Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules.
Journal
Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192
Informations de publication
Date de publication:
07 Jul 2024
07 Jul 2024
Historique:
received:
18
03
2024
accepted:
13
06
2024
medline:
8
7
2024
pubmed:
8
7
2024
entrez:
7
7
2024
Statut:
epublish
Résumé
We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean: 50.9), and containing up to 54 (mean: 28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global and local physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and de novo generation of large (solvated) molecules with pharmaceutical and biological relevance.
Identifiants
pubmed: 38972891
doi: 10.1038/s41597-024-03521-8
pii: 10.1038/s41597-024-03521-8
doi:
Substances chimiques
Solvents
0
Pharmaceutical Preparations
0
Water
059QF0KO0R
Types de publication
Journal Article
Dataset
Langues
eng
Sous-ensembles de citation
IM
Pagination
742Subventions
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 956832
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 956832
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Organisme : Janssen Pharmaceuticals (Janssen Pharmaceuticals, Inc.)
ID : Aquamarine
Informations de copyright
© 2024. The Author(s).
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