DOI: 10.5281/zenodo.11632269
title: modelforge curated dataset: SPICE 2

description: Modelforge Curated SPICE 2 Dataset:- Full dataset limited to elements [H, C, N, O, F]- Version: full_dataset_HCNOF_v1.1

This provides a curated hdf5 file for a subset of the SPICE 2 dataset (release v2.0.1) designed to be compatible with modelforge, an infrastructure to implement and train NNPs. This dataset contains 57037 unique records for 928073 total configurations. The dataset is limited to the elements ['H', 'C', 'N', 'O', 'F'].

When applicable, the units of properties are provided in the datafile,  encoded as strings compatible with the openff-units package. 

This is compatible with modelforge hdf5 schema 2.

For more information about the structure of the data file, please see the following:



https://github.com/choderalab/modelforge/wiki/Dataset-and-curation#curation-module


Source Dataset:

Small-molecule/Protein Interaction Chemical Energies (SPICE).

The SPICE 2 dataset contains roughly 2 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 17 elements, charged and  uncharged molecules, and a wide range of covalent and non-covalent interactions.  SPICE 2 is an update to spice 1, roughly double the total dataset size and including 2 additional elements.  It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, using Psi4 1.4.1 along with other useful quantities such as multipole moments and bond orders.



 


Properties Included:



atomic_numbers 

positions      



"per_atom"

"nanometer"



dft_total_force



"per_atom"

"kilojoule_per_mole / nanometer"



mbis_charges   



"per_atom"

"elementary_charge"



mbis_dipoles   



"per_atom"

"elementary_charge * nanometer"



mbis_quadrupoles       



"per_atom"

"elementary_charge * nanometer ** 2"



mbis_octupoles 



"per_atom"

"elementary_charge * nanometer ** 3"



mayer_indices  



"per_atom"

"dimensionless"



wiberg_lowdin_indices  



"per_atom"

"dimensionless"



total_charge   



"per_system"

"elementary_charge"



dft_total_energy       



"per_system"

"kilojoule_per_mole"



formation_energy       



"per_system"

"kilojoule_per_mole"



scf_dipole     



"per_system"

"elementary_charge * nanometer"



scf_quadrupole 



"per_system""elementary_charge * nanometer ** 2"



smiles 



"meta_data"




 

Citations:



Spice 2 publication:





Eastman, P., Pritchard, B. P., Chodera, J. D., & Markland, T. E. Nutmeg and SPICE: models and data for biomolecular machine learning. Journal of chemical theory and computation, 20(19), 8583-8593 (2024). https://doi.org/10.1021/acs.jctc.4c00794




Original SPICE 1 publication:



Eastman, P., Behara, P.K., Dotson, D.L. et al. SPICE,  A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials. Sci Data 10, 11 (2023). https://doi.org/10.1038/s41597-022-01882-6


Source dataset, released with CCO 1.0 Universal license:













Eastman, P., Behara, P. K., Dotson, D., Galvelis, R., Herr, J., Horton, J., Mao, Y., Chodera, J., Pritchard, B., Wang, Y., De Fabritiis, G., & Markland, T. (2024). SPICE 2.0.1 (2.0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10975225