Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert Protein Data Bank files to Structure Data Format
Convert Structure Data Format files to Protein Data Bank format
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Convert InChI strings into SMILES with batch support and downloadable outputs.
Convert MDL MOL ligand files into canonical SMILES strings for registration, filtering, and downstream analysis.
Convert SDF ligand files, including multi-record batches, into SMILES strings.
Convert SMILES strings into InChI strings with batch support and downloadable outputs.
Convert SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
Convert single SMILES strings or small batches into 3D SDF files with downloadable per-entry files and a combined batch output.
Run Open Babel in the browser to convert chemical and structure files, with coordinate, hydrogen, and pH options where the WASM runtime supports them.
Convert Protein Data Bank files to Structure Data Format
Convert Structure Data Format files to Protein Data Bank format
Configure inputs to begin
Set options on the left, then click “Submit job”.
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.
ProteinIQ generates 3D MOL2 structures server-side, accepting SMILES strings directly from the browser with no RDKit installation needed.
| 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 |
| 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. |
Each input compound produces a separate .mol2 file, downloadable individually and ready to use as ligand input in docking software.
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.