Why do sulfone oxygens have 3 lone pairs by default?
The sulfur in the sulfone group is not sp2 hybridized, so it is not clear which plane the lone pairs should lie in. Due to this ambiguity, three lone pairs are used for the oxygen. This choice of three vectors gives some vector character to the feature and at the same time does not penalize the vector score significantly. The ambiguity could possibly be resolved by the presence of the recptor, but such information cannot a priori be built into the default pharmacophore feature set. This behavior may be overridden by checking the Ignore box for the built-in pattern and then adding a new pattern with the same SMARTS string, but with a different projected point type.
