Comparison of PMX53 structures from the MD simulations of modes 6 (gray; panel A), 3 (gray; panel B), and 30 (gray; panel C) superposed against the lowest binding free energy conformation of complex 22 (red; all panels). The conformations shown have the lowest binding free energy among all snapshots of the corresponding trajectory (in the MM-PBSA approximation). The structures are aligned using the mainchain transmembrane atoms of C5aR. All ligand hydrogen atoms are omitted for clarity. The C5aR segments interacting with the ligand are shown in different colors, in tube representation; the coloring scheme is the same as in Figure 3.