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The side chain of Phe341 is more dynamic in “WT/paroxetine-ABC”. In “WT/paroxetine-ABC”, the Phe341 χ1 rotamer oscillates between trans and gauche- (B), whereas in “ts3/paroxetine-ABC” (A) and “WT/Br-paroxetine-ABC” (C), it does not. Such oscillations affect the RMSD of the ligand (D–F), but not that of the transmembrane domain (G–I). RMSDs were calculated against the last frame in each trajectory, based on the ligand heavy atoms (D–F) or the Cα atoms of TM 1–10 segments (G–I).
