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README.md

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+---
+license: 
+- cc-by-4.0
+license_link: https://creativecommons.org/licenses/by/4.0
+tags:
+- humo-lumo-gaps
+- energy
+- dipole-moments
+- quantum-chemistry
+- pubchem
+- small-molecules
+annotations_creators:
+- crowdsourced
+pretty_name: pubchemqc-b3lyp
+size_categories:
+- 10K<n<100M
+source_datasets:
+- pubchem
+- pubchemqc-b3lyp
+task_categories:
+- tabular-regression
+- other
+task_ids:
+- tabular-single-column-regression
+configs:
+- config_name: b3lyp_pm6
+  data_files:
+  - split: train
+    path: "data/b3lyp_pm6/train/*.json"
+  default: true
+- config_name: b3lyp_pm6_chon300nosalt
+  data_files:
+  - split: train
+    path: "data/b3lyp_pm6_chon300nosalt/train/*.json"
+- config_name: b3lyp_pm6_chon500nosalt
+  data_files:
+  - split: train
+    path: "data/b3lyp_pm6_chon500nosalt/train/*.json"
+- config_name: b3lyp_pm6_chnopsfcl300nosalt
+  data_files:
+  - split: train
+    path: "data/b3lyp_pm6_chnopsfcl300nosalt/train/*.json"
+- config_name: b3lyp_pm6_chnopsfcl500nosalt
+  data_files:
+  - split: train
+    path: "data/b3lyp_pm6_chnopsfcl500nosalt/train/*.json"
+- config_name: b3lyp_pm6_chnopsfclnakmgca500
+  data_files:
+  - split: train
+    path: "data/b3lyp_pm6_chnopsfclnakmgca500/train/*.json"
+---
+# PubChemQC-B3LYP/6-31G*//PM6 Dataset
+
+## Table of Contents
+
+- [PubChemQC-B3LYP/6-31G\*//PM6 Dataset](#pubchemqc-b3lyp6-31gpm6-dataset)
+  - [Table of Contents](#table-of-contents)
+  - [Dataset Description](#dataset-description)
+    - [Dataset Summary](#dataset-summary)
+  - [Dataset Structure](#dataset-structure)
+    - [Data Instances](#data-instances)
+    - [Data Fields](#data-fields)
+    - [Data Splits and Configurations](#data-splits-and-configurations)
+  - [Dataset Creation](#dataset-creation)
+    - [Curation Rationale](#curation-rationale)
+    - [Source Data](#source-data)
+      - [Initial Data Collection and Normalization](#initial-data-collection-and-normalization)
+    - [Personal and Sensitive Information](#personal-and-sensitive-information)
+  - [Considerations for Using the Data](#considerations-for-using-the-data)
+    - [Social Impact of Dataset](#social-impact-of-dataset)
+  - [Additional Information](#additional-information)
+    - [Dataset Curators](#dataset-curators)
+    - [Licensing Information](#licensing-information)
+    - [Citation Information](#citation-information)
+    - [Contributions](#contributions)
+
+## Dataset Description
+
+- **Homepage:** https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html
+- **Repository:** https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html
+- **Paper:** https://doi.org/10.1021/acs.jcim.3c00899
+- **Point of Contact:** [Maho Nakata]([email protected])
+- **Point of Contact:** [Mohammad Mostafanejad]([email protected])
+- **Point of Contact:** [MolSSI-AI Hub]([email protected])
+
+### Dataset Summary
+
+The presented **PubChemQC B3LYP/6-31G*//PM6** data set is composed of the electronic
+properties of 85,938,443 molecules, encompassing a broad spectrum of molecules from
+essential compounds to biomolecules with a molecular weight up to 1000. These molecules
+account for 94.0% of the original PubChem Compound catalog as of August 29, 2016.
+The electronic properties, including orbitals, orbital energies, total energies, dipole
+moments, and other pertinent properties, were computed by using the B3LYP/6-31G* and PM6
+methods.
