MOL2 to SDF Converter
Move structures out of modelling software and into the SDF ecosystem without losing the three-dimensional geometry.
Why SDF rather than SMILES
SDF keeps the coordinates and per-record data fields. If you are moving a modelled or docked structure into a compound database, that context is worth preserving — SMILES would throw away the geometry entirely.
What is lost
SYBYL atom types and partial charges are not part of the SDF specification. If downstream tools need them, re-run atom typing after conversion rather than assuming they survived.
Multi-substructure MOL2 files
Some MOL2 files describe a complex as several named substructures. Converted to SDF, these become one record per molecule in the file.