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VDW Radii

Atomic VDW (van der Waals) radii are used in sphere and ball display. They are also used to calculate molecular surfaces and surface areas. VDW radii are assigned default values according to atom type and can be changed with the size command. See also: surface, measure, contacts

Default Assignments

For C, N, O, and S, the default VDW radii depend on whether explicit hydrogen atoms are present:

Due to differences in how the sets were derived, united-atom radii are not always larger than the corresponding all-atom radii.

For metal and halide ions, ionic radii from The CRC Handbook of Chemistry and Physics, 82nd Edition (2001-2002) are used. If the charge state differs from that listed below, a different radius may be more appropriate.

For P, and for F, Cl, Br, and I in the context of molecules (as opposed to singleton ions), the all-atom radii are used.

The default VDW radii of any remaining atoms are twice their covalent bond radii.

Default VDW Radii

United-Atom Radii
atom description
(see also 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 Radii
atom description
(see also atom type)
Amber atom type radius (Å)b
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 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 Radii
ion coordination number
(default in bold)
radius (Å)d
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 ChimeraX, but not listed above.


UCSF Resource for Biocomputing, Visualization, and Informatics / January 2017