  NE2 HE2#
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG#	FAST	HG1 HG2
			HE2#	FAST	HE21 HE22


	AMINO_ACID  TYR   
		CHAR_CODE	Y
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				CD1  HD1  CD2  HD2  CE1  HE1  CE2 -
				HE2  HD#  HE#  CZ  OH  HH  C  O
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  CD1  HD1  CD2  -
				HD2  CE1  HE1  CE2  HE2  CZ  -
				OH  HH
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG CD1  CG CD2 -
				CD1 CE1  CD2 CE2  CD1 HD1  CD2 HD2  -
				CE1 CZ  CE2 CZ  CE1 HE1  CE2 HE2  -
				CZ OH  OH HH
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HD#     SLOW	HD1 HD2
			HE#     SLOW	HE1 HE2


	AMINO_ACID  HIH   
		CHAR_CODE	H
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				ND1  HD1  CD2  HD2  CE1  HE1  NE2  C  O
		EXCHANGEABLE	HN  HD1
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  ND1  HD1  CD2  -
				HD2  CE1  HE1  NE2
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG CD2  CG ND1 -
				ND1 CE1  CD2 NE2  ND1 HD1  CD2 HD2 -
				CE1 NE2  CE1 HE1
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2


	AMINO_ACID  HIS   
		CHAR_CODE	H
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				ND1  HD1  CD2  HD2  CE1  HE1  NE2  C  O  HE2
		EXCHANGEABLE	HN  HD1
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  ND1  HD1  CD2  -
				HD2  CE1  HE1  NE2
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG CD2  CG ND1 -
				ND1 CE1  CD2 NE2  ND1 HD1  CD2 HD2 -
				CE1 NE2  CE1 HE1
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2


	AMINO_ACID  ASP   
		CHAR_CODE	D
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				OD1  OD2  C  O  HD2
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  OD1  OD2
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG OD1  CG OD2
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2


	AMINO_ACID  GLU   
		CHAR_CODE	E
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				HG1  HG2  HG#  CD  OE1  OE2  C  O HT# -
				HT1  HT2  HT3  HE2
		EXCHANGEABLE	HN
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG1  HG2  HG#  -
				CD  OE1  OE2 HT# HT1  HT2  HT3
		BOND_ATOMS	N HN   N CA  C O  CA HA   CA CB   CB CG -
				CB HB1  CB HB2  CB HB#  CG CD  CG HG1 -
				CG HG2  CG HG#  CD OE1  CD OE2  N HT# -
				N HT1  N HT2  N HT3
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG#	FAST	HG1 HG2
			HT#	FAST	HT1 HT2 HT3


	AMINO_ACID  LYS   
		CHAR_CODE	K
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG  -
				HG1  HG2  HG#  CD  HD1  HD2  HD#  CE  -
				HE1  HE2  HE#  NZ  HZ1  HZ2  HZ3  HZ#  C  O
		EXCHANGEABLE	HN  HZ1  HZ2  HZ3  HZ#
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG1  HG2  HG#  -
				CD  HD1  HD2  HD#  CE  HE1  HE2  HE#  -
				NZ  HZ1  HZ2  HZ3  HZ#
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG CD  CG HG1 -
				CG HG2  CG HG#  CD CE  CD HD1  CD HD2 -
				CD HD#  CE NZ  CE HE1  CE HE2  CE HE# -
				NZ HZ1  NZ HZ2  NZ HZ3  NZ HZ#
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG#	FAST	HG1 HG2
			HD#	FAST	HD1 HD2
			HE#	FAST	HE1 HE2
			HZ#	FAST	HZ1 HZ2 HZ3


	AMINO_ACID  ARG   
		CHAR_CODE	R
		VALID_ATOMS	N  HN  CA  HA  CB  HB1  HB2  HB#  CG    -
				HG1  HG2  HG# CD  HD1  HD2  HD#  NE  HE -
				CZ  NH1  HH11  HH12  HH1#  NH2  HH21    -
				HH22  HH2#  HG1# C  O
		EXCHANGEABLE	HN  HE  HH11  HH12  HH1#  HH21  HH22  HH2#
		SIDE_CHAIN	CB  HB1  HB2  HB#  CG  HG1  HG2  HG# CD -
				HD1  HD2  HD#  NE  HE  CZ  NH1  HH11    -
				HH12  HH1#  NH2  HH21  HH22  HH2#
		BOND_ATOMS	N HN   N CA  C O  CA HA  CA CB  CB CG -
				CB HB1  CB HB2  CB HB#  CG CD  CG HG1 -
				CG HG2  CG HG#  CD NE  CD HD1  CD HD2 -
				CD HD#  NE CZ  NE HE  CZ NH1  CZ NH2 -
				NH1 HH11  NH1 HH12  NH1 HH1#  NH2 HH21 -
				NH2 HH22  NH2 HH2#
		AVRG_ATOM_TBL
		   AVRG_ATOM	Type	True Names
			HB#	FAST	HB1 HB2
			HG#	FAST	HG1 HG2
			HD#	FAST	HD1 HD2
			HH1#	FAST	HH11 HH12
			HH2#	FAST	HH21 HH22
			HG1#	FAST    HG1 HG2