Table 3A.
Molecular docking scores of ligands (napin and cruciferin) and bacterial receptor proteins (1xbp, 3fra, 3fyv, and 4urm).
| Complex name | Sol no | Global Energy | Softened attractive van der Waals energy | Softened repulsive van der Waals energy | Atomic contact energy | Insideness measure |
|---|---|---|---|---|---|---|
| 1xbp and napin | 7 | −0.59 | −1.61 | 0.49 | −0.12 | 2.31 |
| 5 | 9.18 | 0 | 0 | 0 | 13.12 | |
| 6 | 965.84 | −41.1 | 1,273.52 | 3.16 | 5.16 | |
| 9 | 2,121.34 | −24.46 | 2,707.98 | −9.41 | 9.57 | |
| 1 | 5,698.16 | −94.77 | 7,327.33 | −16.89 | 7.82 | |
| 8 | 6,643.37 | −89.32 | 8,488.29 | −11.47 | 7.23 | |
| 3 | 7,793.08 | −87.84 | 9,920.56 | −12.14 | 11.15 | |
| 2 | 8,236.15 | −62.31 | 1,0423.07 | −7.39 | 4.25 | |
| 10 | 95,88.56 | −126.96 | 1,2261.58 | −19.94 | 2.33 | |
| 4 | 12,417.14 | −133.42 | 1,5860.67 | −47.34 | 6.38 | |
| 1xbp and procruciferin | 6 | 1.21 | −8.06 | 2.94 | −2.65 | 21.69 |
| 10 | 8.12 | −1.9 | 0.67 | 0.4 | 14 | |
| 7 | 10.63 | −5.51 | 5.89 | 0.78 | 18.47 | |
| 8 | 11.63 | −1.92 | 0.78 | 1.92 | 15.45 | |
| 4 | 12.24 | −0.37 | 0 | 0.47 | 17.22 | |
| 5 | 931.29 | −24.03 | 1,187.66 | 3.16 | 17.37 | |
| 9 | 2,271.55 | −24.4 | 2,845.58 | 13.27 | 14.93 | |
| 1 | 2,348.57 | −37.17 | 3,007.55 | −9.82 | 20 | |
| 3 | 5,195.91 | −48.03 | 6,616.99 | −21.11 | 11.64 | |
| 2 | 6,642.51 | −46.95 | 8,399.35 | −16.86 | 29.19 | |
| 3FRA and napin | 3 | 9.67 | −5.15 | 0.25 | 4.36 | 12.98 |
| 7 | 11.99 | −18.76 | 6.61 | 15.45 | 18.5 | |
| 6 | 13.94 | −29.11 | 26.56 | 9.82 | 15.85 | |
| 2 | 19.23 | −0.75 | 0 | 2.22 | 21.28 | |
| 10 | 356.25 | −26.03 | 468.74 | −3.02 | 3.91 | |
| 9 | 368.1 | −38.18 | 481.56 | 12.76 | 13.88 | |
| 5 | 437.39 | −38.47 | 571.12 | 7.64 | 9.96 | |
| 1 | 447.54 | −29.03 | 593.26 | 0.16 | 5.97 | |
| 8 | 2,125.92 | −58.88 | 2707.8 | 6.13 | 13.04 | |
| 4 | 2,921.04 | −67.41 | 3751.22 | 7.48 | 12.65 | |
| 3FRA and procruciferin | 3 | −18.4 | −33.53 | 9.14 | 6.63 | 18.39 |
| 9 | 7.07 | −33.19 | 18.05 | 5.11 | 18.86 | |
| 8 | 12.74 | −24.81 | 11.45 | 10.97 | 18.18 | |
| 10 | 13.78 | −26.79 | 8.26 | 10.54 | 15.28 | |
| 1 | 14.38 | −28.27 | 14.14 | 17.54 | 20.42 | |
| 7 | 24.06 | −20.77 | 10.71 | 12.52 | 8.85 | |
| 5 | 31.73 | −16.53 | 7.55 | 9.77 | 9.91 | |
| 6 | 35.27 | −44.71 | 14.99 | 22.79 | 26.12 | |
| 4 | 46.04 | −9.72 | 6.78 | 8.46 | 20.11 | |
| 2 | 1,413.49 | −39.03 | 1752.69 | 13.97 | 16.75 | |
| 3fyv and napin | 7 | 10.1 | −2.74 | 0.6 | 3.02 | 19.22 |
| 10 | 28.13 | −23.99 | 12.28 | 12.2 | 15.36 | |
| 8 | 37.82 | −34.61 | 28.57 | 12.7 | 18.12 | |
| 2 | 39.93 | −29.2 | 26.67 | 18.88 | 15.78 | |
| 3 | 45.64 | −18.73 | 17.01 | 13.08 | 16.78 | |
| 9 | 116.89 | −23.22 | 118.17 | 18.87 | 16.1 | |
| 6 | 956.15 | −39.5 | 1,267.32 | 0.69 | 9.89 | |
| 5 | 1,428.16 | −22.18 | 1,797.91 | 14.11 | 11.47 | |
