Convert a MOL file to SMILES
Free, no sign-up. It runs in your browser on Athanor’s own engine, and your structures never leave your device.
MOL file
SMILES
The result appears here, with a picture of every structure.
How to do it
Open a .mol file, drop it on the box, or paste its text.
Press Convert. Athanor reads the structure and writes its SMILES.
Copy the SMILES or download it as a .smi file.
One line instead of a file
SMILES is the compact way to pass a structure around: in a spreadsheet cell, a search box or a message. Athanor reads V2000 and V3000 MOL files and writes the SMILES in Kekulé form, with explicit single and double bonds in rings, and with stereochemistry when the file has it.
What a conversion keeps
Athanor’s engine was checked on 1,222 structures from its own library, each sent from SMILES to a MOL file and back, and compared by RDKit with stereochemistry included: 1,212 came back as exactly the same molecule, with every R/S and E/Z label. The ten that did not show the three gaps the engine still has: a radical (as in nitric oxide or TEMPO) is not yet written into MOL files; the E/Z of a double bond inside a very large ring can be lost; and a metal sandwich compound such as ferrocene is written with multi-center bonds, which some programs read differently. The converter reads every MOL file it writes back again and marks any structure that does not come back the same.
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