. Author manuscript; available in PMC: 2007 Apr 30.

Published in final edited form as: J Mol Biol. 2006 Nov 3;366(2):687–701. doi: 10.1016/j.jmb.2006.10.095

Table 3.

Comparison of calculated distances and dissociation energies in [MD₆(H₂O)₅]²⁺X complexes in the gas phase with ab initio calculations.^†

	distance (Å)				dissociation energy (kcal/mol)^a
	ENZYMIX				ENZYMIX
Ligand X	reg.^b	pol.^c	AMBER	DFT	reg.^b	pol.^c	AMBER	DFT
H₂O	2.06	2.10	2.09	2.15	41	42	47	34
CH₃OH	2.10	2.11	2.09	2.09	37	43	48	43
PO₃⁻	2.02	2.06	2.15	1.94	237	246	221	200
HPO₄²⁻	1.97	1.97	2.16	1.91	446	418	434	348

^†

The model complexes used are shown schematically in Figure 2. These complexes were minimized using the ENZYMIX or AMBER force field. The force field parameters of MD₆²⁺ (Table I) were fit to reproduce the corresponding values of [Mg(H₂O)₅]²⁺X obtained from DFT calculations at the B3LYP/6-311++G** level.

The energy required to remove the ligand X from the complex (see Figure 2).

reg. designates that the regular, nonpolarizable ENZYMIX force field was used.

pol. designates that the polarizable ENZYMIX force field was used