Table 3.

Docking score and the interactions of the Inhibitors with RdRp

Ligands	Binding Affinity ΔG (Kcal/mol)	Inhibition Constant Ki (µM) 10–6	Interacting Amino acids	Bond Type
Lopinavir	− 7.7	2.8	SER 397, PHE 396, PRO 378, LEU 270, MET 666, THR 324, PHE 326, ALA 382, ALA 379, VAL 398, PRO 328, LEU 271, LEU 329, VAL 330, ALA 383, TYR 273, GLY 327, VAL 341, LEU 387	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Unfavorable Acceptor-Acceptor, Alkyl, Pi-Alkyl
Dexamethasone	− 7.3	5.4	THR 710, GLY 712, SER 709, TYR 129, LEU 240, ALA 125	Conventional Hydrogen Bond, Unfavorable Donor-Donor, Alkyl, Pi-Alkyl
Remdesvir	− 7.2	6.3	TYR 273, LEU 329, LEU 271, ALA 399, SER 325, LEU 387, ALA 383, PHE 396, ALA 379, ALA 382, VAL 398, PRO 378, PHE 326, VAL 330, THR 324, PRO 328	Van der waals, Conventional Hydrogen Bond, Pi-Pi Stacked, Alkyl, Pi-Alkyl
Merimepodib	− 7.2	6.3	ALA 125, TYR 129, GLN 724, HIS 725, TYR 728, GLY 712, THR 710, LEU 708, ASN 705, SER 709, TYR 732, LEU 240, HIS 133, VAL 128, ARG 132	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Pi Stacked, Pi-Pi T-shaped, Pi -Alkyl
Ritonavir	− 7.0	8.8	PRO 461, PRO 677, ASN 459, LEU 460, PHE 326, ARG 349, PHE 321, THR 319, SER 318, SER 255, ARG 249, ALA 252, HIS 256, LEU 261, LEU 265, VAL 320, PRO 322, TRP 268, THR 394, CYS 395, PHE 396, PRO 323	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Cation, Alkyl, Pi-Alkyl, Pi-Sulfur, Pi-Pi T-shaped
EIDD-2801	− 6.2	33.3	ARG 836, ALA 797, ASP 618, LYS 798, ASP 760, SER 759, SER 814, ASP 761, VYS 813, PHE 812, TRP 617, GLU 811, HIS 810	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Anion
Favipiravir	− 5.8	64.8	LYS 798, ASP 618, ALA 762, PHE 812, ASP 761, GLY 616, TRP 617, TRP 800, GLU 811, HIS 810	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Halogen (Floorine), Unfavorable Donor-Donor
Hydroxychloroquine	− 4.5	562.0	LEU 514, TRP 509, LEU 371, PHE 368, ALA 375, PHE 506, LEU 372, TYR 515, LEU 514	Van der waals, Pi-Pi Stacked, Pi-alkyl