On Wed, 2011-03-09 at 11:55 -0500, Pompeu,Yuri Alexey Andreiw wrote:
it is not experiencing interaction in the form of H-bonds. Which I think is concerning.
Well it should not be. There are two possibilities: a) the carbonyl in question is facing solvent. Depending on resolution/degree of solvent disorder you may or may not see the water molecules that make hydrogen bonds b) the carbonyl in question is facing protein. In this case upon binding you simply lose a hydrogen bond that ligand was making to solvent. It is likely to cost some free energy, perhaps 1-2 kcal/mole, but other interactions may be more than enough to produce binding at whatever levels you observe. Of course, it is also possible that you are not modeling it right. Depending on resolution, quality of the map and internal symmetry of the ligand molecule, it may be possible to come up with alternative docking mode. You can get better (more specific) advice if you show your data to an experienced crystallographer. Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs