MOL2 to SMILES Converter
MOL2 is the Tripos format used by docking and modelling software. Convert it to SMILES when you need a compact, portable representation.
Where MOL2 files come from
MOL2 is the native format of SYBYL and is produced by many modelling packages — docking preparation tools, conformer generators and molecular mechanics suites. It carries partial charges and atom types that SMILES cannot express.
What is lost in conversion
- Partial charges — not represented in SMILES at all.
- SYBYL atom types — collapsed into plain elements.
- Substructure names — dropped.
When that matters
If you are moving a structure into a modelling pipeline that needs charges, do not round-trip through SMILES — you will have to re-perceive them. Use SMILES for storage, search, and sharing, and keep the MOL2 for the modelling step.