This archive contains all data necessary to reproduce the results of the article

Jakob Günther, Thomas Weymuth, Moritz Bensberg, Freek Witteveen, Matthew S. Teynor,
F. Emil Thomasen, Valentina Sora, William Bro-Jørgensen, Raphael T. Husistein,
Mihael Erakovich, Marek Miller, Leah Weisburn, Minsik Cho, Marco Eckhoff, Aram
Harrow, Anders Krogh, Troy van Voorhis, Kresten Lindorff-Larsen, Gemma Solomon,
Markus Reiher, Matthias Christandl, "How to Use Quantum Computers for Biomolecular
Free Energies", 2025, to be submitted.

The software used to generate the data in the directories databases, energies,
work_distributions, and mlp is provided in the directory software/pipeline and
the following Zenodo upload: https://zenodo.org/records/14971120

The software used to generate the data in the directory bootstrap_embedding
is presented in the following article: Minsik Cho, Oinam Romesh Meitei, Leah P.
Weisburn, Oskar Weser, Shaun Weatherly, Alexandra Alexiu, Rebecca Hanscam,
Henry K. Tran, Hong-Zhou Ye, Matthew Welborn, Nathan Ricke, Takashi Tsuchimochi,
Aleksandr Trofimov, Temujin Orkhon, Noah Whelpley, Carina Luo, Troy Van Voorhis,
"QuEmb: A Toolbox for Bootstrap Embedding Calculations of Molecular and Periodic
Systems", J. Phys. Chem. A, 2025, accepted.

The software used to generate the data in the directory quantum_computing is
provided in the directory software/quantum-resources and presented in the
following article: Jakob Günther, Freek Witteveen, Alexander Schmidhuber, Marek
Miller, Matthias Christandl, Aram Harrow, "Phase estimation with partially randomized
time evolution", 2025, arXiv:2503.05647 [quant-ph].

This archive is structured as follows:

- bootstrap_embedding:
  - be_complex_data.csv: Bootstrap embedding energies for the GRP78-NKP1339 protein-ligand complex
  - be_ligand_data.csv: Bootstrap embedding energies for the solvated NKP1339 ligand
- databases: The databases containing the structures and QN/QM/MM Hamiltonians. To
             reimport it use the tool `mongoimport`.
  - ru-ligand-solvent.tar.xz: The databases containing the structures and QM/QM/MM Hamiltonians for the GRP78-NKP1339 protein-ligand complex
    - calculations.bson: The calculations collection exported as a BSON file
    - calculations.metadata.json: The metadata of the calculations collection
    - properties.bson: The property collection (i.e., collection of properties such as energies, charges etc.)
    - properties.metadata.json: The metadata of the properties collection
    - structures.bson: The structure collection (i.e., collection of all Cartesian coordinates and element symbols)
    - structures.metadata.json: The metadata of the structures collection
  - ru-complex-shrunk.tar.xz: The databases containing the structures and QM/QM/MM Hamiltonians for the solvated NKP1339 ligand
    - calculations.bson: The calculations collection exported as a BSON file
    - calculations.metadata.json: The metadata of the calculations collection
    - properties.bson: The property collection (i.e., collection of properties such as energies, charges etc.)
    - properties.metadata.json: The metadata of the properties collection
    - structures.bson: The structure collection (i.e., collection of all Cartesian coordinates and element symbols)
    - structures.metadata.json: The metadata of the structures collection
- energies
  - energies_hf_dmrg_nevpt2_loc_protein_pruned: HF, DMRG, and DMRG-NEVPT2 energies for the GRP78-NKP1339 protein-ligand complex
  - energies_hf_dmrg_nevpt2_loc_solvated_pruned: HF, DMRG, and DMRG-NEVPT2 energies for the solvated NKP1339 ligand
  - energies_hf_ump2_uccsd_uccsd_t_protein: HF, MP2, and CCSD(T) energies for the GRP78-NKP1339 protein-ligand complex
  - energies_hf_ump2_uccsd_uccsd_t_solvated: HF, MP2, and CCSD(T) energies for the solvated NKP1339 ligand
  - raw_data: TODO
- mlp
  - grp78-nkp1339_complex_shrunk_ump2: MLP for the GRP78-NKP1339 protein-ligand complex (based on MP2 data)
  - grp78-nkp1339_complex_shrunk_uccsdt: MLP for the GRP78-NKP1339 protein-ligand complex (based on CCSD(T) data)
  - grp78-nkp1339_complex_shrunk_nevpt2: MLP for the GRP78-NKP1339 protein-ligand complex (based on NEVPT2 data)
  - grp78-nkp1339_solvent_ump2: MLP for the solvated NKP1339 ligand (based on MP2 data)
  - grp78-nkp1339_solvent_uccsd: MLP for the solvated NKP1339 ligand (based on CCSD(T) data)
  - grp78-nkp1339_solvent_nevpt2: MLP for the solvated NKP1339 ligand (based on NEVPT2 data)
- quantum_computing: Data underlying the quantum computing resource estimates (gate counts, runtime)
- software: 
  - pipeline: A collection of Python scripts/executables to generate plots, populate the database, and run the active learning
  - quantum-resources: The Python scripts necessary to calculate the quantum resource estimates
- work_distributions
  - ru-complex-shrunk
    - ump2: Work values for the GRP78-NKP1339 protein-ligand complex (MP2 data)
    - ccsdt: Work values for the GRP78-NKP1339 protein-ligand complex (CCSD(T) data)
    - nevpt2: Work values for the GRP78-NKP1339 protein-ligand complex (NEVPT2 data)
  - ru-ligand-solvated
    - ump2: Work values for the solvated NKP1339 ligand (MP2 data)
    - ccsdt: Work values for the solvated NKP1339 ligand (CCSD(T) data)
    - nevpt2: Work values for the solvated NKP1339 ligand (NEVPT2 data)