MOL2 to SMILES

What is MOL2 to SMILES?

MOL2 to SMILES is a small-molecule format converter for turning Tripos MOL2 ligand structures into canonical SMILES text. A MOL2 record holds a molecular graph alongside three-dimensional coordinates, atom types, partial charges, and substructure information. SMILES keeps the molecular graph in a compact line notation, which makes it practical for compound registration, library deduplication, descriptor calculation, and ligand-based workflows.

The converter reads and sanitizes the submitted structure with RDKit, then writes RDKit canonical, isomeric SMILES. Canonical output is useful when comparing molecules represented by different atom orders, but it is not a universal identifier. A different cheminformatics toolkit can write a different canonical string for the same molecule, and salts, tautomers, protonation states, and unspecified stereochemistry remain distinct chemical representations.

MOL2 should remain the working format when coordinates, Tripos atom types, or charge assignments matter. When a workflow needs connectivity rather than geometry, SMILES is the more portable handoff. For example, converted ligands can be passed to molecular descriptor calculation or used to screen a library with the PAINS filter.

How to use MOL2 to SMILES online

ProteinIQ converts each submitted .mol2 ligand into a canonical SMILES string. It accepts one pasted MOL2 block or up to 10 uploaded MOL2 files, and returns a .smi file for every successful conversion. A multi-file job also returns a named TSV batch when at least two ligands convert, plus a curated Run log that records the outcome counts for the submitted entries.

Input

Input	Accepted content	Limits and requirements
Ligand	A pasted MOL2 block or .mol2 file	Up to 10 inputs and 50 MB per file. A ligand must contain @<TRIPOS>MOLECULE and @<TRIPOS>ATOM sections. Multi-atom structures also need a @<TRIPOS>BOND section with counts consistent with their atom and bond records.
Job name	Optional label for the conversion job	Defaults to MOL2 to SMILES batch.

MOL2 records need meaningful three-dimensional coordinates. A multi-atom input whose atoms all occupy the same position is rejected before conversion. A file with several @<TRIPOS>MOLECULE records is converted record by record, and each molecule is counted as one entry.

No conversion settings are required. The input record defines the chemical representation, including formal charges and any stereochemistry that its atom types, bond definitions, and coordinates allow RDKit to interpret. RDKit's MOL2 reader expects the atom-typing scheme used by Corina; files written with other schemes, including some legacy Tripos dbtranslate output, may not parse reliably.

Results and downloads

The result data has one row per submitted ligand. A failed ligand does not prevent other files in the same job from being converted.

Result field	Meaning
input_name	The submitted ligand name used to identify the output.
source_format	The detected source format, mol2 for this tool.
status	success when a SMILES string was written, otherwise failed.
smiles	The canonical SMILES string for a successful conversion.
output_file	The generated .smi filename for a successful conversion.
error	Parsing or sanitization detail when the input could not be converted.

Download	Contents	When available
<ligand-name>.smi	One canonical SMILES string followed by a newline	For each successful ligand
batch.smi.tsv	Tab-separated name and smiles columns	When at least two ligands convert successfully
run.log	Curated run record with the input format, conversion phases, successful and failed entry counts, and stable failure guidance	For every job

The .smi files are convenient for individual downstream jobs. batch.smi.tsv retains each input name next to its SMILES value, which is useful for importing a small library into a spreadsheet or workflow. Successful results are also available as ligand-SMILES artifacts in ProteinIQ workflows.

How the conversion works

RDKit first constructs a molecular graph from the MOL2 atom and bond blocks, then sanitizes that graph before writing the result. Sanitization checks that valence, aromaticity, and related chemical features can be assigned consistently. If direct MOL2 parsing fails, ProteinIQ retries by translating the structure to SDF with Open Babel and then parsing the translated record.

Before exporting text, the converter removes ordinary explicit hydrogen atoms and asks RDKit for canonical SMILES with isomeric information enabled. The result can represent connectivity, bond orders, aromaticity, formal charge, isotopes, and specified stereochemistry. It does not retain the input coordinates, Tripos atom types, partial charges, substructure records, or other MOL2 annotations.

For example, an aspirin MOL2 structure can be written as CC(=O)Oc1ccccc1C(=O)O. Many valid non-canonical SMILES spellings can describe the same molecular graph. RDKit canonicalization selects one RDKit-specific spelling; it does not standardize a salt form, select a preferred tautomer, neutralize charge, or infer missing stereochemistry.

Reading failures and choosing the next step

Common failures come from a truncated file, atom or bond counts that do not match the records, missing bond connectivity, unsupported atom typing, or a structure that cannot be sanitized. The Run log records the failed-entry count for the affected inputs.

Format conversion does not repair chemical identity. It does not choose the protonation state appropriate for a target pH, split or remove counterions, or fix incorrect bond orders. Ligand Fixer is appropriate when a MOL2 ligand needs structural preflight and repair. The repaired structure should be inspected before its SMILES is used in later analysis.

SMILES to MOL2 creates a coordinate-bearing MOL2 file from a trusted SMILES string. That reverse conversion generates a new three-dimensional conformer, so it cannot reconstruct the original MOL2 coordinates, charges, or atom types from a SMILES string.