[phenixbb] Turn off non-bonded interactions to measure distance in case of unknown interaction

[Edward A. Berry]

I have a phenix-specific question and a general chemistry question.
In a ligand-bound structure, S in an aromatic ring (substituted thiophene)
may be H-bonding NH1 of arginine guanidino group.
The general question is whether thiophene S can act as H-bond acceptor
(assuming one lone pair is in the aromatic pi system for a total of 6 e,
the other lone pair is available as H-bond acceptor?).

The phenix-specific question involves whether non-bonded interactions
will push the atoms apart during refinement, and how to turn off the
nonbonded interaction between these two atoms to allow the xray data
to determine the position.
Under geometry_restraints.edits I define a bond, but give a very
large sigma of 1A.
Will this effectively remove non-bonded interactions between these
two atoms?