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C16H17N
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C16H17N
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A17B16C
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data/MD/3195/MD_1065765008166216957433195.json
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data/MD/5202/MD_1086845055867124744315202.json
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PO_1000866583077510975519600
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DS_ctjgc03xdauc_0
| 1
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ORCA 4.0.1
| null | -7,863.695284
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CO_9528207182577771436888640
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C4H11NO
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C4H11NO
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A11B4CD
|
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data/MD/3195/MD_1065765008166216957433195.json
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data/MD/5202/MD_1086845055867124744315202.json
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PO_1000823566977779075044466
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DS_ctjgc03xdauc_0
| 1
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ORCA 4.0.1
| null | -15,624.430333
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C3H12NS
|
C3H12NS
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A12B3CD
|
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[
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A14B3C3D2
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data/MD/3195/MD_1065765008166216957433195.json
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data/MD/3195/MD_1065765008166216957433195.json
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End of preview. Expand
in Data Studio
Cite this dataset
Unke, O. T., and Meuwly, M. solvated protein fragments JCTC 2019. ColabFit, 2023. https://doi.org/10.60732/c4731f07
Cite this dataset
Unke, O. T., and Meuwly, M. solvated protein fragments JCTC 2019. ColabFit, 2023. https://doi.org/10.60732/c4731f07This dataset has been curated and formatted for the ColabFit Exchange
This dataset is also available on the ColabFit Exchange:
https://materials.colabfit.org/id/DS_ctjgc03xdauc_0
Visit the ColabFit Exchange to search additional datasets by author, description, element content and more.
https://materials.colabfit.org
Dataset Name
solvated protein fragments JCTC 2019
Description
The solvated protein fragments dataset was generated as a partner benchmark dataset, along with SN2, for measuring the performance of machine learning models, in particular PhysNet, at describing chemical reactions, long-range interactions, and condensed phase systems. The dataset contains structures for all possible "amons" (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur in different charge states due to (de)protonation (i.e., carboxylic acids that can be negatively charged or amines that can be positively charged), all possible structures with up to a total charge of +-2e are included. In total, the dataset provides reference energies, forces, and dipole moments for 2,731,180 structures calculated at the revPBE-D3(BJ)/def2-TZVP level of theory using ORCA 4.0.1.
Dataset authors
Oliver T. Unke, Markus Meuwly
Publication
https://doi.org/10.1021/acs.jctc.9b00181
Original data link
https://doi.org/10.5281/zenodo.2605372
License
CC-BY-4.0
Number of unique molecular configurations
2730942
Number of atoms
58390211
Elements included
C, H, N, O, S
Properties included
energy, atomic forces
Usage
ds.parquet: Aggregated dataset information.co/directory: Configuration rows each include a structure, calculated properties, and metadata.cs/directory : Configuration sets are subsets of configurations grouped by some common characteristic. Ifcs/does not exist, no configurations sets have been defined for this dataset.cs_co_map/directory : The mapping of configurations to configuration sets (if defined).
ColabFit Exchange documentation includes descriptions of content and example code for parsing parquet files:
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