. Author manuscript; available in PMC: 2015 Jul 30.

Published in final edited form as: J Theor Comput Chem. 2014 Apr 8;13(3):1440006. doi: 10.1142/S0219633614400069

Table 1.

Radii sets used in this work. For the small proteins we used a modification of BONDI (MBONDI2) in which the radius of a hydrogen atom bound to nitrogen is increased to 1.3 Å versus 1.2 Å in the original BONDI set.

	Atomic Radii (Å)
	C	H	N	O	S	P	F	Cl	Br	I
BONDI	1.7	1.2	1.55	1.5	1.8	1.8	1.47	1.75	1.85	1.98
PARSE	1.7	1.0	1.5	1.4	1.85	1.8	1.47	1.75	1.85	1.98
ZAP9	1.87	1.1	1.55^a	1.52^b	2.15	1.8	2.4	1.82	1.85	2.65

1.4 Å for Secondary and Tertiary N

1.76 Å for carbonyl O