Table 3.
Default parameters used for T2F pharmacophore elucidation.
| Grid box | Center | Ligand CoM * or center coordinates |
| Size of the edge of the cubic box | 16 Å | |
| Distance between two grid points | 0.6 Å | |
| Cavity | Occupancy | 0.6 kcal/mol |
| Buriedness (PSP) | 4 | |
| Feature type | Hydrophilic radius | 3 Å |
| Type specific energy cut-off ** | Hydrophobic (H) | −0.4 kcal/mol (−0.6) |
| H-bond donor (HBD) | −0.35 kcal/mol (−0.3) | |
| H-bond acceptor (HBA) | −0.6 kcal/mol (−0.5) | |
| Negative/Positive ionizable (NI/PI) | ±1.0 kcal/mol | |
| Clustering | Neighbor distance cut-off | 1.21 Å |
| Number of common neighbors | 6 (12, 16) *** | |
| Min. number of points per cluster | 15 |
* CoM = center of mass. ** Numbers in parentheses are parameter values used for the hydrophobic pocket of reverse transcriptase (PDB entry 1TVR). *** Numbers in parentheses are parameter values used for splitting larger clusters in second and third rounds.