. Author manuscript; available in PMC: 2012 Jun 27.

Published in final edited form as: J Chem Inf Model. 2011 May 25;51(6):1296–1306. doi: 10.1021/ci2000665

Table 1.

List of 20 atom types in LISA

Atom Type	Description	Hydrogen Bonding Donor/Acceptor?	VDW radii
C3	sp³ hybridized carbon	N/A	1.94
C2	sp² hybridized carbon	N/A	1.90
C1	sp hybridized carbon	N/A	1.80
Car	aromatic carbon	N/A	1.85
N4	positively charged nitrogen	N/A (if no H bonded) / Donor (if H bonded)	1.83
N3	sp³ hybridized nitrogen	N/A (if no H bonded) / Donor (if H bonded)	1.87
N2	sp² hybridized nitrogen	N/A (if no H bonded) / Donor (if H bonded)	1.86
N1	sp hybridized nitrogen	N/A	1.85
Nar	aromatic nitrogen	N/A	1.86
Nam	amide nitrogen	N/A (if no H bonded) / Donor (if H bonded)	1.83
Npl3	trigonal planar nitrogen	N/A (if no H bonded) / Donor (if H bonded)	1.86
O3	sp³ hybridized oxygen	Acceptor (if no H bonded) / Donor-Acceptor (if H bonded)	1.74
O2	sp² hybridized oxygen	Acceptor	1.66
S	sulfur	N/A	2.09
P	phosphor	N/A	2.03
F	fluorine	N/A	1.55
Cl	chlorine	N/A	2.00
Br	bromine	N/A	2.20
I	Iodine	N/A	2.40
Zn	zinc cation	N/A	1.20