Figure 9.

(a) The interactions analysis for the S protein–ligand complexes for the second binding site over the last 40 ns of simulation. The S protein–ligand interactions are categorized into four types: hydrogen bonds (green color), hydrophobic interactions (purple color), ionic interactions (magenta color), and water bridges (blue color). (b) A schematic of detailed ligand atom interactions with the S protein residues. Only interactions that occurred more than 15.0% of the analyzed simulation time are illustrated.