Figure 2.

Protonation of the ligand molecule by analysing the protein environment. Protonation of nitrogen atom N9 of molecule ADE339 depends on three parameters: the distance from ligand atom N9 to protein atom NH1 of ARG163, and the angles H-N9-NH1 and H1-NH1-N9. If hydrogen atoms H and H1 fall within a cone described by a solid angle of 60 degrees, then the hydrogen atom attached to the ligand ADE339 is removed (as indicated with a red X), even though the atom OE2 of GLU160 is in a favourable position to accept a hydrogen bond.