What is the MOL file format?
The .mol file, commonly called a Molfile, is the standard plain-text format for representing a single chemical molecule's 2D or 3D structure in cheminformatics and computational chemistry. Originally created by MDL Information Systems in 1985, it is now maintained by BIOVIA (Dassault Systèmes) as part of the CTfile Formats specification.
A Molfile consists of a three-line header (molecule name, program metadata, comment), a counts line specifying atom and bond totals plus the format version keyword (V2000 or V3000), an atom block with element symbols and coordinates, a bond block with connectivity and bond-order data, and optional property lines terminated by M END.
Two sub-versions exist: V2000 is the legacy format supporting a maximum of 999 atoms and 999 bonds with fixed-width columns - it is frozen with no further extensions planned but remains widely supported; V3000 (introduced 1995) is the current standard, supporting unlimited atom counts, enhanced stereochemistry, and Sgroup definitions.
The closely related .sdf format is simply multiple Molfiles concatenated and separated by $$$$ record delimiters, optionally with appended data fields. Major chemical databases including PubChem, ChEMBL, and the RCSB distribute structures as .mol or .sdf files. Open Babel can interconvert .mol with over 300 other chemical formats.
Security & safety
RISK: LOWMOL is a plain ASCII text file. No executable code, no macros. Safe to open with any text editor. No documented malware delivery via MOL files.
Format details
in a nutshellPrograms that open MOL files
Windows5 apps
Avogadro 2
Open-source File > Open, select the .mol file. Avogadro 2.0.0 (April 2026) supports both V2000 and V3000.
BIOVIA Discovery Studio Visualizer
Free File > Open Molecule, select the .mol file. Full 3D visualization and analysis.
Sybyl (Tripos/Certara)
Paid File > Open, select .mol file. Tripos SYBYL format support being deprecated by Certara. 
macOS1 app
Avogadro 2
Open-source File > Open, select the .mol file. Available as macOS app or via conda-forge. 
Linux2 apps
Avogadro 2
Open-source File > Open, select the .mol file. Available via conda-forge and distribution packages.
Open Babel (CLI)
Open-source obabel input.mol -O output.pdb (also converts between formats). obabel -imol file.mol -display for viewing. Technical details
deep spec| MIME type | chemical/x-mdl-molfile |
| Encoding | Plain text (ASCII) |
| File structure | 3-line header + counts line + atom block + bond block + property lines + M END terminator |
| V2000 atom/bond limit | Max 999 atoms and 999 bonds (fixed-width counts line) |
| V3000 atom/bond limit | Unlimited (variable-width extended format) |
| V2000 status | Frozen legacy - no further extensions planned; widely supported across all cheminformatics tools |
| V3000 status | Active current standard, maintained by BIOVIA / Dassault Systèmes |
| Coordinate types | 2D (x,y,z=0.0) and 3D (x,y,z real values) both supported |
| Typical file size | 1 KB - 100 KB (single molecule) |
| Multi-molecule container | SDF (.sdf) - Molfiles separated by $$$$ record delimiters with optional data fields |
| Specification | CTfile Formats PDF, freely downloadable from BIOVIA / Dassault Systèmes |
| Released | 1985 (MDL MOLGEN program, MDL Information Systems) |
| Latest version | V3000 (MDL CTfile Formats, current; V2000 is legacy frozen) |
| Open standard | Yes · royalty-free |
| Specification | discover.3ds.com |
MOL conversions
Community Q&A
asked by usersNo questions yet - be the first to ask about MOL files.
