Docking Energy Calculation

Docking geometries and energies are best performed using other methods, for example MM, but if you want to model docking using MOPAC, here is a starting strategy:

Geometry optimize the complex; let its Heat of Formation be ΔH_f(complex). Add keyword EPS=78.4 to mimic water solvent. Separate the ligand from the protein by moving the ligand far away (e.g., by adding 100 Ångstroms to every "x" coordinate of the ligand atoms), and run the geometry optimization again.  Let the new HoF be ΔH_f(separate). Then the interaction energy is ΔH_f(complex) - ΔH_f(separate).