Source data for the "Retinal photoisomerization vs counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct"

The archives contain the xyz coordinates (both QM and QM/MM parts) data used to simulate the photochemistry of 13-cis and all-trans (Figure 3) as well as the multi-exponential decay of the K intermediate of bacteriorhodopsin presented in the main text of the paper "Retinal photoisomerization vs counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct" published in Nature Communications, 2024. Specifically:

Figure_3: the directory containing the xyz coordinates (both QM and QM/MM parts) of the structures used to compute the bond relaxation (BLA) profile and phtoisomerization torsional MEP of the Dark adapted (DA) and Light activated (LA) BR at CASSCF//CASPT2/MM level of theory.

Figure_7: The directory containing the xyz coordinates (both QM and QM/MM parts) of the structures used to compute the bond relaxation (BLA) profile of different protomers of K-intermediate of BR at CASSCF//CASPT2/MM level of theory.

Note: The QMpart.xyz and QMMMpart.crd files in the sub-directories contain the optimized coordinates of QM and QM/MM parts, respectively. The QMMMpart.xyz file included in each directory can also be used to distinguish QM (H-layer) and MM (M- and L-layer) parts. These data can be used to reproduce the QM/MM simulations with the COBRAMM pachage (https://gitlab.com/cobrammgroup/cobramm), following the computational details provided in the main text and the Supplementary Information.