Convert a V2000 MOL file to V3000
Free, no sign-up. It runs in your browser on Athanor’s own engine, and your structures never leave your device.
MOL file
MOL file (V3000)
The result appears here, with a picture of every structure.
How to do it
Open the V2000 .mol file or paste its text.
Press Convert. Athanor reads it and writes the V3000 form.
Copy the result or download the new .mol file.
The same structure, the newer layout
V2000 MOL files use fixed columns and stop at 999 atoms and 999 bonds. V3000 writes each atom and bond as its own line of named fields, with no such limit, and carries more, such as enhanced stereochemistry. Athanor reads the V2000 file and writes the same structure as V3000, then reads it back to check nothing changed.
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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