| Target protein | Ligand | Binding affinity (kcal/mol) | Noncovalent interactions | Hydrogen bonds | Hydrophobic |
| Spike protein | Dithymoquinone | −7.5 | — | PHE342, LEU368 | Kaempferol | −7.6 | SER349, LEU441, ASP442, TYR451, ARG509 | ARG346 | Nigelladine A | −7.8 | LEU368 | PHE342, PHE374, PHE375, TRP436 | Nigelladine B | −7.3 | LEU368 | PHE342, LEU371, PHE374, PHE375, TRP436 | Nigellidine | −7.5 | — | PHE342, LEU368, LEU371, ALA372, PHE374, PHE375, TRP436 | Nigellidine sulphate | −7.4 | LEU368 | PHE342, PHE374, PHE375, TRP436 |
| Mpro | Dithymoquinone | −7.2 | THR292 | PHE294 | Kaempferol | −7.2 | HIS41, PHE140, ASN142 | LEU141 | Nigelladine A | −7.8 | — | PRO293, PHE294 | Nigelladine B | −7.2 | — | PHE8, PHE294 | Nigellidine | −7.6 | THR25, HIS164 | HIS41, CYS145 | Nigellidine sulphate | −7.8 | HIS41, ASN142, GLY143 | CYS44, MET49, CYS145 |
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