I have little knowledge that the potential energy is based on the force field being used while kinetic energy is not. but I am not quite convinced that this is the only reason why it the K.E. is not being used. the formula used for the calculation of free energy of binding is

DGbind = a(p - w) + b(p w) ;

p = LJ term for ligand/protein interaction

w = LJ term for ligand/water interaction

p = Electrostatic term for ligand/protein interaction

w = Electrostatic term for ligand/water interaction

with default scaling factors a=0.18 and b=0.50