Extract canonical SMILES strings from MDL MOL ligand files for cheminformatics workflows. Learn more
Input
What is MOL to SMILES?
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.
How to use MOL to SMILES online
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 status in a curated Run log.
Input and output
| 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. |
run.log | Curated run record with the input format, conversion phases, successful and failed entry counts, and stable failure guidance. |
RDKit sanitization checks features such as valence and aromaticity before writing SMILES. A failed entry remains represented in the Run log instead of silently disappearing from the batch.
What the conversion preserves
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:
- Coordinates: A SMILES string does not encode the submitted 2D drawing or 3D pose.
- MOL metadata: Header text and format-specific annotations are not part of ordinary SMILES.
- Undefined stereochemistry: Missing or ambiguous stereochemical information cannot be reconstructed.
- A universal canonical form: Another toolkit may write a different valid canonical SMILES for the same graph.
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.
Common conversion failures
Invalid atom valence, malformed counts or bond blocks, unsupported query atoms, and incomplete V2000 or V3000 records can prevent sanitization. The Run log records the failed-molecule count. When the molecular graph needs repair rather than simple conversion, Ligand Fixer can standardize common ligand-file problems before another attempt.
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