I'm trying to apply restrains to the interactions of cavity residues
with ATP. Apart from electrostatic interactions between atom pairs, a
Tyr residue is always packed parallel with the Adenine ring of ATP, as
shown in this pic:
I'm not sure what the best form would be for a pi-stacking interaction.
For stacking of two 6-membered rings, with Modeller restraints you could
add 6 distance restraints between the pairs of atoms (but that would
prevent rotation, of course) or create two centers of gravity, one for
each ring, and add a single distance restraint between the two (but that
would not force the rings to lie in the same plane - you'd have to add a
few dihedral restraints to do that). If you can't achieve it with
Modeller restraints, you can certainly write your own.