Novus Convert
Convert files
Data format

MOL converter

A .mol file is an MDL Molfile: a chemical structure written as a connection table — a counts line, then one fixed-width line per atom giving its coordinates and element, then one line per bond giving the two atoms it joins and its order. It describes a molecule's topology, not its appearance.

Private for supported formats — processed in your browser

Convert supported files

Runs on your device

Drop MOL files here

Batch files can each use a different output. Nothing uploads for local conversions.

Working inputs include camera RAW, browser-local audio/video, PDF, CBZ/CBR comics, office documents, ebooks, markup, 3D models, structured text, images, and archives.

Where MOL comes from

Molecular Design Limited created the format in the 1980s, and it became the lingua franca of cheminformatics through ISIS/Draw and the CTfile family. The V2000 variant is still overwhelmingly the most common, despite its hard limit of 999 atoms and 999 bonds; V3000 was introduced to lift those limits and remains comparatively rare. Symyx and then BIOVIA inherited the specification, and it has outlived all of them.

How MOL works

  • The first three lines are a title, a program/timestamp line and a comment, before any structural data.
  • The counts line declares atom and bond counts and the version marker, conventionally V2000.
  • Atom lines are fixed width: three ten-character coordinates followed by a left-justified element symbol.
  • Bond lines give two one-based atom indices and a bond order, where 4 means aromatic.
  • V2000 cannot exceed 999 atoms or 999 bonds — a hard limit that V3000 exists to remove.
  • M END terminates the connection table; property lines may precede it.

When to use MOL

  • Exchanging a single molecular structure between chemistry applications
  • Depositing or retrieving structures from chemical databases
  • Converting a structure into coordinates or a rendered diagram
  • Inspecting connectivity and stereochemistry as plain text

Strengths and limitations

Strengths

  • The universal interchange format in cheminformatics
  • Fixed-width layout makes it parseable without a library
  • Carries explicit connectivity and stereochemistry rather than inferring them

Limitations

  • V2000's 999-atom limit rules out proteins and large systems
  • Fixed-width columns are unforgiving — a one-character shift silently changes meaning
  • Multiple structures require the SDF container, not the molfile itself

Compatibility

Read by RDKit, Open Babel, ChemDraw, PubChem, Avogadro and effectively all chemistry software. Novus Convert parses the connection table locally and converts to XYZ coordinates, JSON and an SVG depiction.

Atom coordinates, element symbols, bond orders and the title line are preserved. Property blocks after the connection table are not carried into every target.

Convert MOL to another format