Table 1.

Molecular Constructs studied with MD simulations

PDB code	3F3A			3GJD		3GJD-K288A
Constructsa	S1 - Trp S2 - Øb	S1 - Trp S2 - Trp	S1 - Trp S2 – Trp, OG, C14c	S1 - Leu S2 - Ø	S1 - Leu S2 - OG	S1 - Leu S2 - Ø
Time (ns)d	95	89	104	96	87	113
NPOPE	534	534	534	534	534	534
NPOPG	161	161	161	160	160	160
NW	58541	58541	58541	57529	57529	57367
NCl−	6	6	6	5	5	4
NNa+	159	159	159	158	158	158

^a- 3F3A structure contained 2 Na+ ions, and 3GJD had 2 Na+ and 1 Cl− ions, all retained in MD simulations;

^b- Ø denotes empty S2 site ;

^c– S2 site contains TPR, OG and C14;

^d– production run, excludes equilibration phase.