Default VDW Radii

United Atom Radii
atom description
(see also Chimera atom type)		 # hydrogens attached radius (Å)
sp2 C 0 1.61a
sp2 C 1 1.76a
sp3 C 1-3 1.88a
any other C 1.88
sp2 N 0-2 1.64a
sp3 N 3 1.64a
any other N 1.64
sp2 O 0 1.42a
sp3 O 1 1.46a
sp3 O 0 1.46
any other O 1.42
sp3 S 0-1 1.77a
any other S 1.77
a Tsai et al., J Mol Biol 290:253 (1999)

All Atom Radiib
atom description
(see also Chimera atom type)		 Amber atom type radius (Å)
C all C types 1.700
N all N types 1.625
sp2 O O, O2 1.480
sp3 O OS 1.500
S S, SH 1.782
H (see notec) 1.000
P P 1.871
F F 1.560
Cl Cl 1.735
Br Br 1.978
I I 2.094
b Derived from the Amber parm99 parameters: RVDW = (R*)/(21/6)
c Amber parm99 includes many H types with VDW radii ranging from 0.0 to 1.325 Å; smaller radii are assigned to hydrogens bonded to more electron-withdrawing moieties. The Chimera atom types only distinguish between hydrogen bonded to carbon and hydrogen bonded to “other,” so a compromise value of 1.0 has been used for all hydrogens.

Selected Ionic Radiid
ion coordination number
(default in bold)		 radius (Å)
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
d 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.