What does the three terms 'Energy', 'Score' and 'mscore' mean?

Solution:

Score stands for RankScore (this should be the value considered for evaluation), Mscore for MatchScore and the energy is purely a forcefield energy and should not be used to compare different compounds with different composition.

In practice, the score is used to compare different ligands together and the energy is used to identify the best pose for the same ligand. So out of the three runs, one should consider the pose with the best energy and compare this score to other ligands. The mscore is the MatchScore which is a score of the interactions of the ligand and the protein. This matchscore provides information about the complementarity of the ligand and the active site defined as the Interaction Spheres (IS).