Convert CDXML to CDX
Free, no sign-up. It runs in your browser on Athanor’s own engine, and your structures never leave your device.
ChemDraw CDXML in
or paste it
ChemDraw CDX out
How to do it
Choose a file, or paste it.
Athanor’s own engine reads it in your browser and writes the new format.
Download the result. It is read back and checked first.
How it works
Turn a ChemDraw CDXML file into the binary .cdx form, for programs and journals that ask for it. Athanor reads and writes ChemDraw’s CDX and CDXML formats with its own engine, the one in the Athanor app, so nothing is uploaded and you need no ChemDraw license. After converting, it reads the result back and compares the structure by its InChIKey, and says so plainly if anything did not survive.
Measured on November 12, 2026 over all 1,128 structures in Athanor’s compound library, each converted out and read back: CDX and CDXML both returned the same structure 1,128 times out of 1,128, and MOL V3000 and SDF did too. MOL V2000 cannot hold 26 of them (radicals, fixed hydrogen counts, some metal bonds) and says so rather than changing them.
To edit the structure rather than only convert it, open the file in Athanor, which opens and saves CDX and CDXML as they are. See the CDX and CDXML formats.
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