Table 3.

Minima found by MCSS in the active site of rat nNOS

MCSS functional groups	Initial number of copies	Number of Minima	Range of Ubinda for minima (kcal/mol)		Selected minima
			from	To	Ubind; Pocket	residues/cofactors involved
Benzene	2500	27	-1.75	-24.16	No.1: -24.16; S	V567, F584, heme
					No.7: -13.47; C1	M336, L337, Y706, W306 (the other NOS monomer)
					No.8: -12.99; M	D597, heme propionate A
Cyclohexane	5000	98	-0.09	-9.80	No.1: -9.80; S	V567, F584, heme
					No.3: -9.02; M	D597, heme propionate A
					No.6: -7.08; C1	M336, L337, Y706, W306 (the other NOS monomer)
isobutene	5000	22	-5.75	-11.29	No.1: -11.29; S	V567, F584, heme
					No.3: -7.33; M	D597, heme propionate A
					No.13: -6.12; C1	M336, L337, Y706, W306 (the other NOS monomer)
n-butane	5000	224	-2.82	-10.86	No.1: -10.85; S	V567, F584, heme
					No.12: -7.79; M	D597, heme propionate A
					No.52: -5.70; C1	M336, L337, Y706, W306 (the other NOS monomer)
Propane	5000	84	-1.55	-9.99	No.1: -9.99; S	V567, F584, heme
					No.6: -6.50; M	D597, heme propionate A
					No.14: -5.71; C1	M336, L337, Y706, W306 (the other NOS monomer)
trimethylamine ion	5000	28	-2.18	-87.43	No.1: -87.43; M	D597, E592
					No.2: -82.79; M	heme propionate A and D
					No.4: -80.64; M	heme propionate A
					No.7: -73.98; M	heme propionate D
					No.22: -32.36; S	E592
dimethylamine ion	5000	35	-0.31	-131.52	No.1: -131.52; M	heme propionate A and D
					No.6: -126.30; M	E592, D597
					No.8: -110.59; M	heme propionate A
					No.11: -102.92; M	heme propionate D

^aU_bind, the binding energy for a given functional group in each minimized replica obtained from the MCSS calculations, 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.