Table 3.

Ligand–protein interaction energies based on the optimized additive and Drude polarizable force fields.

PDB	Opt-CGenFF		Opt-Drude
Metdodb	Einter	E1inter	E2inter	E3inter	E4inter
2ZC9	−59.1 ± 1.3	−106.1 ± 1.6	−104.5 ± 2.0	−177.1 ± 0.4	−66.4 ± 0.8
2UW8	−54.8 ± 0.6	−136.2 ± 7.22	−135.9 ± 6.1	−117.8 ± 2.2	−68.0 ± 2.1
4DT6	−119.9 ± 0.3	−195.3 ± 6.7	−192.6 ± 7.0	−344.6 ± 2.8	−85.5 ± 1.2
4N1T	−37.2 ± 0.6	−42.6 ± 2.9	−42.0 ± 3.1	−57.2 ± 2.5	−44.3 ± 3.0
31X8	−75.6 ± 0.2	−96.5 ± 0.1	−96.7 ± 0.2	−99.2 ± 0.2	−92.6 ± 0.4
2AG6	−53.8 ± 0.1	−77.0 ± 0.2	−71.6 ± 0.5	−146.9 ± 3.2	−74.6 ± 0.2
3JUM	−83.3 ± 6.8	−149.8 ± 3.2	−145.0 ± 2.4	−345.9 ± 10.9	−83.2 ± 4.0

^aErrors shown are standard errors based on three independent simulations for each system.

^bPolarizable E1_inter, E2_inter, and E3_inter are based on equations 1, 2 and 3, respectively (Figure 2). CGenFF E_inter and E4inter are directly calculated using INTER command in the CHARMM program.^52–54