Table 2.

Docking score and the interactions of the Inhibitors with 3CLpro

Ligands	Binding Affinity ΔG (Kcal/mol)	Inhibition Constant Ki (µM) 10–6	Interacting Amino acids	Bond Type
Lopinavir	− 9.5	0.14	THR 196, ASP 197, THR 198, ASN 238, LYS 236, TYR 237, LEU 272, LEU 271, GLY 275, LEU 287, MET 276, ARG 131, TYR 239, VAL 204, ASP 289, THR 199, LEU 286, GLU 290, GLU 288, LYS 137	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Sigma, Pi-Sulfur, Pi-Alkyl
Dexamethasone	− 9.4	0.16	TYR 237, THR 199, GLU 290, ASP 289, ARG 131, ASP 197, LYS 137, GLU 288, LEU 286, LEU 287, TYR 239, LEU 272	Van der waals, Conventional hydrogen bond, Alkyl
Merimepodib	− 8.8	0.44	ASN 238, LYS 137, ASP 289, ARG 131, GLU 288, GLY 275, LEU 272, TYR 237, LEU 286, LEU 287, TYR 239, VAL 204, THR 199, ASP 197, THR 198	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Anion, Pi-Cation, Pi-Alkyl
Remdesvir	− 8.2	1.2	LEU 272, MET 276, LEU 287, THR 196, TYR 239, LEU 286, GLU 288, GLU 290, ASP 289, ARG 131, THR 199, TYR 237, THR 198, ASP 197, ASN 238	Van der waals, Conventional Hydrogen Bond, Pi-Sigma, Pi-Sulfur, Pi-Alkyl
Ritonavir	− 8.1	1.4	LEU 286, LEU 287, MET 276, LYS 137, ARG 131, THR 199	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Sigma, Alkyl, Pi-Alkyl
EIDD-2801	− 7.8	2.3	LEU 272, THR 199, LEU 287, THR 198, ARG 131, ARG 131, GLU 288, LYS 5, GLU 290, ASP 289, LYS 137, LEU 286, TYR 239	Van der waals, Conventional Hydrogen Bond, Pi-Anion
Hydroxychloroquine	− 6.9	10.4	MET 276, GLY 275, LEU 271, LEU 272, LEU 286, ARG 131, ASP 289, LYS 137, GLU 290, LYS 5, GLU 288, THR 199, LEU 287, TYR 239	Van der waals, Conventional Hydrogen Bond, Pi-Cation, Pi-Anion
Favipiravir	− 5.6	90.3	LEU 271, ASN 277, ASN 274, GLY 275, ARG 279, LEU 220, ASN 221, TRP 218, PHE 219, GLU 270, SER 267	Van der waals, Conventional Hydrogen Bond, Halogen (Fluorine), Pi-Pi T-shaped, Pi-Alkyl