Input
10 credits
Output
Configure input settings on the left, then click "Submit job"
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 MOL2 ligand files into 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 MOL2 files for docking and molecular modeling workflows.
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
SMILES to PDB converts SMILES strings into three-dimensional PDB format files using RDKit. While SMILES encodes molecular connectivity as a text string, PDB carries explicit 3D atomic coordinates, making it suitable for molecular visualization alongside protein structures in viewers such as PyMOL, VMD, and UCSF Chimera.
ProteinIQ performs the conversion server-side, generating 3D coordinates and producing one PDB file per input compound without requiring RDKit or any local chemistry software.
| 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). Recommended for accurate geometry. |
Optimize geometry | Runs a short UFF force field minimization after coordinate generation (default: on). Improves coordinate quality for strained or flexible structures. |
Each input compound produces a separate PDB file containing 3D atomic coordinates, downloadable individually and ready to load into molecular visualization software alongside protein structures.
RDKit's AllChem.EmbedMolecule places atoms in 3D space using distance geometry. When Add hydrogens is enabled, Chem.AddHs is called first so hydrogen positions are included in the embedding. When Optimize geometry is enabled, a short Universal Force Field (UFF) minimization via AllChem.UFFOptimizeMolecule relaxes bond lengths, angles, and torsions. The resulting conformer is then written in PDB format.