MOL to SMILES converts an MDL MOL structure into a canonical SMILES string with RDKit. A MOL file stores an atom and bond table, optional stereochemical annotations, and usually 2D or 3D coordinates. SMILES keeps the molecular graph in a compact text form that is easier to register, search, filter, and pass to cheminformatics models.
The conversion does not preserve coordinates because standard SMILES describes connectivity rather than a particular conformation. The resulting string is canonical within RDKit, but canonical SMILES are toolkit-specific and should not be treated as a universal compound identifier.
Upload as many as ten .mol or .mdl files, or paste one MDL MOL block, to convert MOL structures to canonical SMILES online. ProteinIQ parses and sanitizes each molecule with RDKit, returns one .smi file per successful entry, combines batch results in a TSV file, and records conversion failures in a JSON report.
| Item | Description |
|---|---|
Ligand | One pasted MOL block or up to 10 uploaded .mol or .mdl files. Each file may be up to 50 MB. |
Per-entry .smi | Canonical isomeric SMILES followed by a newline. |
batch.smi.tsv | Combined name and SMILES table, returned when more than one entry converts successfully. |
mol_to_smiles_report.json | Machine-readable status, output filename, SMILES, and error message for every submitted entry. |
RDKit sanitization checks features such as valence and aromaticity before writing SMILES. A failed entry remains in the report instead of silently disappearing from the batch.
Canonical SMILES generated by RDKit preserves the interpreted molecular graph, including atom elements, formal charges, bond orders, isotopes, and supported stereochemistry. Isomeric SMILES output is enabled, so tetrahedral and double-bond stereochemistry are included when the MOL record defines them unambiguously.
The conversion does not preserve:
For a multi-record structure file, SDF to SMILES is the appropriate converter. To create a fresh 3D structure from the resulting text, SMILES to SDF generates coordinates, but those coordinates are a new conformer rather than the geometry from the original MOL file.
Invalid atom valence, malformed counts or bond blocks, unsupported query atoms, and incomplete V2000 or V3000 records can prevent sanitization. The JSON report gives the error for each failed molecule. When the molecular graph needs repair rather than simple conversion, Ligand Fixer can standardize common ligand-file problems before another attempt.
Convert InChI strings into SMILES with batch support and downloadable outputs.
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 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
MOL to SMILES converts an MDL MOL structure into a canonical SMILES string with RDKit. A MOL file stores an atom and bond table, optional stereochemical annotations, and usually 2D or 3D coordinates. SMILES keeps the molecular graph in a compact text form that is easier to register, search, filter, and pass to cheminformatics models.
The conversion does not preserve coordinates because standard SMILES describes connectivity rather than a particular conformation. The resulting string is canonical within RDKit, but canonical SMILES are toolkit-specific and should not be treated as a universal compound identifier.
Upload as many as ten .mol or .mdl files, or paste one MDL MOL block, to convert MOL structures to canonical SMILES online. ProteinIQ parses and sanitizes each molecule with RDKit, returns one .smi file per successful entry, combines batch results in a TSV file, and records conversion failures in a JSON report.
| Item | Description |
|---|---|
Ligand | One pasted MOL block or up to 10 uploaded .mol or .mdl files. Each file may be up to 50 MB. |
Per-entry .smi | Canonical isomeric SMILES followed by a newline. |
batch.smi.tsv | Combined name and SMILES table, returned when more than one entry converts successfully. |
mol_to_smiles_report.json | Machine-readable status, output filename, SMILES, and error message for every submitted entry. |
RDKit sanitization checks features such as valence and aromaticity before writing SMILES. A failed entry remains in the report instead of silently disappearing from the batch.
Canonical SMILES generated by RDKit preserves the interpreted molecular graph, including atom elements, formal charges, bond orders, isotopes, and supported stereochemistry. Isomeric SMILES output is enabled, so tetrahedral and double-bond stereochemistry are included when the MOL record defines them unambiguously.
The conversion does not preserve:
For a multi-record structure file, SDF to SMILES is the appropriate converter. To create a fresh 3D structure from the resulting text, SMILES to SDF generates coordinates, but those coordinates are a new conformer rather than the geometry from the original MOL file.
Invalid atom valence, malformed counts or bond blocks, unsupported query atoms, and incomplete V2000 or V3000 records can prevent sanitization. The JSON report gives the error for each failed molecule. When the molecular graph needs repair rather than simple conversion, Ligand Fixer can standardize common ligand-file problems before another attempt.
Convert InChI strings into SMILES with batch support and downloadable outputs.
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 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