Table 1. The definition of protein and ligand atom types.

IDNo.	AtomType	Radius(Å)	Description
1	NH1	1.65	Backbone NH
2	C	1.76	Backbone C
3	CH1E	1.87	Backbone CA(exc. Gly)
4	O	1.40	Backbone O
5	CH0	1.76	Arg CZ, Asn CG, Asp CG, Gln CD, Glu CD
6	CH1S	1.87	Side chain CH1:Ile CB, Leu CG, Thr CB, Val CB
7	CH2E	1.87	Tetrahedral CH2(except CH2P,CH2G) All CB
8	CH3E	1.87	Tetrahedral CH3
9	CR1E	1.76	Aromatic CH(except CR1W,CRHH,CR1H)
10	OH1	1.40	Alcohol OH(Ser OG, Thr OG1,Tyr OH)
11	OC	1.40	CarboxylO(Asp OD1,OD2,Glu OE1,OE2)
12	OS	1.40	Side chain O: Asn OD1,Gln OE1
13	CH2G	1.87	Gly CA
14	CH2P	1.87	Pro CB,CG,CD
15	NH1S	1.65	Side chain NH: Arg NE, His ND1,NE1,Trp NE1
16	NC2	1.65	Arg NH1,NH2
17	NH2	1.65	Asn ND2,Gln NE2
18	CR1W	1.76	Trp CZ2,CH2
19	CY2	1.76	Tyr CZ
20	SC	1.85	Cys S
21	CF	1.76	Phe CG
22	SM	1.85	Met S
23	CY	1.76	Tyr CG
24	CW	1.76	Trp CD2,CE2
25	CRHH	1.76	His CE1
26	NH3	1.50	Lys NZ
27	CR1H	1.76	His CD2
28	C5	1.76	His CG
29	N	1.65	Pro N
30	C5W	1.76	Trp CG
31	HOH	1.40	Water
32	C.3	1.91	sp3 carbon
33	C.2	1.91	sp2 carbon
34	C.1	1.91	sp carbon
35	C.ar	1.91	aromatic carbon
36	C.cat	1.91	carbocation used only in a guadinium group
37	O.3	1.68	sp3 oxygen
38	O.2	1.66	sp2 oxygen
39	O.co2	1.66	oxygen in carboxylate or phosphate group
40	N.4	1.82	sp3 positively charged nitrogen
41	N.3	1.82	sp3 nitrogen
42	N.2	1.82	sp2 nitrogen
43	N.1	1.82	sp nitrogen
44	N.ar	1.82	aromatic nitrogen
45	N.pl3	1.82	trigonal planar nitrogen
46	N.am	1.82	amide nitrogen
47	P.3	2.10	sp3 phosphorous
48	S.3	2.00	sp3 sulfur
49	S.2	2.00	sp2 sulfur
50	S.O2	2.00	Sulfone sulfur
51	F	1.75	F fluorine
52	Cl	1.95	Cl chlorine
53	Br	2.22	Br bromine

The protein atom types (1–31) have been previously defined.