Figure 7.

Average interaction-free energies (kcal/mol) decomposed into polar (blue or gray) and nonpolar (orange or yellow) components for AhR interacting residues and molecular graphics images of the lowest association-free energy binding modes of 4′,5,7-trimethoxyisoflavone and 4′,5,7-trimethoxyflavone in complex with AhR. (A) AhR interacting residues in complex with 4′,5,7-trimethoxyflavone (second bar/residues). The sum of the polar and nonpolar components corresponds to the total average per AhR residue interaction-free energy. Only per residue interactions with total interaction-free energies less than −1.0 kcal/mol are considered in the plot. The average polar and nonpolar interaction-free energy component values and their standard deviation values were calculated over four measurements in which the first, second, third, and fourth measurements correspond to the individual average interaction-free energy component of the first, second, third, and fourth 6.5 ns segment of the last 25 ns of the 30 ns MD simulation production run. Image of the lowest association-free energy binding modes of 4′,5,7 trimethoxyisoflavone (B) and 4′,5,7-trimethoxyflavone (C) in complex with the AhR binding pocket. For both panels, the ligand is shown in licorice representation; AhR is shown in transparent cyan new cartoon representation, and key AhR residues are shown in thin licorice representation.