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.
benzene
NovusEx 3D synthetic idealised geometry
V3000 extended connection table.
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 12 12 0 0 0
M V30 BEGIN ATOM
M V30 1 C 1.3970 0.0000 0.0000 0
M V30 2 C 0.6985 1.2098 0.0000 0
M V30 3 C -0.6985 1.2098 0.0000 0
M V30 4 C -1.3970 0.0000 0.0000 0
M V30 5 C -0.6985 -1.2098 0.0000 0
M V30 6 C 0.6985 -1.2098 0.0000 0
M V30 7 H 2.4810 0.0000 0.0000 0
M V30 8 H 1.2405 2.1486 0.0000 0
M V30 9 H -1.2405 2.1486 0.0000 0
M V30 10 H -2.4810 0.0000 0.0000 0
M V30 11 H -1.2405 -2.1486 0.0000 0
M V30 12 H 1.2405 -2.1486 0.0000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 4 1 2
M V30 2 4 2 3
M V30 3 4 3 4
M V30 4 4 4 5
M V30 5 4 5 6
M V30 6 4 6 1
M V30 7 1 1 7
M V30 8 1 2 8
M V30 9 1 3 9
M V30 10 1 4 10
M V30 11 1 5 11
M V30 12 1 6 12
M V30 END BOND
M V30 END CTAB
M END
Specifications
- Format
- MDL Molfile V3000
- Atoms
- 12
- Bonds
- 12
- Aromatic Bond Type
- 4
- Counts Line Atoms
- 0
- Trap
- the V2000 counts line reads 0 atoms — the real counts are in the V30 block
- Idealised Geometry
- true
Testing contract
Expected to pass- Scenario
- Detect the V3000 marker on the counts line and parse the M V30 blocks instead of the fixed-column V2000 blocks.
- Expected result
- You read 12 atoms and 12 bonds with the six ring bonds typed as 4 (aromatic); a V2000-only parser reports zero atoms because the legacy counts line says 0.
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
“Benzene — Molfile V3000 Extended Connection Table (.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 V3000. 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.
Scientific fixtures are small, valid, and fully synthetic — no real organism, patient, sample, or observation. Point your parser or loader at the file and check it reads the documented records, variables, or headers; binary formats ship a readable twin or metadata listing for comparison.
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