atom_def

药物开发中的基于结构的从头设计代码

# Data cited from the Tripos force field as implemented in SYBYL 6.3
# The 1st column: numeric ID
# The 2nd column: atom type symbol
# The 3rd column: van der Waals radius
# The 4th column: van der Walls epsilon value
# The 5th column: atomic weight
# The 6th column: description
#
1	C.3	1.7	0.107	12	carbon sp3
2	C.2	1.7	0.107	12	carbon sp2
3	C.1	1.7	0.107	12	carbon sp
4	C.cat	1.7	0.107	12	carbocation (C+) used in guadinium
5	C.ar	1.7	0.107	12	carbon aromatic
6	H	1.00	0.042	1	hydrogen
7	N.4	1.55	0.095	14	nitrogen sp3 positively charged
8	N.3	1.55	0.095	14	nitrogen sp3
9	N.2	1.55	0.095	14	nitrogen sp2
10	N.1	1.55	0.095	14	nitrogen sp
11	N.ar	1.55	0.095	14	nitrogen aromatic
12	N.pl3	1.55	0.095	14	nitrogen trigonal planar
13	N.am	1.55	0.095	14	nitrogen amide
14	O.3	1.52	0.116	16	oxygen sp3	
15	O.2	1.52	0.116	16	oxygen sp2
16	O.co2	1.52	0.116	16	oxygen in carboxylate and phosphate
17	P.3	1.8	0.314	31	phosphorous sp3
18	S.3	1.8	0.314	32	sulfur sp3
19	S.2	1.8	0.314	32	sulfur sp2
20	S.o	1.7	0.314	32	sulfoxide sulfur
21	S.o2	1.7	0.314	32	sulfone sulfur
22	F	1.47	0.109	19	fluorine
23	Cl	1.75	0.314	35	chlorine
24	Br	1.85	0.434	80	bromine
25	I	1.98	0.623	127	iodine
26	Du	0	0.000	0	dummy atom
27	Un	0	0.000	0	unknown atom
28	H.spc	1.00	0.042	1	seed hydrogen
#
# Notice: the VDW radius of hydrogen has been changed from original 1.5 to 
# current 1.0 to reproduce reasonable conformations
#