SMILES to MOL2 Converter
MOL2 is the Tripos format used by docking preparation and molecular mechanics tools. This conversion also generates a 3D conformer.
What MOL2 adds over MOL
MOL2 assigns a SYBYL atom type to every atom and carries partial charges in the atom block. That lets force-field and docking software act on the structure without re-perceiving it. It also supports multiple named substructures per record, so a protein–ligand complex can live in one file.
3D geometry is required
MOL2 is used almost exclusively for three-dimensional work. This converter generates a conformer, so the output has real coordinates rather than a flat 2D layout.
Check before docking
- Hydrogens should be explicit — enable the option if they are missing.
- Charges from atom typing are preliminary; most docking tools re-assign them.