SMILES to MOL Converter
Turn a one-line SMILES into a MOL file you can open in a structure editor, attach to a report, or hand to a colleague.
Why convert SMILES to MOL?
SMILES is compact and machine-friendly, but many desktop tools — ChemDraw, MarvinSketch, Avogadro, PyMOL — expect a MOL file with an explicit atom and bond table. Converting gives you a file with fixed 2D coordinates that opens exactly as drawn, rather than being re-laid-out by the receiving application.
What the output contains
The result is a V2000 MOL block: a header line, a counts line (number of atoms and bonds), the atom block with element symbols and coordinates, and the bond block. Hydrogens are implicit unless you enable the option to add them.
Things to watch for
- MOL files hold exactly one molecule — if your SMILES describes a salt or mixture, only the disconnected structure is written.
- Aromatic rings are written in Kekulé form (alternating double bonds), which is what MOL requires.
- If you need 3D coordinates for docking, tick “3D coordinates”.