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Table 6 Docking results of Template molecule, designed molecule with the highest activity, first, second, and third generation approved direct-acting antiviral agents

From: Computer-aided identification of a series of novel ligands showing high potency as hepatitis C virus NS3/4A protease inhibitors

The compound from Table 5 Binding energy kCal/mol Residues interacting with ligand Types of interaction Bond length (Å)
1 − 7.5 THR298, SER229 Conventional Hydrogen Bond 2.17, 3.60
   SER297 Carbon Hydrogen Bond 3.69
   GLU291 Pi-Anion 3.51
   SER294, TRP501 Pi-Donor Hydrogen Bond 3.78, 3.54
   ALA497, PRO230, HIS293 Pi-Alkyl 4.48, 4.79, 5.48
7 − 10.7 THR416, THR416, SER294, THR295, GLY484 Conventional Hydrogen Bond 2.91, 2.79, 3.02, 2.85, 3.10
   TYR391, HIS293 Carbon Hydrogen Bond 3.70, 3.10
   ASP454 Pi-Anion 3.43
   SER457, THR295, SER483 Pi-Donor Hydrogen Bond 3.75, 4.05, 3.56
   ARG393, VAL456 Pi-Alkyl 4.69, 4.64
14 − 9.5 ARG481, MET485, GLY484, THR295, THR295, HIS369 Conventional Hydrogen Bond 3.18, 1.95, 3.11, 3.31, 3.10, 2.32
   VAL490, VAL490, PRO523, VAL456 Alkyl 4.99, 4.71, 4.34, 4.61
   VAL432 Pi-Alkyl 5.01
15 − 10.0 ALA413, GLN434 Conventional Hydrogen Bond 2.80, 3.21
   ASN556, SER489, GLU493 Carbon Hydrogen Bond 3.58, 3.14, 3.63
   ASP454 Pi-Anion 4.09
   THR295, THR433 Pi-Donor Hydrogen Bond 3.71, 3.88
   VAL456, VAL490 Alkyl 3.96, 3.57
   VAL456 Pi-Alkyl 4.93
16 − 10.5 GLU493, TRP501, TYR502, GLY253 Conventional Hydrogen Bond 2.39, 3.16, 2.50, 3.17
   THR269 Carbon Hydrogen Bond 3.47
   ASP412, ASP412 Halogen (Fluorine) 3.31, 3.40
   GLY271 Amide-Pi Stacked 4.59
   ALA413, PRO558 Alkyl 4.19, 4.50
   ALA497, TRP501 Pi-Alkyl 4.86, 5.06
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