Table 1. Experimental and Calculated Binding Free Energies Using Microstate Energies Obtained with ff94 Scoring in Conjunction with the Implicit GB Solvent Model, ff99SB Scoring with the GB Solvent Model, and Semiempirical PM6DH2 Scoring with COSMO Solvent Modela.
| ff94/GB |
ff99SB/GB |
PM6DH2/COSMO |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| PDB | ligand | exptl. ΔGbind | ΔGbind | cor. | unc. | ΔGbind | cor. | unc. | ΔGbind | cor. | unc. |
| 181L | benzene | –5.2 | –8.63 | 0.43 | 3.61 | –8.64 | 0.43 | 3.46 | –10.45 | –0.39 | 0.77 |
| 182L | 2,3-benzofuran | –5.5 | –10.43 | 1.12 | 4.64 | –10.48 | 1.12 | 4.75 | –15.51 | –0.96 | 0.89 |
| 183L | indene | –5.1 | –12.17 | 0.99 | 4.51 | –12.10 | 0.99 | 4.58 | –15.86 | –0.47 | 0.77 |
| 184L | i-butyl benzene | –6.5 | –19.18 | 1.10 | 5.06 | –19.24 | 1.10 | 5.28 | –19.90 | –0.95 | 0.95 |
| 185L | indole | –4.9 | –9.70 | 1.19 | 5.00 | –9.68 | 1.19 | 5.04 | –14.04 | –0.94 | 0.99 |
| 186L | n-butyl benzene | –6.7 | –20.60 | 1.19 | 5.22 | –20.55 | 1.19 | 5.09 | –19.84 | –0.97 | 1.03 |
| 187L | p-xylene | –4.7 | –15.78 | 0.84 | 4.03 | –15.66 | 0.84 | 4.07 | –13.93 | –0.68 | 0.71 |
| 188L | o-xylene | –4.6 | –14.09 | 1.37 | 5.51 | –14.06 | 1.37 | 5.57 | –13.68 | –0.81 | 0.87 |
a
The systematic and random errors for each level of theory are also shown. “cor.” stands for the overall systematic correction to binding free energies, and “unc.” represents the uncertainty in those. All the numbers are in kcal/mol.