What is a .MOL2 file?
MOL2 is Tripos's molecule format, and unlike a Molfile it records the atom TYPE rather than just the element - "C.ar" for aromatic carbon, "N.4" for a quaternary nitrogen - which is the information a force field needs.
- Did you know
- The format comes from SYBYL, and its atom typing is why MOL2 is still the usual currency of molecular docking software.
- MOL2 organises a molecule into labelled record blocks such as @<TRIPOS>ATOM and @<TRIPOS>BOND, which is how parsers locate each section.
- Its atom types encode chemical detail like hybridisation and aromaticity, making MOL2 a richer description than a bare list of coordinates.
- What Analyser reads
- Open chemical structures and see the molecule: MOL and SDF connection tables, MOL2, plain XYZ coordinates, Protein Data Bank entries and mmCIF/CIF crystallographic files, all drawn in an interactive 3D viewer you can rotate, zoom and restyle. Small molecules come up as ball-and-stick with the standard element colours; proteins and nucleic acids get a cartoon instead, drawing each chain as a ribbon along its backbone with helices and sheets picked out and any bound ligand still shown as sticks - which is the only way a structure of tens of thousands of atoms is readable at all. Alongside the picture, the composition is worked out from the atoms actually present rather than from any label in the file: molecular formula in Hill notation, molecular weight, net charge, element counts, and for a macromolecule the chain, residue and secondary-structure counts plus every non-polymer group - bound drugs, cofactors, metal ions and crystallisation buffer. PDB headers give up the entry ID, title, experimental method and resolution; an SDF is stepped through record by record with each molecule's tagged data fields read out.
- Depth of analysis
- .MOL2 is an identification-grade format: Analyser recognises it from its bytes and decodes the header metadata it carries, rather than opening it in a full viewer. Formats that do get a full viewer are marked "Full" on the formats page.
- Open a .MOL2 file
- Drag a .MOL2 file onto the Analyser home page (or tap to pick one). It is identified entirely in your browser - nothing is uploaded, there is no account, and it works offline once installed.