+
+## Dataset Structure
+
+### Data Instances
+
+An example of a data instance is as follows:
+
+```json
+{'cid': 1,
+  'state': 'S0',
+  'pubchem-inchi': 'InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3',
+  'pubchem-charge': 0,
+  'pubchem-version': '20160829',
+  'name': '[email protected]',
+  'coordinates': [
+    4.543149670829423,
+   -2.8411897941733857,
+   -1.6418598810432616,
+   ...,
+   4.345629685137421
+   ],
+  'atomic-numbers': [
+   6,
+   6,
+   8,
+   ...,
+   1
+   ],
+  'atom-count': 31,
+  'heavy-atom-count': 14,
+  'core-electrons': [
+   0,
+   0,
+   0,
+   ...,
+   0
+   ],
+  'bond-order': [
+   1,
+   1,
+   1,
+   ...,
+   1
+   ],
+  'connection-indices': [
+   15,
+   1,
+   17,
+   ...,
+   30],
+  'formula': 'C9H17NO4',
+  'version': '1.0',
+  'obabel-inchi': 'InChI=1S/C9H17NO4/c1-7(11)14-8(5-9(12)13)6-10(2,3)4/h8H,5-6H2,1-4H3/t8-/m0/s1',
+  'pm6-obabel-canonical-smiles': '[O]C(=O)C[C@@H](C[N](C)(C)C)OC(=O)C',
+  'charge': 0,
+  'energy-beta-gap': 4.34837933099,
+  'energy-beta-homo': -4.60960862747,
+  'energy-beta-lumo': -0.2612292964799998,
+  'energy-alpha-gap': 4.34837933099,
+  'energy-alpha-homo': -4.60960862747,
+  'energy-alpha-lumo': -0.2612292964799998,
+  'total-energy': -19286.973573267132,
+  'homos': [54],
+  'orbital-energies': [
+    [
+      -522.303488065215,
+      -521.209590386205,
+      -518.042185166385,
+      ...,
+      127.37105114203999
+    ]
+  ],
+  'mo-count': 244,
+  'basis-count': 244,
+  'multiplicity': 1,
+  'molecular-mass': 203.23557999999983,
+  'number-of-atoms': 31,
+  'lowdin-partial-charges': [
+   -0.459759,
+   0.210106,
+   -0.286001,
+   ...,
+   0.169819
+   ],
+  'mulliken-partial-charges': [
+   -0.542286,
+   0.622923,
+   -0.486172,
+   ...,
+   0.185706
+  ],
+  'dipole-moment': 11.419443262233626,
+  'pubchem-multiplicity': 1,
+  'pubchem-obabel-canonical-smiles': '[O-]C(=O)CC(C[N+](C)(C)C)OC(=O)C',
+  'pubchem-isomeric-smiles': 'CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C',
+  'pubchem-molecular-weight': 203.23558,
+  'pubchem-molecular-formula': 'C9H17NO4'
+}
+```
+
+### Data Fields
+
+  | Field                           | Description                                                                                                                     |
+  | ------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- |
+  | cid                             | Pubchem Compound ID                                                                                                             |
+  | state                           | Electronic state                                                                                                                |
+  | pubchem-inchi                   | InChI extracted from PubChem Compound entry                                                                                     |
+  | pubchem-charge                  | Molecular charge extracted from PubChem Compound entry                                                                          |
+  | pubchem-version                 | PubChem Compound Database version                                                                                               |
+  | name                            | Name of the input file used for the B3LYP/6-31G*//PM6 calculation                                                               |
+  | coordinates                     | Cartesian coordinates of the molecular geometry optimized with PM6 method in Angstroem                                          |
+  | atomic-numbers                  | An array of atomic numbers                                                                                                      |
+  | atom-count                      | Number of atoms in the molecule                                                                                                 |
+  | heavy-atom-count                | Number of heavy atoms in the molecule                                                                                           |
+  | core-electrons                  | The number of core electrons in each atom's pseudopotentials                                                                    |
+  | bond-order                      | Bond order                                                                                                                      |
+  | connection-indices              | Connection indices between atoms                                                                                                |
+  | formula                         | Chemical formula                                                                                                                |
+  | version                         | Version number                                                                                                                  |
+  | obabel-inchi                    | InChI of the structure generated by Open Babel                                                                                  |
+  | pm6-obabel-canonical-smiles     | Canonical SMILES for the structure generated by Open Babel                                                                      |
+  | charge                          | Molecular charge                                                                                                                |
+  | energy-beta-gap                 | HOMO-LUMO energy gap for beta spin orbitals                                                                                     |
+  | energy-beta-homo                | Energy of the highest-occupied molecular orbital (HOMO) of beta spin symmetry                                                   |
