Article ID: 1036 - Last Modified: November 5, 2012
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. For example, bending benzene (folding along the line connecting para carbons) by 5 degrees takes only 0.5 kcal/mol. The lowest vibrational motions of benzene are out-of-plane motions, and the frequency is only a bit over 400 cm-1. Thus, it is fairly easy for rings to bend out of plane by several degrees.
However, crystallographers generally enforce planarity, and these distortions are easy to notice visually. If you are concerned about them, one way to remove nonplanarity is to turn off PDM (in 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.
Another option that is available as of Suite 2011 is to apply an extra potential term that increases the energetic penalty for nonplanarity. You can do this in the Settings tab with the "Enhance planarity of conjugated pi groups" option (Suite 2012 on) or "Use enhanced planarity force field parameters" option (Suite 2011).
#244: Sometimes I find distorted phenol rings coming out of a Glide docking run. Why is that and how should I get rid of th...
#1470: Sometimes the results returned from Glide have slightly distorted aromatic rings. Can I prevent this?
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