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vdw.radii
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vdw.radii
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#vdw_start
# NACCESS standard residue library
#
# Format:
#
# RESIDUE starts off each residue. It must be followed by one of
# a) ATOM - amino acids
# b) NUCL - nucleic acids
# c) HETA - heteroatoms (e.g.HEMES)
# d) WATER - solvent (eg, HOH, WAT, MOH)
# After this label, a 3 letter residue name must be supplied. It must be
# 3 letters, and if it is preceded by spaces (see the nucleic acids for
# example) the spaces should be replaced by underscores (_).
#
# ATOM begins each atom of a residue. All ATOM records between residue
# statments are counted for each residue. The format of this line is
# important, and is *not* free format. After ATOM there should be one
# space followed by the 4-character atom name corresponding to the 13th
# to 16th column of a standard PDB file. After the atom name, format is
# free, and should contain a real number (the van der Waals radius) and
# a 1 digit integer (0 or 1) where 1 implies this atom is deemed to be
# polar.
#
RESIDUE ATOM ALA 5
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
RESIDUE ATOM ARG 11
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM CD 1.87 0
ATOM NE 1.65 1
ATOM CZ 1.76 0
ATOM NH1 1.65 1
ATOM NH2 1.65 1
RESIDUE ATOM ASP 8
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM OD1 1.40 1
ATOM OD2 1.40 1
RESIDUE ATOM ASN 8
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM OD1 1.40 1
ATOM ND2 1.65 1
RESIDUE ATOM CYS 6
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM SG 1.85 0
RESIDUE ATOM GLU 9
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM CD 1.76 0
ATOM OE1 1.40 1
ATOM OE2 1.40 1
RESIDUE ATOM GLN 9
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM CD 1.76 0
ATOM OE1 1.40 1
ATOM NE2 1.65 1
RESIDUE ATOM GLY 4
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
RESIDUE ATOM HIS 10
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM ND1 1.65 1
ATOM CD2 1.76 0
ATOM CE1 1.76 0
ATOM NE2 1.65 1
RESIDUE ATOM ILE 8
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG1 1.87 0
ATOM CG2 1.87 0
ATOM CD1 1.87 0
RESIDUE ATOM LEU 8
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM CD1 1.87 0
ATOM CD2 1.87 0
RESIDUE ATOM LYS 9
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM CD 1.87 0
ATOM CE 1.87 0
ATOM NZ 1.50 1
RESIDUE ATOM MET 8
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM SD 1.85 0
ATOM CE 1.87 0
RESIDUE ATOM PHE 11
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM CD1 1.76 0
ATOM CD2 1.76 0
ATOM CE1 1.76 0
ATOM CE2 1.76 0
ATOM CZ 1.76 0
RESIDUE ATOM PRO 7
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.87 0
ATOM CD 1.87 0
RESIDUE ATOM SER 6
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM OG 1.40 1
RESIDUE ATOM THR 7
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM OG1 1.40 1
ATOM CG2 1.87 0
RESIDUE ATOM TRP 14
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM CD1 1.76 0
ATOM CD2 1.76 0
ATOM NE1 1.65 1
ATOM CE2 1.76 0
ATOM CE3 1.76 0
ATOM CZ2 1.76 0
ATOM CZ3 1.76 0
ATOM CH2 1.76 0
RESIDUE ATOM TYR 12
