#
# This file contains the information about amino acids required
# by the program thermo and edpdb in the stc package.
#
# Last update: Jan 27, 2006 
#

###################################################################
#
# Format Description
#
# Each residue in this table is defined in the following manner.
# Lines preceding with '#' are comments and are skipped.
# Field delimiters are denoted with white space or tabs.
#
# Residue Description Line:
#
#    Field #1 - RESIDUE (required keyword)
#    Field #2 - residue type (ATOM or NUCL or HETA or WATER)
#                  ATOM = amino acid, 
#                  NUCL = nucleic acids
#                  HETA = heteroatoms (e.g.HEMES)
#                  WATER = solvent (eg, HOH, WAT, MOH)
#    Field #3 - a residue name (1, 2, or 3 characters in length) 
#
# Following the residue description line are entries which follow
# one of the formats below. Entries for the above residue are read
# until the next RESIDUE line is found or end of file reached. 
#
# Format #1 (thermodynamics parameters)
#
#    Field #1 - THERMO (required keyword)
#    Field #2 - Residue ID number
#                  -99 means all residue IDs in the sequence apply
#    Field #3 - ASAsc 
#                  if not set to 0.0, use field #4 in SBuEx calculation
#                  if not set to 0.0, use field #5 in SeXu calculation
#    Field #4 - dSBuEx
#    Field #5 - dSeXu
#    Field #6 - dSBB
#
# Format #2 (atom descriptions)
#
#    Field #1 - ATOM (required keyword identifying each atom of a residue). 
#    Field #2 - Atom name (1, 2, 3, or 4 letter character string)
#    Field #3 - van der waals radius
#    Field #4 - 0 or 1 where polar = 1, non-polar = 0
#    Field #5 - 0 or 1 where backbone atom = 1, sidechain atom = 0
#
#
###################################################################
#
# Regular amino acids
#
RESIDUE ATOM ALA
THERMO -99    67.0    0.0    0.00  4.10
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
#
RESIDUE ATOM ARG
THERMO -99    196.0    7.11  -0.84  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  CD  1.87 0 0
ATOM  NE  1.65 1 0
ATOM  CZ  1.76 0 0
ATOM  NH1 1.65 1 0
ATOM  NH2 1.65 1 0
#
RESIDUE ATOM ASN
THERMO -99    113.0    3.29   2.24  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  OD1 1.40 1 0
ATOM  ND2 1.65 1 0
#
RESIDUE ATOM ASP 
THERMO -99    106.0    2.00   2.16  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  OD1 1.40 1 0
ATOM  OD2 1.40 1 0
#
RESIDUE ATOM CYS
THERMO -99    104.0    3.55   0.61  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  SG  1.85 0 0
#
RESIDUE ATOM GLN 
THERMO -99    144.0    5.02   2.12  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 0
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  CD  1.76 0 0
ATOM  OE1 1.40 1 0
ATOM  NE2 1.65 1 0
#
RESIDUE ATOM GLU
THERMO -99    138.0    3.53   2.27  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  CD  1.76 0 0
ATOM  OE1 1.40 1 0
ATOM  OE2 1.40 1 0
#
RESIDUE ATOM GLY
THERMO -99    0.0   0.00   0.00  6.50 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
#
RESIDUE ATOM HIS
THERMO -99    151.0    3.44   0.79  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  ND1 1.65 1 0
ATOM  CD2 1.76 0 0
ATOM  CE1 1.76 0 0
ATOM  NE2 1.65 1 0
#
RESIDUE ATOM ILE
THERMO -99    140.0    1.74   0.67  2.18 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG1 1.87 0 0