+  | energy-beta-lumo                | Energy of the lowest-unoccupied molecular orbital (LUMO) of beta spin symmetry                                                  |
+  | energy-alpha-gap                | HOMO-LUMO energy gap for alpha spin orbitals                                                                                    |
+  | energy-alpha-homo               | Energy of the highest-occupied molecular orbital (HOMO) of alpha spin symmetry                                                  |
+  | energy-alpha-lumo               | Energy of the lowest-unoccupied molecular orbital (LUMO) of alpha spin symmetry                                                 |
+  | total-energy                    | Total electronic energy of the molecule calculated at the B3LYP/6-31G* level of theory                                          |
+  | homos                           | 1D index array of the highest occupied molecular orbital (HOMOs) with one (two) element(s) for the (un)restricted wavefunctions |
+  | orbital-energies                | 1D array of orbital energies in hartree with one (two) member(s) for the (un)restricted wavefunction                            |
+  | mo-count                        | Number of molecular orbitals                                                                                                    |
+  | basis-count                     | Number of basis functions                                                                                                       |
+  | multiplicity                    | Spin multiplicity                                                                                                               |
+  | molecular-mass                  | Molecular mass                                                                                                                  |
+  | number-of-atoms                 | Number of atoms in the molecule                                                                                                 |
+  | lowdin-partial-charges          | Lowdin partial atomic charges                                                                                                   |
+  | mulliken-partial-charges        | Mulliken partial atomic charges                                                                                                 |
+  | dipole-moment                   | Dipole moment                                                                                                                   |
+  | pubchem-multiplicity            | Spin multiplicity of the molecule extracted from PubChem Compound                                                               |
+  | pubchem-obabel-canonical-smiles | Canonical SMILES of the molecule extracted from PubChem Compound generated by Open Babel                                        |
+  | pubchem-isomeric-smiles         | Isomeric SMILES of the molecule extracted from PubChem Compound calculated by the OpenEye's OEChem Toolkit                      |
+  | pubchem-molecular-weight        | Molecular weight extracted from the PubChem Compound entry                                                                      |
+  | pubchem-molecular-formula       | Molecular formula extracted from the PubChem Compound entry                                                                     |
+
+### Data Splits and Configurations
+
+The dataset has only one ``train`` split. The PubChemQC B3LYP/6-31G*//PM6 dataset
+has six configurations/subsets:
+- ``b3lyp_pm6`` (default)
+- ``b3lyp_pm6_chon300nosalt``
+- ``b3lyp_pm6_chon500nosalt``
+- ``b3lyp_pm6_chnopsfcl300nosalt``
+- ``b3lyp_pm6_chnopsfcl500nosalt``
+- ``b3lyp_pm6_chnopsfclnakmgca500``
+
+## Dataset Creation
+
+### Curation Rationale
+
+The present version of PubChemQC B3LYP/6-31G*//PM6 dataset has been extracted
+from its original Postgresql database, transformed into a dictionary and
+stored in the ``.json`` format.
+
+### Source Data
+
+The link to the original PubChemQC B3LYP/6-31G*//PM6 dataset repository can be
+found [here](https://nakatamaho.riken.jp/pubchemqc.riken.jp/b3lyp_pm6_datasets.html)
+
+#### Initial Data Collection and Normalization
+
+Other than the changes detailed in Sec. [Curation Rationale](#curation-rationale),
+no data modification has been performed on the PubChemQC B3LYP/6-31G*//PM6 dataset.
+
+### Personal and Sensitive Information
+
+The PubChemQC B3LYP/6-31G*//PM6 dataset does not involve any personal or sensitive information.
+
+## Considerations for Using the Data
+
+### Social Impact of Dataset
+
+The PubChemQC B3LYP/6-31G*//PM6 dataset paves the way for applications in drug discovery and materials science, among others.
+
+## Additional Information
+
+### Dataset Curators
+
+- **Maho Nakata**, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
+- **Toshiyuki Maeda**, Software Technology and Artificial Intelligence Research Laboratory, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan
+
+### Licensing Information
+
+[Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0)
+
+### Citation Information
+
+```tex
+@article{Nakata:2023:5734,
+   author = {Maho Nakata and Toshiyuki Maeda},
+   doi = {10.1021/ACS.JCIM.3C00899},
+   issn = {1549960X},
+   issue = {18},
+   journal = {Journal of Chemical Information and Modeling},
+   pages = {5734-5754},
+   publisher = {American Chemical Society},
+   title = {{PubChemQC B3LYP/6-31G*//PM6 Data Set: The Electronic Structures of 86 Million Molecules 
+   Using B3LYP/6-31G* Calculations}},
+   volume = {63},
+   url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.3c00899},
+   year = {2023},
+}
+```
+
+### Contributions
+
+- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)