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Sometimes I find distorted phenyl rings coming out of a Glide docking run. Why is that and how should I get rid of the distortion?

Ring distortions of several degrees out of plane are not unphysical, as it takes less than 1 kcal/mol to produce such a distortion. It's also possible this is a result of Glide's post-docking minimization (on the Output tab). If Glide produces a pose with some strain, the post-docking minimization can distribute some of the strain energy into ring distortions. However, such distortions can still occur because the receptor structure is fixed. If they are a concern, post processing (e.g., running the constrained minimization step of the Protein Preparation Wizard on the complex) should be able to eliminate the unphysical distortions.

You can increase the force constant for out-of-plane distortions, by selecting the option "Enhance planarity of conjugated pi groups". This should eliminate most, if not all, ring distortions.

You can also try running an Impact or MacroModel minimization on just the ligand, to determine whether the ring itself prefers to be nonplanar. The OPLS force fields used in these calculations reproduce closely the results of high-level quantum mechanical calculations, so the results of the minimization should be reliable.

Related Articles:

#1036: Why are there nonplanar aromatic rings in docked poses?
#1470: Sometimes the results returned from Glide have slightly distorted aromatic rings. Can I prevent this?

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