Table 2.
Lowest and average binding energies and corresponding ligand rankings.
| Molecule | Rank(calc)a | min(u)b | min(u)-rankc | 〈u〉1d | 〈u〉1-ranke |
|---|---|---|---|---|---|
| L99A Apolar Cavity | |||||
| iso-butylbenzene | 1 | -27.3 | 1 | -20.4 | 1 |
| benzene | 2 | -17.8 | 7 | -12.5 | 7 |
| toluene | 3 | -20.2 | 5 | -14.8 | 5 |
| indole | 4 | -22.9 | 4 | -16.3 | 4 |
| ter-butylbenzene | 5 | -24.7 | 2 | -18.4 | 2 |
| cyclohexane | 6 | -19.6 | 6 | -14.1 | 6 |
| 1,3,5-trimethylbenzene | 7 | -22.9 | 3 | -16.8 | 3 |
| phenol | 8 | -17.5 | 8 | -11.7 | 8 |
| Rank order CC:f | 0.36 | 0.36 | |||
| L99A/M102Q Polar Cavity | |||||
| toluene | 1 | -20.0 | 6 | -14.8 | 6 |
| phenol | 2 | -21.4 | 5 | -16.1 | 3 |
| 3-chlorophenol | 3 | -23.5 | 2 | -17.6 | 1 |
| catechol | 4 | -22.9 | 3 | -16.7 | 2 |
| 4-vinylpiridine | 5 | -18.7 | 7 | -13.6 | 7 |
| 4-chloro-1h-pyrazole | 6 | -18.7 | 8 | -12.4 | 8 |
| 2-aminophenol | 7 | -22.9 | 4 | -15.0 | 5 |
| phenylhydrazine | 8 | -26.2 | 1 | -15.7 | 4 |
| Rank order CC:f | -0.21 | 0.38 | |||
a
Ligand rankings based on the calculated binding free energies (from Table 1).
b
Lowest binding energy found over the conformations sampled from the HREM simulation.
c
Ligand rankings based on lowest binding energy values.
d
Average binding energy at λ = 1.
e
Ligand rankings based on average binding energy values.
f
Rank order correlation coefficients between lowest/average binding energy rankings (4th and 6th column, respectively) and binding free energy rankings (2nd column).