SMILES to MOL2 Converter
In short: Convert SMILES strings into MOL2 format for docking and med-chem workflows. It is free, works in your web browser and needs no download.
Convert SMILES strings to MOL2 format for docking and pipeline compatibility.
Input and output formats
| Input: SMILES | Output: MOL2 | |
|---|---|---|
| Full name | SMILES (Simplified Molecular Input Line Entry System) | MOL2 (Tripos Mol2) |
| What it holds | Atoms, bonds, rings, charges and stereo as one line of text. No coordinates. | 3D coordinates, bonds, atom types and partial charges. |
| File or form | .smi or plain text | .mol2 |
File Format Explained
SMILES stores molecule connectivity in a short line of text. It is useful for identifiers, but it does not carry Tripos atom typing or molecule sections.
MOL2 is the Tripos Mol2 format. It can store atoms, bonds, substructures, atom types, coordinates, and charges, which makes it useful in docking, molecular modeling, and medicinal chemistry workflows.
Use MOL2 when a docking or modeling tool expects Tripos atom types or charge fields. Validate protonation, charges, and generated coordinates before production docking.
When you need MOL2
MOL2 is a common input format for docking, virtual screening, and molecular mechanics. Besides coordinates, it stores SYBYL atom types and partial charges, which many modelling programs rely on. Converting a SMILES string to MOL2 is a quick way to prepare a ligand when you only have its structure as text.
How to use it
- Paste the SMILES of your ligand, for example ibuprofen
CC(C)CC1=CC=C(C=C1)C(C)C(=O)O. - Convert and download the .mol2 file.
- Open it in your modelling or docking software.
Before docking
- Protonation: decide what charge state is relevant at your target pH. A carboxylic acid such as ibuprofen is mostly deprotonated at pH 7.4.
- Stereochemistry: specify @ or @@ in the SMILES for chiral centres; otherwise the generated geometry may pick one arbitrarily.
- Geometry: generated 3D coordinates are a starting conformer; energy minimisation in your modelling package is usually recommended.
For docking programs that need PDBQT, see SMILES to PDBQT. To go back, use MOL2 to SMILES.
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