Source Data for the publication: “Energy transfer pathways in plant Photosystem I from first-principles modeling”

The dataset contains the data underlying all of the Figures of the main text and other supporting data that can be used to reproduce our results.

• Hamiltonian_CT.csv : site energies and couplings computed for the 156 pigments on the refined structure.
• dipoles.dat : transition dipoles for the 156 pigments (x,y,z components for each Chl, in the same order of the Hamiltonian).
• PSI_refined.pdb : refined structure used for QM/MMPol calculations. The numbering of the resIDs is that obtained upon system preparation. The correspondence with the labels used in the work can be found in nomenclature.dat file.
• domains.dat: composition of the Redfield-Forster domains (by index in the Hamiltonian and by name).
• rates_calculation : a zipped folder containing the python scripts compute_rates.py and compute_rates_CT.py to compute rates for the CT and noCT model respectively. The results are collected in rates and rates_CT folders. Note that in rates_calculation/data/ we report all the input data needed for the calculation of rates, including the ensemble of Hamiltonians for CT and noCT models as well as the spectral density files and transition dipoles.

Other data made available here:

• abs_spec_CT_noCT.csv : frequency axis and absorption intensity for the CT and noCT model shown in Fig.3. abs_spec_contributions_CT.csv and abs_spec_contributions_noCT.csv contain the contributions of each Chl to the total spectra.
• pop_CT.csv, pop_noCT.csv : time evolution of the population of each pigment upon homogeneous excitation in the CT and noCT models. Their sum is shown in Fig.3.
• flows_core.csv, flows_Lhca1.csv, flows_Lhca2.csv, flows_Lhca3.csv, flows_Lhca4.csv contain the data underlying Fig.4.
• pop_core.csv, pop_LHCIblue.csv : time evolution of the population of each pigment in the CT model upon excitation of the core and LHCI respectively (data in Fig.5).
• MFPT_CT_noCT.csv: mean first passage times computed for the CT and noCT model.

We also deposit the full pyQME package in the version used in this work for future reference in pyQME_version_PSI.zip.