# # 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