| Compound/ligand | Binding affinity (kcal/mol) | H-bond | Residual amino acid interactions | Hydrophobic/electrostatic | Van der Waals |
| 3 | −9.9 | Asp-831, Glu-839, His-1005, Glu-712, and Ile-715 | Arg-672, Glu-712, Glu-839, Phe-1003 Pro-724, and Leu-829 | Met-669, Arg-673, Gly-1007, Asn-708, Lys-676, Trp-840, Lys-728, Glu-837, Arg-727, Lys-723, Pro-716, and Ser-717 | 4 | −7.5 | Gly-1007 and Met-669 | Arg-672, Arg-673, Glu-712, and Phe-1003 | Pro-724, Arg-727, Ser-717, Lys-676, and Cys-1008 | 5 | −8.7 | Met-669, Glu-839, and Glu-712 | Arg-672, Arg-673, Glu-712, Phe-1003, Met-669, and Pro-724 | Trp-840, Leu-829, Glu-837, Arg-727, Ser-717, Leu-722, Pro-716, Lys-723, Ile-715, Gly-1007, Asn-708, Lys-676, Val-1006, and Lys-827 | 6 | −9.2 | Arg-673, Gly-1007, Arg-727, and Glu-837 | Leu-829, Pro-724, and Glu-712 | Pro-838, Glu-839, Asp-831, Lys-827, Lys-676, Arg-672, Phe-1003, Lys-723, Pro-716, Leu-722, Ile-715, and Ser-717 | Etoposide | −9.4 | Lys-827, Glu-839, His-1005, and Met-669 (C-H bond) | Arg-672, Arg-673, Pro-724, Lys-676, and Phe-1003 | Glu-682, Leu-829, Gly-1007, Trp-840, Asp-1004, Ser-717, Arg-727, Lys-723, Pro-716, Glu-712, and Ile-715 |
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