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM CD1 1.76 0
ATOM CD2 1.76 0
ATOM CE1 1.76 0
ATOM CE2 1.76 0
ATOM CZ 1.76 0
ATOM OH 1.40 1
RESIDUE ATOM VAL 7
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG1 1.87 0
ATOM CG2 1.87 0
RESIDUE ATOM ASX 8
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM AD1 1.50 0
ATOM AD2 1.50 0
RESIDUE ATOM GLX 9
ATOM N 1.65 1
ATOM CA 1.87 0
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CB 1.87 0
ATOM CG 1.76 0
ATOM CD 1.87 0
ATOM AE1 1.50 0
ATOM AE2 1.50 0
RESIDUE ATOM ACE 3
ATOM C 1.76 0
ATOM O 1.40 1
ATOM CH3 1.87 0
RESIDUE NUCL __A 21
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM C1* 1.80 0
ATOM N9 1.60 1
ATOM C8 1.80 0
ATOM N7 1.60 1
ATOM C5 1.80 0
ATOM C6 1.80 0
ATOM N6 1.60 1
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM N3 1.60 1
ATOM C4 1.80 0
RESIDUE NUCL __C 19
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM C1* 1.80 0
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM O2 1.40 1
ATOM N3 1.60 1
ATOM C4 1.80 0
ATOM N4 1.60 1
ATOM C5 1.80 0
ATOM C6 1.80 0
RESIDUE NUCL __G 22
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM C1* 1.80 0
ATOM N9 1.60 1
ATOM C8 1.80 0
ATOM N7 1.60 1
ATOM C5 1.80 0
ATOM C6 1.80 0
ATOM O6 1.40 1
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM N2 1.60 1
ATOM N3 1.60 1
ATOM C4 1.80 0
RESIDUE NUCL __T 20
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM C1* 1.80 0
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM O2 1.40 1
ATOM N3 1.60 1
ATOM C4 1.80 0
ATOM O4 1.40 1
ATOM C5 1.80 0
ATOM C5M 1.80 0
ATOM C6 1.80 0
RESIDUE NUCL __U 20
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM O2* 1.40 1
ATOM C1* 1.80 0
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM O2 1.40 1
ATOM N3 1.60 1
ATOM C4 1.80 0
ATOM O4 1.40 1
ATOM C5 1.80 0
ATOM C6 1.80 0
RESIDUE NUCL 2MG 24
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM O2* 1.40 1
ATOM C1* 1.80 0
ATOM N9 1.60 1
ATOM C8 1.80 0
ATOM N7 1.60 1
ATOM C5 1.80 0
ATOM C6 1.80 0
ATOM O6 1.40 1
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM N2 1.60 1
ATOM C2A 1.80 0
ATOM N3 1.60 1
ATOM C4 1.80 0
RESIDUE NUCL H2U 20
ATOM P 1.90 0
ATOM O1P 1.40 1
ATOM O2P 1.40 1
ATOM O5* 1.40 1
ATOM C5* 1.80 0
ATOM C4* 1.80 0
ATOM O4* 1.40 1
ATOM C3* 1.80 0
ATOM O3* 1.40 1
ATOM C2* 1.80 0
ATOM O2* 1.40 1
ATOM C1* 1.80 0
ATOM N1 1.60 1
ATOM C2 1.80 0
ATOM O2 1.40 1
ATOM N3 1.60 1
ATOM C4 1.80 0
ATOM O4 1.40 1
ATOM C5 1.80 0
ATOM C6 1.80 0
RESIDUE HETATM HEM 43
ATOM FE 1.47 0
ATOM CHA 2.00 0
ATOM CHB 2.00 0
ATOM CHC 2.00 0
ATOM CHD 2.00 0
ATOM N A 1.55 1
ATOM C1A 1.78 0
ATOM C2A 1.78 0
ATOM C3A 1.78 0
ATOM C4A 1.78 0
ATOM CMA 1.90 0
ATOM CAA 1.90 0
ATOM CBA 1.90 0
ATOM CGA 1.90 0
ATOM N B 1.55 1
ATOM C1B 1.78 0
ATOM C2B 1.78 0
ATOM C3B 1.78 0
ATOM C4B 1.78 0
ATOM CMB 1.90 0
ATOM CAB 1.90 0
ATOM CBB 1.90 0
ATOM N C 1.55 1
ATOM C1C 1.78 0
ATOM C2C 1.78 0
ATOM C3C 1.78 0
ATOM C4C 1.78 0
ATOM CMC 1.90 0
ATOM CAC 1.90 0
ATOM CBC 1.90 0
ATOM N D 1.55 1
ATOM C1D 1.78 0
ATOM C2D 1.78 0
ATOM C3D 1.78 0
ATOM C4D 1.78 0
ATOM CMD 1.90 0
ATOM CAD 1.90 0
ATOM CBD 1.90 0
ATOM CGD 1.90 0
ATOM O1A 1.35 1
ATOM O2A 1.35 1
ATOM O1D 1.35 1
ATOM O2D 1.35 1
RESIDUE WATER HOH 1
ATOM O 1.40 1
#vdw_end