. Author manuscript; available in PMC: 2011 Jul 8.

Published in final edited form as: J Phys Chem B. 2010 Jul 8;114(26):8701–8712. doi: 10.1021/jp9109699

TABLE 1.

Overview of the MD simulations performed here. The presence of ligand in the active site and the charge of the acid-base groups differing in protonation state are indicated.

			GlcN6P	GlcN6P	Simulation length [ns]
Simulation name	cofactor	G40	amino group	phosphate
G40⁻/GlcN⁺6P²⁻	yes	−1	+1	−2	20
G40⁻/GlcN⁺6P⁻	yes	−1	+1	−1	20
G40/GlcN⁰6P²⁻	yes	0	0	−2	20
G40/GlcN⁺6P²⁻	yes	0	+1	−2	50
G40/GlcN⁺6P⁻(G1)^a	yes	0	+1	−1	20
G40/GlcN⁺6P⁻(P2.2)^a	yes	0	+1	−1	20
G40/GlcN⁺6P⁻(bulk)^a	yes	0	+1	−1	20
G40/free	no	0	-	-	50

The labels “G1”, “P2.2”, or “bulk” in parentheses indicate initial orientation of the hydroxyl of the GlcN⁺6P⁻ phosphate toward G1, P2.2 stem and bulk solvent, respectively.