Figure 6.

Interaction energies for UQ (blue) and anionic SQ^– (red) headgroups using the GROMACS explicit solvent analysis (top) and MCCE Poisson–Boltzmann implicit solvent analysis (bottom). All energies are averaged over the 45 SMD trajectories for each redox state. The black dashed lines show the 5 selected time points: 2000, 4800, 5800, 6400, and 8000 ps. (A) Sum of the pairwise electrostatic and van der Waals interaction energies between quinone and the reaction center. This does not include interactions with the explicit water in the GROMACS analysis. For the MCCE analysis, the solvation energy is not included, but the pairwise interactions with the protein are screened by the protein dielectric constant of 4 and the implicit solvent with a dielectric constant of 80. (B) Specific interaction energies with Fe⁺² (solid lines), which become less negative during the unbinding trajectories and with the solvent (dots for explicit and dashed line for implicit), which becomes more negative. The isolated points on the right axis (*) show the implicit reference GCMC solvation energy for UQ (blue) and SQ^– (red) in the unbound state.