Table 4. Comparison of RMSD along MDs in refined and non-refined docked complexes.

Solution	RMSD NO-REF	RMSD REF
1	2.62	2.38
2	2.67	2.41
3	2.69	2.36
4	3.01	2.89
5	2.99	2.76
6	2.65	2.33
7	2.77	2.40
8	2.62	2.32
9	2.98	2.53
10	2.78	2.43

The RMSD from the first snapshot of the MDs were calculated for the 10 docked solutions with and without refinement. In all cases the difference in terms of RMSD is less than .5 Å meaning that the refinement procedure does not introduce distortions in the structures. For both refined and non-refined MDs we calculated the RMSD over the 1 ns unrestrained MDs. NO-REF: solutions not refined. REF: solutions refined.