Table 2.

Interactions between the highest binding affinity ligands with the human Toll-like receptor 4 (TLR4).

Ligand	Binding Energy (kcal/mol)	Interacting Amino Acids	Interaction	Type	Location of Interaction	Common Amino Acid LPS and Ligands Interacted with
IP	−10	ILE52, PHE121, PHE151, LEU61, ILE32, VAL48	Hydrophobic	Pi-sigma and Pi-alkyl, Pi-Pi stacked, Pi-Pi T-shaped, Pi-alkyl, Pi-alkyl, Pi-alkyl	Chain D of TLR4	4: Val48, ILE52, ILE32 and LEU61
DahA	−9.2	PHE121, PHE119	Hydrophobic	Pi-Pi stacked, Pi-Pi stacked	Chain D of TLR4	1: PHE119
BkF	−8.9	PHE119, PHE121, ILE52, LEU61	Hydrophobic	Pi-Pi stacked, Pi-Pi stacked, Pi-Alkyl, Pi-Alkyl respectively	Chain D of TLR-4	3: PHE119, ILE52, and LEU61
BaP	−8.9	PHE119, PHE121, ILE52, LEU61	Hydrophobic	Pi-Pi stacked, Pi-Pi stacked, Pi-Alkyl, Pi-Alkyl respectively	Chain D of TLR-4	3: PHE119, ILE52, and LEU61