| 1 | 2,298.62 | −51.15 | 2,982.34 | −1.48 | 10.44 | |
| 4 | 4,226.41 | −53.66 | 5,383.38 | 3.23 | 11.43 | |
| 3fyv and procrucifrerin | 3 | −18.35 | −31 | 19.02 | 6.1 | 18.91 |
| 1 | −12.47 | −36.55 | 20.82 | 6.23 | 20.75 | |
| 2 | −7.57 | −20.79 | 17.3 | 6.92 | 16.75 | |
| 8 | −1.86 | −18.25 | 4.4 | 4.97 | 15.95 | |
| 7 | 6.68 | −19.44 | 19.24 | 8.98 | 13.41 | |
| 10 | 12.21 | −23.53 | 23.31 | 11.27 | 17.97 | |
| 5 | 35.64 | −22.45 | 10.36 | 11.19 | 21.6 | |
| 9 | 39.63 | −24.11 | 8.84 | 15.88 | 20 | |
| 6 | 684.27 | −43.27 | 942.18 | 1.59 | 15.88 | |
| 4urm and napin | 7 | −9.16 | −23.05 | 4.03 | 13.03 | 10.4 |
| 6 | −6.66 | −7.2 | 0.69 | 0.73 | 3.46 | |
| 8 | −3.81 | −25.16 | 11.33 | 15.72 | 17.27 | |
| 5 | −3.23 | −14.12 | 3.96 | 5.69 | 8.62 | |
| 2 | 1 | −3.22 | 0 | 1.48 | 11.06 | |
| 10 | 6.79 | −7.07 | 0.22 | 7.88 | 9.47 | |
| 3 | 12.67 | −1.61 | 0 | 1.56 | 16.15 | |
| 9 | 14.97 | −18.85 | 13.87 | 14.34 | 12.75 | |
| 1 | 58.84 | −12.38 | 36.52 | 5.95 | 7.38 | |
| 4 | 317.09 | −46.6 | 421.44 | 16.89 | 10.47 | |
| 4urm and procruciferin | 10 | 2.83 | −2.08 | 0 | 3.29 | 10.25 |
| 6 | 6 | −8.97 | 3.59 | 1.89 | 16.23 | |
| 2 | 6.62 | −8.84 | 6.65 | −0.29 | 19.8 | |
| 4 | 11.86 | −31.63 | 10.19 | 15.62 | 16.63 | |
| 5 | 20.54 | −4.71 | 0.12 | −0.24 | 22.41 | |
| 3 | 34.18 | −7.81 | 0.91 | 5.68 | 16.7 | |
| 9 | 42.57 | −18.89 | 2.96 | 13.63 | 16.95 | |
| 1 | 55.59 | −32.57 | 24.05 | 7.35 | 21.79 | |
| 8 | 85.15 | −27.61 | 93 | 13.49 | 20.4 | |
| 7 | 1,252.18 | −18.68 | 1,600.34 | −0.04 | 6.92 |
Solution numbers are arranged according to the order of the input transformations or models by default settings of online docking server. Global Energy is the binding energy of the solution complex. aVdW, rVdW, softened attractive and repulsive van der Waals energy; ACE, atomic contact energy; inside, insideness measure; aElec, rElec, attractive and repulsive short-range Coulomb electrostatics; laElec, lrElec, attractive and repulsive long-range Coulomb electrostatics; HB, hydrogen and disulfide bonds; CHB, Conventional Hydrogen Bond; piS, PI-PI stacking; catpiS, cation-PI stacking; aliph, aliphatic interactions; Transformation, ligand transformation after refinement. Analysis of the binding interactions of napin and procruciferin with bacterial enzymes showed that the ligand (napin and procruciferin) is surrounded by the amino acids of the bacterial enzymes mentioned in column H. Elec, Electrostatic; AC, Attractive Charge. 1XBP is the 50S ribosomal subunit from Deinococcus radiodurans, 3FRA is Staphylococcus aureus dihydrofolate reductase, 4URM is S. aureus gyrase B, and 3FYV is S. aureus dihydrofolate reductase. Bacterial receptor proteins were selected by efficient global search of relative receptor-ligand interactions (Andrusier et al., 2007; Barakat et al., 2016).