| Target | Ligand | Binding affinity | H-bonding | Hydrophobic and electrostatic | Van der Waals |
| 7P2M | 3 | −7.8 | Thr-165 | Alkyl: Ile-78, 94 | Leu-98, Val-93, 97, 120, Gly-119, 75, 77, Asn-46, Asp-73, Glu-50, Arg-76, Pro-79 | 4 | −6.8 | — | Pi-sigma: Phe-196; alkyl and pi-alkyl: Arg-192, Leu-197, Phe-196 | Glu-193, Ser-195, His-217, Phe-216, Tyr-218 | 5 | −6.4 | Asn-46, Arg-76, Asp-49 | Pi-sigma: Ile-78; alkyl and pi-alkyl: Ala-47, Ile-94, Val-120, Ala-53; carbon hydrogen bond: Asp-73 | Gly-119, Val-93, 167, 97, Pro-79, Thr-165, Met-95, Glu-50, Leu-98 | 6 | −7.6 | Arg-76, Asn-46, Val-120 | Pi-sigma: Thr-165; alkyl and pi-alkyl: Val-167, 120, 43, Ile-78, 84; carbon hydrogen bond: Val-71, 97, Thr-165 | Pro-79, Arg-136, Ala-90, 53, 47, Gly-77, 119, Asp-49, 73, Val-93, Leu-98, Met-166, Glu-50 | 7 | −7.9 | Asp-73, Val-120, Ser-121 | Pi-sigma: Thr-165; alkyl and pi-alkyl: Ala-47, Val-43, 97, 93, Ile-94, 78; carbon hydrogen bond: Val-71, Thr-165, Asp-73, Gly-119 | Val-167, Asn-46, Asp-49, His-83, Arg-76, 136, Pro-79, Gly-77, Glu-50 | Ciprofloxacin | −7.4 | Arg-76 | Halogen: Asp-73; amide-pi stacked: Gly-77; alkyl and pi-alkyl: Ile-78, 94, Pro-79; carbon hydrogen bond: Asp-73 | Arg-136, Ala-47, Asn-46, Val-43, 167, 120, Glu-50, Trh-165 |
| 5OE4 | 3 | −9.0 | — | Pi-sigma: Phe-209, Trp-233; alkyl and pi-alkyl: Pro-205, Trp-233 | Val-254, Ile-204, Pro-234, 236, Ser-235, Phe-208 | 4 | −8.8 | — | Pi-sigma: Phe-209, Trp-233; alkyl and pi-alkyl: Pro-205, Phe-209, Trp-233 | Val-254, Pro-234, Phe-208, Lys-206, Ile-204 | 5 | −8.3 | Ser-226, Gly-198, Arg-200, 200 | Pi-anion: Asp-17, 19; pi-sigma: Ala-21; alkyl and pi-alkyl: Arg-249, 200, Ala-21; pi-donor and carbon hydrogen bond: Asp-199, 19, Ala-21, Arg-247 | Thr-29, 29, 20, 20, His-24, 24, Asp-199, 19, 17, Gly-198, Pro-248, Ser-31, 226 | 6 | −8.7 | Arg-200, 200, His-24, Ser-226 | Pi-anion and cation: Arg-200, Asp-19; alkyl, pi-alkyl, and pi-sigma: Arg-249, Ala-21; carbon and pi-donor hydrogen bond: Gly-198, 224, Arg-247, Asp-19, Ala-21 | Pro-248, Thr-20, 20, 29, 29, Gly-198, Ala-125, 21, 197, Asp-199, 19, 17, His-24 | 7 | −8.4 | Gln-34, Ser-31, Arg-200, 200, Ala-21 | Pi-cation: Arg-200; pi-sigma: Thr-29; alkyl and pi-alkyl: Ala-245, 21, 21; carbon hydrogen bond: His-24, Asp-117 | Leu-228, 30, Phe-246, His-24, Thr-29, 20, 20, Ser-31, Asp-19, 19, Gly-198, 27 | Ciprofloxacin | −7.2 | Arg-200 | Halogen: Asp-19, Arg-200; alkyl: Ala-21; carbon hydrogen bond: Gly-198, Asp-17 | His-24, Ser-226, Thr-29, 20, Arg-249, Gly-198 |
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