Structural Dynamics and Optical Spectra of the Phycobiliprotein PC612 Complex

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. 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 DBV478 2 DBV 60/61D DBV482 3 PCB 20A CYC477 4 PCB 20C CYC481 5 PCB 158B CYC479 6 PCB 158D CYC483 7 PCB 82B CYC480 8 PCB 82D CYC484