Table 1.
The binding affinity (kcal/mol) of various compounds 1 to 8 and reference with OmpU after molecular docking.
| Structure | Binding affinity (kcal/mol) | Docked complex (amino acid -ligand) interactions | Distance (Å) | |
|---|---|---|---|---|
| Ref |
|
−10.7 | H-bonds | |
| Reference—TYR20: HH | 2.03 | |||
| Reference—TYR20: HH | 2.48 | |||
| Reference—SER239: HG | 2.38 | |||
| Reference—GLY218: O | 2.49 | |||
| 1 |
|
−8.0 | H-bonds | |
| Compound 1—ASP126: OD2 | 2.03 | |||
| π-π interactions | ||||
| Compound 1—PHE85 | 3.88 | |||
| Compound 1—PHE85 | 5.05 | |||
| π-cation interactions | ||||
| Compound 1—ARG107: NH1 | 4.07 | |||
| Compound 1—ARG155: NH1 | 5.77 | |||
| Compound 1—TYR108 | 6.17 | |||
| 2 |
|
−9.6 | H-bonds | |
| Compound 2—TYR110:OH | 2.08 | |||
| π-π interactions | ||||
| Compound 2—PHE85 | 3.86 | |||
| Compound 2—PHE85 | 5.07 | |||
| π-cation interactions | ||||
| Compound 2—ARG107: NH1 | 6.63 | |||
| Compound 2—ARG155: NH1 | 5.79 | |||
| Compound 2—TYR108 | 4.07 | |||
| 3 |
|
−10.6 | H-bonds | |
| Compound 3—ASN125:OD1 | 2.36 | |||
| π-π interactions | ||||
| Compound 3—PHE85 | 3.91 | |||
| Compound 3—PHE85 | 5.10 | |||
| π-cation interactions | ||||
| Compound 3—ARG107:NH1 | 6.64 | |||
| Compound 3—ARG155:NH1 | 5.75 | |||
| Compound 3—TYR108 | 4.07 | |||
| Compound 3—TYR108 | 6.02 | |||
| 4 |
|
−10.0 | H-bonds | |
| Compound 4—ASP29:H | 2.06 | |||
| π-cation interactions | ||||
| Compound 4—ARG107:NH1 | 6.62 | |||
| Compound 4—ARG107:NH1 | 6.79 | |||
| Compound 4—ARG155:NH1 | 5.44 | |||
| Compound 4—ARG155:NH1 | 5.96 | |||
| 5 |
|
−9.0 | π-cation interactions | |
| Compound 5—ARG155:NH1 | 5.96 | |||
| Compound 5—ARG155:NH1 | 6.08 | |||
| 6 |
|
−9.5 | H-bonds | |
| Compound 6—ASP126:OD2 | 2.42 | |||
| π-π interactions | ||||
| Compound 6—PHE85 | 3.88 | |||
| Compound 6—PHE85 | 5.08 | |||
| π-cation interactions | ||||
| Compound 6—ARG107:NH1 | 6.67 | |||
| Compound 6—ARG155:NH1 | 5.75 | |||
| Compound 6—TYR108 | 4.07 | |||
| 7 |
|
−8.8 | π-π interactions | |
| Compound 7—PHE85 | 3.88 | |||
| Compound 7—PHE85 | 5.02 | |||
| π-cation interactions | ||||
| Compound 7—ARG155:NH1 | 5.77 | |||
| Compound 7—TYR108 | 6.71 | |||
| 8 |
|
−8.7 | H-bonds | |
| Compound 8—ALA14:H | 2.24 | |||
| π-cation interactions | ||||
| Compound 8—LYS172:NZ | 6.25 | |||
| π-sigma interactions | ||||
| Compound 8—LYS163:HB2 | 2.76 |
The 8 molecules (1-8) with the best binding affinity are represented with docking interactions in the table showing H-bonding, pi-pi, pi-cation, and pi-sigma interactions.