Why are there nonplanar aromatic rings in docked poses?
When docking a ligand, Glide must accommodate a rigid receptor structure, so some ligand strain is allowed in order to fit the ligand in the active site. If you run the optional post-docking minimization (PDM) step of Glide, close intra-ligand contacts can be relieved, but this can sometimes happen at the expense of transferring the energy from van der Waals clashes into distortions of the aromatic ring structures. There is actually not much of an energy penalty for minor deviations from planarity in aromatic rings, as shown by quantum mechanical calculations. However, crystallographers generally enforce planarity, and these distortions are easy to notice visually. If you are concerned about them, we suggest turning off PDM (on the Output tab). You may end up with some close contacts in the ligand conformations, but the bond lengths and bond angles will be fixed at their input values.
