Default VDW Radius Tables

Selected Ionic Radiia
ion coordination number
(default in bold)		 radius (Angstroms)
Al+3 4
5
6		 0.39
0.48
0.54
As+3 6 0.58
Au+1 6 1.37
Ba+2 6
8
12		 1.35
1.42
1.61
Be+2 4
6		 0.27
0.45
Bi+3 5
6
8		 0.96
1.03
1.17
Ca+2 6
8
10
12		 1.00
1.12
1.23
1.34
Cd+2 4
6
8
12		 0.78
0.95
1.10
1.31
Co+2 4
6
8		 0.56
0.65
0.90
Cr+2 6 0.73
Cs+ 6
8
10
12		 1.67
1.74
1.81
1.88
Cu+2 4
6		 0.57
0.73
Fe+2 4
6
8		 0.63
0.61
0.92
Ga+3 4
6		 0.47
0.62
Ge+2 6 0.73
Hg+2 2
4
6
8		 0.69
0.96
1.02
1.14
K+ 4
6
8
12		 1.37
1.38
1.51
1.64
Li+ 4
6
8		 0.59
0.76
0.92
Mg+2 4
6
8		 0.57
0.72
0.89
Mn+2 4
6
8		 0.66
0.83
0.96
Mo+3 6 0.69
Na+ 4
6
8
9
12		 0.99
1.02
1.18
1.24
1.39
Ni+2 4
6		 0.49
0.69
Pb+2 6
8
10
12		 1.19
1.29
1.40
1.49
Pd+2 4
6		 0.64
0.86
Pt+2 4
6		 0.60
0.80
Rb+ 6
8
10
12		 1.52
1.61
1.66
1.72
Sb+3 4
6		 0.76
0.76
Sc+3 6
8		 0.75
0.87
Sn+4 4
6
8		 0.55
0.69
0.81
Sr+2 6
8
10
12		 1.18
1.26
1.36
1.44
Tc+4 6 0.65
Ti+2 6 0.86
V+2 6 0.79
Zn+2 4
6
8		 0.60
0.74
0.90
Zr+4 4
6
8
9		 0.59
0.72
0.84
0.89
F- 6 1.33
Cl- 6 1.81
Br- 6 1.96
I- 6 2.20
a CRC Handbook of Chemistry and Physics, 82nd Edition (2001-2002). Additional ionic radii from the same reference (for more rarely encountered ions) are also used as defaults in Chimera, but not listed above.

"All Atom" Radius Setb
element name/residue radius (Angstroms)
H 1.00
C C/*
CD/GLN,GLU
CG/ASN,ASP
CZ/ARG
(non-aromatic sp2 C in standard residues)		 1.50
C C2,C4,C5,C6,C8,CD2,CE1,CE2,CE3,
CH2,CZ2,CZ3/*
CD1/not-ILE
CG/HIS,PHE,TRP,TYR
CZ/not-ARG
(aromatic sp2 C in standard residues)		 1.70
C any other C
(sp3 C in standard residues;
any C not matching the preceding patterns)		 1.25
N NZ/LYS
(sp3 ammonium N in lysine)		 1.25
N N,N4,ND2,NE,NH1,NH2/*
NE2/GLN
(non-aromatic sp2 N in standard residues)		 1.45
N any other N
(aromatic sp2 N in standard residues;
any N not matching the preceding patterns)		 1.70
O 1.35
P 1.70
S 1.70
b Based on the "vdw.hydrogen" set of radii used in MidasPlus; assignments are made according to standard atom and residue names.

"United Atom" Radius Set
atom center # of attached hydrogens radius (Angstroms)
sp2 C 0 1.61*
sp2 C 1 1.76*
sp3 C 1-3 1.88*
any other C 1.88
sp2 N 0-2 1.64*
sp3 N 3 1.64*
any other N 1.64
sp2 O 0 1.42*
sp3 O 0 1.46
sp3 O 1 1.46*
any other O 1.42
P 1.70
sp3 S 0-1 1.77*
any other S 1.77
*Tsai et al., J Mol Biol, 290, 253 (1999).