Table 5.
Dipole moments and RMS fluctuations (Debye) of each neutral ligand and their halogenated aromatic groups (Ar-X) in the aqueous solution and in the ligand-protein (w/Protein) simulations for the optimized Drude and additive force fields.
| PDBID | Aqueous | w/Protein | Watera (Aqueous) | Waterb (w/Protein) | |
|---|---|---|---|---|---|
| Full ligand | |||||
| Additive | |||||
| 4N1T | 5.14 ± 0.73 | 4.18 ± 1.63 | |||
| 31X8 | 6.63 ± 0.62 | 7.83 ± 0.50 | |||
| 2AG6 | 15.04 ± 0.33 | 14.91 ± 0.36 | |||
| Drude | 2.46 ± 0.16c | ||||
| 4N1T | 7.17 ± 0.99 | 4.32 ± 1.06 | 2.46 ± 0.16 | 2.42 ± 0.19 | |
| 31X8 | 9.70 ± 1.02 | 9.00 ± 0.60 | 2.48 ± 0.16 | 2.36 ± 0.22 | |
| 2AG6 | 16.10 ± 0.88 | 15.96 ± 0.74 | 2.46 ± 0.16 | 2.44 ± 0.18 | |
| Halogenated aromatic group | |||||
| Additive | |||||
| PDBid | Ar-Xd | ||||
| 4N1T | CL | 3.11 ± 0.07 | 3.11 ± 0.07 | ||
| 31X8 | CL | 2.29 ± 0.08 | 2.29 ± 0.07 | ||
| BR | 2.50 ± 0.09 | 2.52 ± 0.09 | |||
| 2AG6 | BR | 0.73 ± 0.08 | 0.72 ± 0.08 | ||
| Drude | |||||
| PDBid | Ar-Xd | ||||
| 4N1T | CL | 3.94 ± 0.46 | 3.50 ± 0.60 | ||
| 31X8 | CL | 3.46 ± 0.42 | 3.61 ± 0.29 | ||
| BR | 3.08 ± 0.45 | 3.72 ± 0.35 | |||
| 2AG6 | BR | 1.17 ± 0.50 | 0.86 ± 0.41 | ||
a
Dipole of waters within 3 Å of the full ligand are calculated.
b
Dipole of waters within 3 Å of both the protein and the full ligand are calculated.
c
Average and RMS fluctuations of the dipole moment of water in pure aqueous solution.
d
Ar-X indicates which halogen is included. The halogenated aromatic group includes all the functional groups on the same aromatic ring.