Generate 3D SDF files from SMILES strings with batch conversion and downloadable combined outputs. Learn more
Generate 3D SDF files from SMILES strings with batch conversion and downloadable combined outputs. Learn more
Generate 3D SDF files from SMILES strings with batch conversion and downloadable combined outputs. Learn more
Convert SDF ligand files, including multi-record batches, into SMILES strings.
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 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 SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
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 SDF ligand files, including multi-record batches, into SMILES strings.
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 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 SMILES strings into 3D PDB files for molecular visualization and downstream docking preparation.
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 SDF converts SMILES strings into three-dimensional SDF (Structure Data File) format using RDKit. SDF is the standard input format for most docking and cheminformatics workflows — while SMILES encodes connectivity, SDF carries 3D atomic coordinates that downstream tools require.
ProteinIQ runs the conversion server-side, generating 3D coordinates without requiring RDKit or any other software to be installed locally.
Paste one SMILES per line into the text area, or use name–SMILES pairs separated by a tab (name<TAB>SMILES). Free workspaces can convert up to 3 entries per job; paid plans support larger batches. Alternatively, upload .txt, .csv, .tsv, .smi, or .smiles files, or fetch compounds directly from PubChem by name or CID.
| Format | Example |
|---|---|
| Bare SMILES | CC(=O)Oc1ccccc1C(=O)O |
| Named SMILES | aspirin\tCC(=O)Oc1ccccc1C(=O)O |
| File upload | .smi, .smiles, .csv, .tsv, .txt |
| PubChem fetch | Compound name or CID |
| 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 structures. |
Each entry produces an individual .sdf file. A combined batch.sdf containing all successfully converted structures is also generated for workflows that accept multi-record SDF input.
RDKit's AllChem.EmbedMolecule places atoms in 3D space using distance geometry, seeding initial coordinates from a random conformation. When Optimize geometry is enabled, Universal Force Field (UFF) minimization refines bond lengths, angles, and torsions. The resulting conformation is a reasonable starting geometry but represents a single local energy minimum, not necessarily the global one.