DOI: 10.5281/zenodo.15429129
title: modelforge curated dataset: SPICE 2

description: Modelforge Curated SPICE 2 Dataset:- 1000 configuration test set, limited to elements [H, C, N, O, F, Cl, S]- Version: nc_1000_HCNOFClS_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 374 unique records for 1000 total configurations, with a maximum of 10 configurations per record. The dataset is limited to the elements that are compatible with the ANI2x NNP architecture, namely:  [H, C, N, O, F, Cl, S].

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