Hi

I have docked 20 ligands to a protein using Autodock vina (with 10 poses for each ligand).

Now I want to choose the "best" mode for each ligand and then best ligands (based on the selection of 1). I Know that just these numbers will not be accurate and I will have to look at the 3D as well.

My questions:

1. I know that the first thing to consider is the lowest binding energy BUT the first one is always comapred to self. Does it mean that I should chose the 2nd?

2. Then, which RMSD I should chose? (upper or lower?)

for example, I have the following result for 1 ligand, What is the report that I should chose from the example for affinity and RMSD? (-9.0 and 2.27??)

mode |   affinity | dist from best mode
     | (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
   1         -9.2      0.000      0.000
   2         -9.0      2.275      3.262
   3         -8.9      2.759      7.245
   4         -8.8      2.113      4.472
   5         -8.5      4.396      8.519
   6         -8.5      2.421      4.606
   7         -8.5     24.699     27.660
   8         -8.5     22.339     25.282
   9         -8.3     16.071     19.273