MDL Molfile — Water (.mol)
An MDL Molfile (V2000) of a water molecule with standard geometry — a counts line, atom block with 2D coordinates, and bond block — for testing cheminformatics parsers and MOL/SDF converters.
Water
Novus 2D
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7570 0.5860 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7570 0.5860 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 3 1 0
M END
Specifications
- Format
- MDL Molfile V2000
- Molecule
- H2O (water)
- Atoms
- 3
- Bonds
- 2
What is a .mol file?
An MDL Molfile (.mol) is a plain-text chemical structure format describing a single molecule: a counts line, an atom block with element symbols and 2D or 3D coordinates, and a bond block listing connections and orders. It is a core part of the SDF format and is read by nearly every cheminformatics tool.
How to use this file
Use an example .mol file to test molecule parsers and viewers (RDKit, Open Babel, Jmol), structure-format converters (MOL to SMILES, SDF, or PDB), and cheminformatics pipelines.
How to use this file for testing
“MDL Molfile — Water (.mol)” is a deterministic Novus Examples fixture for Scientific data, Editor testing. Citation catalogs (BibTeX, RIS), chemistry structures (MDL Molfile, PDB), and gridded binary data (NetCDF, FITS) — for testing reference managers, molecule viewers, and scientific-data loaders.
Documented properties for this file: MDL Molfile V2000. Compare results against paired or grouped companions on this page when present (clean↔damaged, searchable↔scanned, or format twins) so scores stay reproducible across runs.
Download the file once, keep the path stable in CI or local scripts, and treat the spec table as the contract: dimensions, seeds, field lists, and roles are intentional. Corrupt or invalid samples are labelled as such — expect parsers to fail loudly rather than silently accept them.
Data fixtures document their exact quirks — delimiters, encodings, null handling, schema, and row counts — in the spec table. Point your parser or importer at the file and assert it handles the documented edge cases; clean and deliberately-messy siblings make before/after diffs straightforward.
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