ATOM  CG2 1.87 0 0
ATOM  CD1 1.87 0 0
#
RESIDUE ATOM LEU
THERMO -99    137.0    1.63   0.25  3.40 
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  CD1 1.87 0 0
ATOM  CD2 1.87 0 0
#
RESIDUE ATOM LYS
THERMO -99    167.0    5.86   1.02  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  CD  1.87 0 0
ATOM  CE  1.87 0 0
ATOM  NZ  1.50 1 0
#
RESIDUE ATOM MET
THERMO -99    160.0    4.55   0.58  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  SD  1.85 0 0
ATOM  CE  1.87 0 0
#
RESIDUE ATOM PHE
THERMO -99    175.0    1.40   2.89  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  CD1 1.76 0 0
ATOM  CD2 1.76 0 0
ATOM  CE1 1.76 0 0
ATOM  CE2 1.76 0 0
ATOM  CZ  1.76 0 0
#
RESIDUE ATOM PRO
THERMO -99    105.0    0.00   0.00  0.00
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.87 0 0
ATOM  CD  1.87 0 0
#
RESIDUE ATOM SER
THERMO -99    80.0    3.68   0.55  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  OG  1.40 1 0
#
RESIDUE ATOM THR
THERMO -99    102.0    3.31   0.48  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  OG1 1.40 1 0
ATOM  CG2 1.87 0 0
#
RESIDUE ATOM TRP
THERMO -99    217.0    2.74   1.15  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  CD1 1.76 0 0
ATOM  CD2 1.76 0 0
ATOM  NE1 1.65 1 0
ATOM  CE2 1.76 0 0
ATOM  CE3 1.76 0 0
ATOM  CZ2 1.76 0 0
ATOM  CZ3 1.76 0 0
ATOM  CH2 1.76 0 0
#
RESIDUE ATOM TYR
THERMO -99    187.0    2.78   3.12  3.40
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  CD1 1.76 0 0
ATOM  CD2 1.76 0 0
ATOM  CE1 1.76 0 0
ATOM  CE2 1.76 0 0
ATOM  CZ  1.76 0 0
ATOM  OH  1.40 1 0
#
RESIDUE ATOM VAL
THERMO -99    117.0    0.12   1.29  2.18
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG1 1.87 0 0
ATOM  CG2 1.87 0 0
#
###################################################################
#
# unusual residues
#
###################################################################
#
RESIDUE ATOM ASX
THERMO -99    0.0        0.00   0.00  0.00
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  AD1 1.50 0 0
ATOM  AD2 1.50 0 0
#
RESIDUE ATOM GLX 
THERMO -99    0.0        0.00   0.00  0.00
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.87 0 0
ATOM  CG  1.76 0 0
ATOM  CD  1.87 0 0
ATOM  AE1 1.50 0 0
ATOM  AE2 1.50 0 0
#
RESIDUE ATOM MDH 
THERMO -99    0.0        0.00   0.00  0.00
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CB  1.76 0 0
ATOM  CM  1.87 0 0
#
RESIDUE ATOM ADD 
THERMO -99    387.0    8.70   0.00  0.00
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  C1  1.87 0 0
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  C2  1.87 0 0
ATOM  CB  1.76 0 0
ATOM  CG  1.76 0 0
ATOM  CD  1.76 0 0
ATOM  C3  1.87 0 0
ATOM  CE  1.76 0 0
ATOM  CF  1.76 0 0
ATOM  C4  1.87 0 0
ATOM  CH  1.87 0 0
ATOM  O5  1.40 1 0
ATOM  C5  1.87 0 0
ATOM  CI  1.87 0 0
ATOM  CJ  1.76 0 0
ATOM  CP  1.76 0 0
ATOM  CK1 1.76 0 0
ATOM  CK2 1.76 0 0
ATOM  CM1 1.76 0 0
ATOM  CM2 1.76 0 0
#
RESIDUE ATOM MAS 
THERMO -99    0.0        0.00   0.00  0.00
ATOM  N   1.65 1 1
ATOM  CA  1.87 0 1
ATOM  CB  1.87 0 0
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CG  1.87 0 0
ATOM  C1  1.76 0 0
ATOM  O1  1.40 1 0
ATOM  O2  1.40 1 0
#
RESIDUE ATOM ACE
THERMO -99    0.0        0.00   0.00  0.00
ATOM  C   1.76 0 1
ATOM  O   1.40 1 1
ATOM  CH3 1.87 0 0
#
###################################################################
