Structure Downloader

Choose how to access chemical database information, particularly geometries which are available in tarballs.

Database Information Options

  • Primary source of truth are database files containing geometries GEOS (Å if unlabeled), reference reaction energy BIND in kcal/mol, and stoichiometry ACTV & RXNM
  • Programmatically, geometries, energies, and reaction information can be accessed through QCDB . The recommended installation path is conda create -n bfdbenv python=2.7 jupyter matplotlib qcdb=0.8 bfdb-jupyter=1.0 -c psi4, though other routes (clone & installer) and detailed instructions are at BFDb SuppMat . In particular, structures can be extracted via the snippet below:

    import qcdb
    
    for db in ['UBQ', 'ACHC']:
        asdf = qcdb.Database(db, loadfrompickle=True)
        asdf.write_xyz_files()
  • Website access to geometries can be had through the "Reactions" page on this site (one system at a time) or through the XYZ-file tarballs below (en masse). For reference reaction energies, consult the "Model Chemistries" page and "Model Chemistry Energies and Errors" section, from which a CSV table is downloadable.
  • Geometry Information

    • Coordinates in Å
    • Second line contains charge and multiplicity
    XYZ Tarball Description Geometry/Database DOI
     A24 interaction energies for small bimolecular complexes 10.1021/ct400057w
     ACHC interaction energy curves for adenine-cytosine stacked nucleobases through six translations and rotations 10.1021/acs.jctc.5b00588 named 10.1021/acs.jpclett.6b00780
     ACONF conformation energies for alkanes 10.1021/jp903640h named 10.1021/ct900489g
     BBI interaction energies for peptide backbone-backbone complexes 10.1063/1.5001028
     CYCONF conformation energies for cysteine 10.1021/ct900005c named 10.1021/ct900489g
     HBC6 interaction energies for dissociation curves of doubly hydrogen-bonded bimolecular complexes 10.1021/ct100469b
     HSG interaction energies for bimolecular complexes from protein-indinavir reaction site 1HSG 10.1021/ct100563b
     JSCH interaction energies for nucleobase pairs 10.1039/b600027d
     NBC10 interaction energies for dissociation curves of dispersion-bound bimolecular complexes NBC10 10.1063/1.3545971 NBC10ext 10.1021/acs.jpclett.6b00780
     PCONF conformation energies for tripeptides 10.1002/chem.200500465 named 10.1021/ct900489g
     S22 interaction energies for organic bimolecular complexes 10.1039/b600027d
     S22by7 interaction energies for dissociation curves of organic bimolecular complexes S22by5 10.1021/ct1002253 S22by7 10.1021/acs.jpclett.6b00780
     S66 interaction energies for organic bimolecular complexes 10.1021/ct2002946
     SCONF conformation energies for sugars 10.1021/ct8004479 named 10.1021/ct900489g
     SSI interaction energies for peptide sidechain-sidechain complexes 10.1063/1.5001028
     UBQ interaction energies for bimolecular complexes from native 1UBQ protein fold 10.1371/journal.pone.0018868