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What is SMILES to MOL2?
SMILES to MOL2 converts SMILES strings into three-dimensional MOL2 (Tripos MOL2) files using RDKit. MOL2 is the standard ligand format for many molecular docking programs — AutoDock, DOCK6, GOLD, and Glide all accept it. While SMILES encodes only 2D connectivity, MOL2 carries Tripos atom types, partial charges, and 3D coordinates required by these tools.
How to use SMILES to MOL2 online
ProteinIQ generates 3D MOL2 structures server-side, accepting SMILES strings directly from the browser with no RDKit installation needed.
Input
| Input type | Format details |
|---|---|
| SMILES strings | One SMILES per line, or name<TAB>SMILES pairs for named compounds |
| File upload | .txt, .csv, .tsv, .smi, .smiles files |
| PubChem fetch | Compound names or CIDs fetched in batch from PubChem |
| Batch limit | Up to 10 entries per job |
Settings
| Setting | Description |
|---|---|
Add hydrogens | Adds explicit hydrogens before 3D embedding (default: on). Required for accurate geometry and most docking pipelines. |
Optimize geometry | Runs a short UFF force field minimization after embedding (default: on). Improves coordinate quality for strained or flexible structures. |
Output
Each input compound produces a separate .mol2 file, downloadable individually and ready to use as ligand input in docking software.
How it works
RDKit's AllChem.EmbedMolecule generates 3D coordinates using distance geometry. When Add hydrogens is on, Chem.AddHs is called first so hydrogen positions are included. When Optimize geometry is on, Universal Force Field (UFF) minimization via AllChem.UFFOptimizeMolecule refines bond lengths, angles, and torsions. The structure is then written in Tripos MOL2 format.
Limitations
- A single conformer is generated per molecule. For ensemble docking or conformer sampling, generate multiple conformers separately.
- Very large or highly flexible macrocycles can fail distance geometry embedding.
- Tautomer and protonation state are taken as given from the input SMILES. Adjust ionization state before conversion if target pH matters.