Table 3.
Calculated and Experimental ΔΔGbind (kcal/mol) of Benzimidazole Inhibitors in FtFabI using 1 ns MD simulations
| Amber Algorithm | Transformation Step | No. of Windows | 91→177 ΔΔG(expt)a = −1.27 | 91→135 ΔΔG(expt) = −1.04 | 135→138 ΔΔG(expt) = −1.53 | 135→166 ΔΔG(expt) = 0.76 | RMSD (kcal/mol) | RMSDall (kcal/mol)b | ΔRMSD (1ns–2ns) (kcal/mol)c |
|---|---|---|---|---|---|---|---|---|---|
| Sander | 3 | 6 | −0.45±0.08d | −1.37±0.10 | −2.26±0.17 | 0.74±0.11 | 0.57±0.12 | 0.44±0.10 | −0.03 |
| Sander | 3 | 11 | −0.47±0.08 | −0.88±0.10 | −2.34±0.18 | 1.33±0.11 | 0.64±0.12 | 0.50±0.10 | −0.14 |
| Sander | 3 | 15 | −0.33±0.08 | −0.80±0.10 | −2.01±0.18 | 1.69±0.11 | 0.71±0.12 | 0.67±0.10 | −0.11 |
| Sander | 3 | 17 | −0.36±0.08 | −0.72±0.10 | −1.89±0.18 | 1.71±0.11 | 0.70±0.12 | 0.68±0.10 | −0.05 |
| Sander | 3 | 21 | −0.27±0.08 | −0.67±0.10 | −1.61±0.13 | 1.77±0.12 | 0.74±0.11 | 0.73±0.10 | −0.07 |
|
| |||||||||
| Sander | 1 | 6 | −0.78±0.09 | −0.62±0.19 | −1.14±0.27 | 1.86±0.24 | 0.67±0.21 | 0.64±0.18 | −0.12 |
| Sander | 1 | 11 | −0.43±0.08 | −0.65±0.19 | −1.12±0.27 | 2.05±0.24 | 0.82±0.21 | 0.79±0.18 | −0.01 |
| Sander | 1 | 15 | −0.44±0.08 | −0.61±0.19 | −0.95±0.27 | 2.03±0.24 | 0.84±0.21 | 0.79±0.18 | −0.03 |
| Sander | 1 | 17 | −0.41±0.08 | −0.55±0.19 | −1.00±0.27 | 2.00±0.24 | 0.84±0.21 | 0.79±0.18 | −0.02 |
| Sander | 1 | 21 | −0.31±0.08 | −0.51±0.18 | −1.01±0.28 | 2.09±0.25 | 0.90±0.21 | 0.86±0.18 | 0.01 |
|
| |||||||||
| pmemd | 3 | 6 | −0.87±0.05 | −0.82±0.07 | −3.10±0.12 | 1.06±0.11 | 0.83±0.09 | 0.27±0.08 | −0.05 |
| pmemd | 3 | 11 | −0.60±0.05 | −0.73±0.07 | −2.46±0.12 | 1.20±0.11 | 0.63±0.09 | 0.43±0.08 | −0.08 |
| pmemd | 3 | 15 | −0.52±0.05 | −0.83±0.07 | −2.16±0.12 | 1.48±0.12 | 0.62±0.10 | 0.53±0.09 | −0.05 |
| pmemd | 3 | 17 | −0.41±0.05 | −0.80±0.07 | −2.15±0.12 | 1.48±0.12 | 0.65±0.10 | 0.57±0.09 | −0.05 |
| pmemd | 3 | 21 | −0.42±0.05 | −1.03±0.07 | −1.95±0.12 | 1.45±0.11 | 0.59±0.09 | 0.55±0.08 | −0.03 |
|
| |||||||||
| pmemd | 1 | 6 | −0.18±0.10 | −1.05±0.11 | −1.75±0.19 | 2.80±0.18 | 1.16±0.15 | 1.16±0.13 | −0.13 |
| pmemd | 1 | 11 | −0.04±0.10 | −1.19±0.11 | −1.98±0.19 | 2.45±0.18 | 1.07±0.15 | 1.05±0.13 | −0.01 |
| pmemd | 1 | 15 | −0.01±0.09 | −1.11±0.11 | −1.67±0.19 | 2.11±0.18 | 0.93±0.15 | 0.92±0.13 | 0.01 |
| pmemd | 1 | 17 | −0.05±0.09 | −1.12±0.11 | −1.79±0.19 | 2.14±0.18 | 0.93±0.15 | 0.92±0.13 | 0.01 |
| pmemd | 1 | 21 | −0.1±0.09 | −1.06±0.11 | −1.68±0.19 | 2.09±0.17 | 0.89±0.15 | 0.89±0.13 | 0 |
a
Experimental ΔΔG values
b
RMSD excluding the 135→ 138.
c
RMSD (excluding the 135→ 138) in 1 ns MD simulation trajectories minus RMSD (excluding the non-converged 135→ 138) in 2 ns MD simulation trajectories.
d
The error estimate using the standard error of the mean in Equation 7.