Table 8. Binding affinity and RMSD values of the different poses of DAPH and Ni-DAPH complex in the active site of 2X08 and 1OAF enzymes.
| PDB code | Mode | DAPH | Ni–DAPH complex | ||||
|---|---|---|---|---|---|---|---|
| Affinity (kcal mol−1) | Dist from RMS dl.b | Best mode RMSD du.b | Affinity (kcal mol−1) | Dist from RMS dl.b | Best mode RMSD du.b | ||
| CCP (2X08) | 1 | −6.0 | 0.000 | 0.000 | −9.5 | 0.000 | 0.000 |
| 2 | −5.9 | 14.755 | 15.339 | −9.5 | 0.481 | 8.519 | |
| 3 | −5.9 | 22.984 | 25.594 | −9.0 | 0.822 | 7.513 | |
| 4 | −5.8 | 23.033 | 25.668 | −9.0 | 3.620 | 7.998 | |
| 5 | −5.8 | 23.546 | 25.801 | −9.0 | 0.339 | 6.904 | |
| 6 | −5.8 | 24.346 | 25.786 | −9.0 | 0.887 | 7.202 | |
| 7 | −5.7 | 2.029 | 3.402 | −8.7 | 0.485 | 4.843 | |
| 8 | −5.4 | 2.106 | 3.475 | −8.5 | 1.318 | 6.758 | |
| 9 | −5.4 | 24.398 | 26.768 | −8.4 | 3.160 | 8.729 | |
| APX (1OAF) | 1 | −5.3 | 0.000 | 0.000 | −7.9 | 0.000 | 0.000 |
| 2 | −5.1 | 2.216 | 4.794 | −7.9 | 0.172 | 6.543 | |
| 3 | −5.0 | 1.622 | 4.161 | −7.7 | 0.304 | 7.685 | |
| 4 | −5.0 | 3.064 | 4.934 | −7.7 | 0.254 | 5.233 | |
| 5 | −4.9 | 2.771 | 5.338 | −7.6 | 1.547 | 7.508 | |
| 6 | −4.9 | 1.941 | 4.777 | −7.6 | 1.542 | 5.966 | |
| 7 | −4.8 | 2.067 | 3.246 | −7.4 | 1.426 | 5.795 | |
| 8 | −4.8 | 1.925 | 4.785 | −7.3 | 1.623 | 5.855 | |
| 9 | −4.8 | 2.260 | 2.629 | −7.0 | 2.103 | 7.881 | |