You mean which binding "pose" should be considered, right?

RMSD should be considered only if the docked molecule has structural similarity with the co-crystallized ligand.

Atleast if your docked molecule has a substructure similar to the cocrystallized ligand, try to filter out the poses, where that substructure is having low RMSD with that of cocryst. ligand. Among those filtered poses, focus on the one with lowest binding energy.

Uddipta Ghosh Dastidar, thanks for your answer.

I think I couldn’t explain my question correctly. I am talking about self docking Or redocking with the same ligand from the crystal structure. After docking, I got 9 to 10 docked structures with highest to lowest docking scores. The one with highest d. Score (1st pose) had rmsd above 2 A*, while the one with lower score (5th pose) had RMSD below 1 A* and this one actually matched to the highest extent with the crystal structure. In this kind of situation, I was thinking, I should go with the 5th pose with lower score but better rmsd. Just trying to know if I am thinking correctly.

Try to optimize the docking parameters, so that the pose with best RMSD comes within the top 3 poses (scorewise).

Otherwise proceed with the 5th pose. No big deal.

Along with the lowest binding energy, and RMSD values, the number of clusters formed should be considered.

Binding energy and RMSD value will tell the better binding pose. Still, the docking pose showing the maximum number of clusters and lowest binding energy will not only tell about a better binding confirmation but also justify the probability of ligand binding to that position most of the time.

Uddipta Ghosh Dastidar Thank you very much.