mol
What is a .mol file?
chemical/x-mdl-molfile
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 a .mol 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.
Download example .mol files
- 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.
- Ethanol — MDL Molfile V2000 (.mol)Ethanol as a V2000 molfile with fixed-column 3D coordinates, a nine-atom counts line and an eight-bond block. The column widths are part of the format rather than a convention, so it is a genuine test of fixed-width parsing rather than of whitespace splitting.
- Benzene — Molfile V3000 Extended Connection Table (.mol)Benzene written in the V3000 extended format, where the legacy counts line reports zero atoms and the real counts live in an M V30 COUNTS record. A parser that trusts the old counts line reads an empty molecule and reports no error whatsoever.
- Intentionally Corrupt Molfile — Counts Line Disagrees With the Atom Block (.mol)An intentionally corrupt molfile whose counts line declares twelve atoms while the atom block contains nine, so a parser reading by count consumes three bond lines as atoms. Everything else about the file is well formed, which is what makes the failure quiet.