pH-Dependent Vibrational Dynamics Drives Excited-State Quenching in the Phycobiliprotein Complex PC645

The dataset contains the system setup, equilibration procedures, initial configurations, molecular dynamics trajectories, excitation energies, and spectral densities generated in the present study of the PC645 complex based on QM/MM MD simulations, as well as QM/MM-optimized structures. In addition, classical MD trajectories, along with the corresponding TrESP charges, are provided and were used for excitonic coupling calculations. The molecular dynamics data include the mdp files required for equilibration, as well as the tpr and xtc trajectory files from a 1 μs classical MD simulation (with only 1000 frames retained). For each pigment molecule, tpr and xtc trajectory files from a 1 ns QM/MM simulation (also reduced to 1000 frames) are included, together with the corresponding QM/MM-optimized structures. All data are provided for both protonated and deprotonated systems. The correspondence between the ordering of the eight bilin molecules and their names in the manuscript and in the MD files is as follows: ID Name in manuscript Name in gro/xtc 1 DBV 50/61B DBV475 2 DBV 60/61D DBV479 3 MBV 18A M1V474 4 MBV 18C M1V478 5 PCB 158B CYC476 6 PCB 158D CYC480 7 PCB 82B CYC477 8 PCB 82D CYC481