. Author manuscript; available in PMC: 2010 Aug 29.

Published in final edited form as: J Am Chem Soc. 2008 Mar 6;130(12):3900–3914. doi: 10.1021/ja0772041

Table 2.

Minima Found by MCSS in the Active Site of Rat nNOS

MCSS functional groups	initial no. of copies	no. of minima	range of U_bind^a for minima (kcal/mol)		selected minima
MCSS functional groups	initial no. of copies	no. of minima	from	to	U_bind; pocket	residues/cofactors involved
benzene	2500	27	−1.75	−24.16	no. 1: −24.16; S	V567, F584, heme
					no. 8: −12.99; M	D597, heme
cyclohexane	5000	98	−0.09	−9.80	no. 1: −9.80; S	V567, F584, heme
					no. 3: −9.02; M	D597, heme
isobutane	5000	22	−5.75	−11.29	no. 1: −11.29; S	V567, F584, heme
					no. 3: −7.33; M	D597, heme
N-methylacetamide	5000	85	−2.44	−54.77	no. 8: −43.97; M	heme
					no. 12: −42.15; M	heme, R603
					no. 13: −41.91; M	Q478, E592
methanol	5000	64	−3.19	−32.66	no. 3: −30.65; M	heme
					no. 5: −29.52; M	D597, Q478
					no. 7: −25.26; S	E592
ether	5000	27	−3.21	− 25.20	no. 2: −19.91; M	Q478, R603
acetate ion	5000	42	−5.93	−79.51	no. 1: −79.51; C1	R481
					no. 2: −77.73; S	heme Fe
					no. 5: −42.93; M	Q478, R481
methylammonium	5000	16	−0.75	−121.90	no. 1: −121.90;M	heme
					no. 4: −115.83; M	E592, heme
					no. 6: −85.32; M	D597
					no. 9: −73.97; S	E592
trimethylamine ion	5000	28	−2.18	−87.43	no. 1: −87.43; M	D597, E592
					no. 2: −82.79; M	heme
					no. 22: −32.36; S	E592

U_bind, the binding energy for a given functional group in each minimized replica obtained from the MCSS calculation, is defined as U_bind= U_{protein–group} + U_group⁰, where U_{protein–group} represents the nonbonded interactions between nNOS and the given functional group. U_group represents the internal energy of the functional group within the complex, and U_group⁰ represents the internal energy of the isolated functional group in vacuum.