Hi everyone. I am studying two different ligands bound to the same enzyme. I want to find out which one has a more favorable interaction using ONIOM energy calculations in Gaussian.

I did not perform geometry optimization, only single-point energy calculations. The structures come from molecular docking and are already pre-optimized. The system is the same in both cases, only the ligand changes.

In the ONIOM model, I placed the ligand and several key residues of the active site in the high layer. The low layer contains the rest of the enzyme. For the high layer, I used DFT (B3LYP) and for the low layer, molecular mechanics with the UFF force field.

I calculated the ONIOM energy of the full system for each ligand. I also calculated energies separately for the high and low layers using the same ONIOM setup.

My question is how to interpret the ONIOM energy values. Can I directly compare the energies between the two ligands? Should I use other calculations to complement the ONIOM energy results in order to determine which ligand has a better interaction with the enzyme? I appreciate your help since this has been a mostly independent work and I’m learning as I go.