What does the ZZE tag in an Chemical Table file refer to?
The current version of the CTFile spec can be downloaded for free from Accelrys. Based on the files you have, you'll want to look at the "V2000" section.

Short answer: I believe [M  ZZE] is a vendor-specific property key, possibly introduced by ACD Labs, given it's the package cited in the header on line 2. The CTFile format spec for V2000 files says nothing about an "M  ZZE" property key.

The CTFile spec says that property keys that are not recognized by parsing software are to be ignored. This makes vendor-specific extensions feasible.

You seem to be on the right track in your interpretation. The Galactobuxin entry has this line in the properties block:


  M  ZZE  1  31  23


Breaking this down:

{M  ZZE} is the mystery properties key.

{1} is the number of data entries on the line.

{31} is the 1-based index of either an atom or bond.

Atom 31 is one of the rather boring methoxy groups.

On the other hand, bond 31 is a real problem child:



This file is abusing the meaning of 'wedge bonds' by trying to use them to indicate chair conformation perspective, rather that what they're intended for - flat stereoprojection. My guess is that the file is trying to annotate this bond.

The only question left is - what does {23} refer to?

Bond 23 is unremarkable. Atom 23 is one of the origins of a wonky wedge bond. But it's not clear why it should be associated with bond 31.

My best guess is that the software that created this file knew it was abusing wedge bonds and wanted to include a flag on bond 31 so that software reading the file wouldn't misinterpret.

Given that you're seeing the same {23} in every file, this could be a code to specially process bond 31's stereo flag.