Table 4.

Ligand–protein interaction self-energies (E_self) based on the optimized Drude polarizable force field.^a Errors shown are standard errors based on the three independent simulations for each system.

PDB	Opt-Drude-El	Opt-Drude-E2	Opt-Drude-E3
Metdod	E1self	E2self	E3self
2ZC9	−101.0 ± 2.7	−5.6 ± 7.6	15.7 ± 6.1
2UW8	−42.0 ± 12.0	−93.3 ± 11.4	−99.2 ± 11.6
4DT6	−126.2 ± 6.9	39.9 ± 12.0	51.0 ± 13.4
4N1T	2.2 ± 1.6	8.9 ± 5.5	13.1 ± 6.5
3IX8	−2.5 ± 0.8	−11.3 ± 2.5	−6.0 ± 2.3
2AG6	78.6 ± 15.7	9.2 ± 24.9	24.9 ± 35.2
3JUM	−237 ± 25.3	292.7 ± 21.8	334.0 ± 17.3

^aIn methods 1–3, each self-energy contribution from the complex, protein and ligand were obtained (e.g. E_{self, comp}, E_{self, prot}, and E_{self, ligand}). The self-energy for each component is calculated from the total bond energy minus the bond energy with the Drude particles omitted based on the geometry after Drude particles are relaxed in the SCF calculation. E_self is calculated as E_{self, comp} - E_{self, prot} - E_{self, ligand}. Self-energies from method 4 are zero, i.e. E_{self, comp} = E_{self, prot} + E_{self, ligand}, as no relaxation of Drude particles is performed.