[phenixbb] ambiguous ligand density

Ed Pozharski epozh001 at umaryland.edu
Wed Mar 9 10:41:48 PST 2011

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.



"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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