MOL2 to SMILES Converter
In short: Convert MOL2 text to SMILES using a best-effort public resolver workflow. It is free, works in your web browser and needs no download.
Convert MOL2 content to SMILES. Best for smaller ligand MOL2 blocks.
Input and output formats
| Input: MOL2 | Output: SMILES | |
|---|---|---|
| Full name | MOL2 (Tripos Mol2) | SMILES (Simplified Molecular Input Line Entry System) |
| What it holds | 3D coordinates, bonds, atom types and partial charges. | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. |
| File or form | .mol2 | .smi or plain text |
File Format Explained
MOL2 is a Tripos structure format used in docking and modeling. It can include atom coordinates, atom types, substructure records, bonds, and charge values.
SMILES is a one-line molecular identifier focused on connectivity. Converting MOL2 to SMILES is useful when you need a searchable string for a ligand from a modeling workflow.
MOL2 files can contain atom-type and charge information that SMILES will not preserve. Check stereochemistry and protonation after conversion.
About MOL2 files
The Tripos MOL2 format is common in molecular modelling and docking. Unlike a MOL file, it stores SYBYL atom types (such as C.ar for aromatic carbon or N.am for amide nitrogen), partial charges, and substructure information in sections that start with tags like @<TRIPOS>MOLECULE, @<TRIPOS>ATOM, and @<TRIPOS>BOND. Docking programs and ligand libraries often supply molecules in MOL2.
Why convert to SMILES
SMILES is far easier to read, store, and search. Converting a docked ligand or library entry to SMILES lets you check its identity, paste it into a spreadsheet, or redraw it for a figure.
How to use it
- Open the .mol2 file in a text editor and copy one molecule, from
@<TRIPOS>MOLECULEthrough the bond section. - Paste and convert.
- Check the SMILES by drawing it with SMILES to Structure.
Watch out: files prepared for docking often include explicit hydrogens and a specific protonation state, so the SMILES may show charged groups such as a protonated amine.
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