#
# Nucleic Acids and others
#
###################################################################
#
RESIDUE NUCL A
THERMO -99  278.0        0.00   0.00  0.00
ATOM  P   1.90 1 1
ATOM  O1P 1.40 1 1
ATOM  O2P 1.40 1 1
ATOM  O5* 1.40 1 1
ATOM  C5* 1.87 0 1
ATOM  C4* 1.87 0 1
ATOM  O4* 1.40 1 1
ATOM  C3* 1.87 0 1
ATOM  O3* 1.40 1 1
ATOM  C2* 1.87 0 1
ATOM  C1* 1.87 0 1
ATOM  N9  1.60 1 0
ATOM  C8  1.80 0 0
ATOM  N7  1.60 1 0
ATOM  C5  1.76 0 0
ATOM  C6  1.76 0 0
ATOM  N6  1.60 1 0
ATOM  N1  1.60 1 0
ATOM  C2  1.76 0 0
ATOM  N3  1.60 1 0
ATOM  C4  1.76 0 0
#
RESIDUE NUCL C
THERMO -99  244.0        0.00   0.00  0.00
ATOM  P   1.90 1 1
ATOM  O1P 1.40 1 1
ATOM  O2P 1.40 1 1
ATOM  O5* 1.40 1 1
ATOM  C5* 1.87 0 1
ATOM  C4* 1.87 0 1
ATOM  O4* 1.40 1 1
ATOM  C3* 1.87 0 1
ATOM  O3* 1.40 1 1
ATOM  C2* 1.87 0 1
ATOM  C1* 1.87 0 1
ATOM  N1  1.60 1 0
ATOM  C2  1.76 0 0
ATOM  O2  1.40 1 0
ATOM  N3  1.60 1 0
ATOM  C4  1.76 0 0
ATOM  N4  1.60 1 0
ATOM  C5  1.76 0 0
ATOM  C6  1.76 0 0
#
RESIDUE NUCL G
THERMO -99  287.0        0.00   0.00  0.00
ATOM  P   1.90 1 1
ATOM  O1P 1.40 1 1
ATOM  O2P 1.40 1 1
ATOM  O5* 1.40 1 1
ATOM  C5* 1.87 0 1
ATOM  C4* 1.87 0 1
ATOM  O4* 1.40 1 1
ATOM  C3* 1.87 0 1
ATOM  O3* 1.40 1 1
ATOM  C2* 1.87 0 1
ATOM  C1* 1.87 0 1
ATOM  N9  1.60 1 0
ATOM  C8  1.80 0 0
ATOM  N7  1.60 1 0
ATOM  C5  1.76 0 0
ATOM  C6  1.76 0 0
ATOM  O6  1.40 1 0
ATOM  N1  1.60 1 0
ATOM  C2  1.76 0 0
ATOM  N2  1.60 1 0
ATOM  N3  1.60 1 0
ATOM  C4  1.76 0 0
#
RESIDUE NUCL T
THERMO -99  256.0        0.00   0.00  0.00
ATOM  P   1.90 1 1
ATOM  O1P 1.40 1 1
ATOM  O2P 1.40 1 1
ATOM  O5* 1.40 1 1
ATOM  C5* 1.87 0 1
ATOM  C4* 1.87 0 1
ATOM  O4* 1.40 1 1
ATOM  C3* 1.87 0 1
ATOM  O3* 1.40 1 1
ATOM  C2* 1.87 0 1
ATOM  C1* 1.87 0 1
ATOM  N1  1.60 1 0
ATOM  C2  1.76 0 0
ATOM  O2  1.40 1 0
ATOM  N3  1.60 1 0
ATOM  C4  1.76 0 0
ATOM  O4  1.40 1 0
ATOM  C5  1.76 0 0
ATOM  C5M 1.80 0 0
ATOM  C6  1.76 0 0
#
RESIDUE NUCL U
THERMO -99  235.0        0.00   0.00  0.00
ATOM  P   1.90 1 1                     
ATOM  O1P 1.40 1 1
ATOM  O2P 1.40 1 1
ATOM  O5* 1.40 1 1
ATOM  C5* 1.87 0 1
ATOM  C4* 1.87 0 1
ATOM  O4* 1.40 1 1
ATOM  C3* 1.87 0 1
ATOM  O3* 1.40 1 1
ATOM  C2* 1.87 0 1
ATOM  O2* 1.40 1 1
ATOM  C1* 1.87 0 1
ATOM  N1  1.60 1 0
ATOM  C2  1.76 0 0
ATOM  O2  1.40 1 0
ATOM  N3  1.60 1 0
ATOM  C4  1.76 0 0
ATOM  O4  1.40 1 0
ATOM  C5  1.76 0 0
ATOM  C6  1.76 0 0
#
RESIDUE HETATM HEM
THERMO -99    0.0        0.00   0.00  0.00
ATOM FE   1.47 0 0
ATOM  CHA 2.00 0 0
ATOM  CHB 2.00 0 0
ATOM  CHC 2.00 0 0
ATOM  CHD 2.00 0 0
ATOM  N_A 1.55 1 0
ATOM  C1A 1.78 0 0
ATOM  C2A 1.78 0 0
ATOM  C3A 1.78 0 0
ATOM  C4A 1.78 0 0
ATOM  CMA 1.90 0 0
ATOM  CAA 1.90 0 0
ATOM  CBA 1.90 0 0
ATOM  CGA 1.90 0 0
ATOM  N_B 1.55 1 0
ATOM  C1B 1.78 0 0
ATOM  C2B 1.78 0 0
ATOM  C3B 1.78 0 0
ATOM  C4B 1.78 0 0
ATOM  CMB 1.90 0 0
ATOM  CAB 1.90 0 0
ATOM  CBB 1.90 0 0
ATOM  N_C 1.55 1 0
ATOM  C1C 1.78 0 0
ATOM  C2C 1.78 0 0
ATOM  C3C 1.78 0 0
ATOM  C4C 1.78 0 0
ATOM  CMC 1.90 0 0
ATOM  CAC 1.90 0 0
ATOM  CBC 1.90 0 0
ATOM  N_D 1.55 1 0
ATOM  C1D 1.78 0 0
ATOM  C2D 1.78 0 0
ATOM  C3D 1.78 0 0
ATOM  C4D 1.78 0 0
ATOM  CMD 1.90 0 0
ATOM  CAD 1.90 0 0
ATOM  CBD 1.90 0 0
ATOM  CGD 1.90 0 0
ATOM  O1A 1.35 1 0
ATOM  O2A 1.35 1 0
ATOM  O1D 1.35 1 0
ATOM  O2D 1.35 1 0
#
RESIDUE WATER HOH
THERMO -99    0.0        0.00   0.00  0.00
ATOM  O   1.40 1 0