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. 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 4.

Comparison of calculated distances in [MD6(H2O)5]2+X complexes in solution with experimental data.†

distance (Å)
ENZYMIX
Ligand X reg.a pol.b AMBER Experiment
H2O 2.05 2.07 2.09 2.07c
CH3OH 2.09 2.09 2.08 2.19c
PO3− 2.02 2.07 2.14 2.03–2.19d
HPO42− 2.02 2.04 2.07
†

For these calculations, the complexes were immersed in a surface-constrained42 20 Å radius sphere of TIP3P43 water molecules, a 22 Å radius sphere of Langevin dipoles, and a surrounding continuum solvent model.22 For comparison, the corresponding distances in X-ray crystal structures are given.

a

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

b

pol. designates that the polarizable ENZYMIX force field was used.

c

These values are taken from Harding;41 the ligands in protein X-ray crystal structures corresponding to methanol are serine and threonine.

d

These values are taken from the pol β structures recently published by Batra et al.;9 the ligands in the X-ray crystal structure corresponding to PO3− and HPO42− are different magnesium-coordinating, nonbridging triphosphate oxygens.