---
license:
  - cc-by-4.0
license_link: https://creativecommons.org/licenses/by/4.0
tags:
  - homo-lumo-gaps
  - energy
  - dipole-moments
  - quantum-chemistry
  - pubchem
  - small-molecules
  - ir-frequencies
  - ir-intensities
annotations_creators:
  - crowdsourced
pretty_name: pubchemqc-pm6
size_categories:
  - 10K<n<300M
source_datasets:
  - pubchem
  - pubchemqc-pm6
task_categories:
  - tabular-regression
  - other
task_ids:
  - tabular-single-column-regression
viewer: false
configs:
  - config_name: pm6opt
    data_files:
      - split: train
        path: "data/pm6opt/train/*.json"
    default: true
  - config_name: pm6opt_chon300nosalt
    data_files:
      - split: train
        path: "data/pm6opt_chon300nosalt/train/*.json"
  - config_name: pm6opt_chon500nosalt
    data_files:
      - split: train
        path: "data/pm6opt_chon500nosalt/train/*.json"
  - config_name: pm6opt_chnops500nosalt
    data_files:
      - split: train
        path: "data/pm6opt_chnops500nosalt/train/*.json"
  - config_name: pm6opt_chnopsfcl300nosalt
    data_files:
      - split: train
        path: "data/pm6opt_chnopsfcl300nosalt/train/*.json"
  - config_name: pm6opt_chnopsfcl500nosalt
    data_files:
      - split: train
        path: "data/pm6opt_chnopsfcl500nosalt/train/*.json"
  - config_name: pm6opt_chnopsfclnakmgca500
    data_files:
      - split: train
        path: "data/pm6opt_chnopsfclnakmgca500/train/*.json"
---

# PubChemQC PM6 Dataset

## Table of Contents

- [PubChemQC PM6 Dataset](#pubchemqc-pm6-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)
  - [How to Use the Dataset](#how-to-use-the-dataset)
    - [Prerequisites](#prerequisites)
    - [Accessing the Data](#accessing-the-data)
  - [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/pm6_datasets.html
- **Repository:** https://nakatamaho.riken.jp/pubchemqc.riken.jp/pm6_datasets.html
- **Paper:** https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740
- **Point of Contact:** [Maho Nakata](maho@riken.jp)
- **Point of Contact:** [Mohammad Mostafanejad](smostafanejad@vt.edu)
- **Point of Contact:** [MolSSI-AI Hub](hub@molssi.org)

### Dataset Summary

The **PubChemQC PM6** dataset consists of optimized molecular geometries
and electronic properties calculated by the PM6 method for 94.0% of the 91.6 million
molecules cataloged in PubChem Compounds retrieved on August 29, 2016. In addition to
neutral states, the cationic, anionic, and spin flipped electronic states of respectively
56.2%, 49.7%, and 41.3% of the molecules have also been studied. As such, the grand total
of the PM6 calculations amounted to 221 million.

## 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": "000000001.PM6.S0",
  "coordinates": [4.543146, -2.8411939999999998, -1.641861, ..., 4.345637],
  "atomic-numbers": [6, 6, 8, ..., 1],
  "atom-count": 31,
  "heavy-atom-count": 14,
  "core-electrons": [0, 0, 0,..., 0],
  "version": "2.0",
  "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": 8.458931156643,
  "energy-beta-homo": -8.8325434733795,
  "energy-beta-lumo": -0.37361231673649903,
  "energy-alpha-gap": 8.458931156643,
  "energy-alpha-homo": -8.8325434733795,
  "energy-alpha-lumo": -0.37361231673649903,
  "total-energy": -7.558832783207512,
  "enthalpy": -0.021744,
  "homos": [40],
  "orbital-energies": [
    [-34.149199782348006,
     -32.51760513475,
     -30.809274381311,
     ...,
     6.947610830966
    ]
  ],
  "mo-count": 73,
  "basis-count": 73,
  "temperature": 298.15,
  "multiplicity": 1,
  "number-of-atoms": 31,
  "mulliken-partial-charges": [-0.5888869999999999,
  0.6862539999999999,
  -0.580137,
  ...,
  0.18249
  ],
  "dipole-moment": 13.22226250268841,
  "frequencies": [26.1465, 37.9831, 50.1099, ..., 2779.2147],
  "intensities": [0.771, 11.6909, 2.5082, ..., 111.8945],
  "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 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                                                                    |
| 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 using PM6 method                                                             |
| enthalpy                        | Enthalpy                                                                                                                        |
| 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                                                                                                       |
| temperature                     | Temperature (in K)                                                                                                              |
| multiplicity                    | Spin multiplicity                                                                                                               |
| number-of-atoms                 | Number of atoms in the molecule                                                                                                 |
| mulliken-partial-charges        | Mulliken partial atomic charges                                                                                                 |
| dipole-moment                   | Dipole moment                                                                                                                   |
| frequencies                     | Infrared (IR) frequencies (in cm$^{-1}$)                                                                                        |
| intensities                     | Infrared intensities                                                                                                            |
| 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 PM6 dataset
has seven configurations/subsets:

- `pm6opt` (default)
- `pm6opt_chon300nosalt`
- `pm6opt_chon500nosalt`
- `pm6opt_chnops500nosalt`
- `pm6opt_chnopsfcl300nosalt`
- `pm6opt_chnopsfcl500nosalt`
- `pm6opt_chnopsfclnakmgca500`

## How to Use the Dataset

### Prerequisites

We recommend isolating your work in a virtualenv or conda environment.
You can create a new conda environment, `pubchemqc`,

```bash
  conda create -n pubchemqc python=3.12
```

and activate it using the following command

```bash
  conda activate pubchemqc
```

Once the conda environment is activated, you can
install the dependencies in it as shown below

```bash
  pip install huggingface_hub ijson
```

### Accessing the Data

Once the required packages are installed, you can run the following code
to access the data

```python
  # import the modules
  from datasets import load_dataset

  # load the dataset with streaming
  hub_ds = load_dataset(path="molssiai-hub/pubchemqc-pm6",
                        name="pm6opt",
                        split="train",
                        streaming=True,
                        cache_dir="./tmp",
                        trust_remote_code=True)

  # fetch a batch of 32 samples from the dataset
  ds = list(hub_ds.take(32))
```

The argument `name` by default is set to `pm6opt` which refers to
the entire dataset. Other configurations (subsets), listed in
Sec. [Data Splits and Configurations](#data-splits-and-configurations),
can also be selected.

The `split` must be set to `train` as it is the only split in our dataset.
We recommend using `streaming=True` to avoid downloading the entire dataset
on disk. The `cache_dir` allows us to store the Hugging Face datasets' and
models' artifacts in a non-default directory (by default, it is set to
`~/.cache/huggingface`). As we are using a custom
[load script](https://huggingface.co/datasets/molssiai-hub/pubchemqc-pm6/blob/main/pubchemqc-pm6.py), the `trust_remote_code` argument should also be set to `True`.

## Dataset Creation

### Curation Rationale

The present version of PubChemQC 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 PM6 dataset repository can be
found [here](https://nakatamaho.riken.jp/pubchemqc.riken.jp/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 PM6 dataset.

### Personal and Sensitive Information

The PubChemQC PM6 dataset does not involve any personal or sensitive information.

## Considerations for Using the Data

### Social Impact of Dataset

The PubChemQC 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
- **Tomomi Shimazaki**, Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, JAPAN
- **Masatomo Hashimoto**, Software Technology and Artificial Intelligence Research Laboratory, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, 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:2020:5891,
   author = {Maho Nakata and Tomomi Shimazaki and Masatomo Hashimoto and Toshiyuki Maeda},
   doi = {10.1021/acs.jcim.0c00740},
   issn = {1549960X},
   issue = {12},
   journal = {Journal of Chemical Information and Modeling},W
   month = {12},
   pages = {5891-5899},
   pmid = {33104339},
   publisher = {American Chemical Society},
   title = {PubChemQC PM6: Data Sets of 221 Million Molecules with Optimized Molecular Geometries and Electronic Properties},
   volume = {60},
   url = {https://pubs.acs.org/doi/abs/10.1021/acs.jcim.0c00740},
   year = {2020},
}
```

### Contributions

- **Mohammad Mostafanejad**, The Molecular Sciences Software Institute (MolSSI)