GDB-BSIE

Dataset of small molecules with up to 7 heavy atoms from the GDB-11 and GDB-13 datasets. For each molecule included, a minimized geometry as well as 10 geometries sampled from MD are included. For each data point, RHF and B3LYP energies are computed using the basis sets STO-3G, cc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z in Psi4.

The following files/folders are found in the tarball GDB-BSIE.tar.

molecule.smi
List of all the molecules found in the dataset.

First column: a unique molecular index index (0 - 13220)
Second column: smiles string canonicalized in rdkit

index_map.txt
mapping from the unique identifier to the molecular index and geometry index of any data point. For each molecule there are one minimum geometry (geometry index = 0) and up to ten geometries sampled from dynamics. The molecule indices correspond to the indices in molecule.smi.

XYZ/
Folder containing all xyz files for all geometries included in the dataset. All files are named after the unique index.

Energies/
Contains the RHF/B3LYP computed energies in Hartrees. Each column of the csv file corresponds to a specific basis set that can be identified in the header line. The index column contains the unique index of all data points. All energies are computed using the Psi4 computational chemistry package.

Psi4 output files are found separately in Psi4OutputFilesB3LYP.tar.gz and Psi4OutputFilesRHF.tar.gz.

All original smiles strings are obtained from either the GDB-11 or GDB-13 datasets
Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physico-chemical properties, compound classes and drug discovery. Fink, T.; Reymond, J.-L. J. Chem. Inf. Model. 2007, 47, 342-353.
Virtual Exploration of the Small Molecule Chemical Universe below 160 Daltons. Fink, T.; Bruggesser, H.; Reymond, J.-L. Angew. Chem. Int. Ed. 2005, 44, 1504-1508.
970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13. Blum L. C.; Reymond J.-L. J. Am. Chem. Soc., 2009, 131, 8732-8733.