Atom Query feature export: System creates invalid mol file if custom query present - export to Mol file/RXN V2000/SDF V2000

**Describe the bug**
Atom Query feature export: System creates invalid mol file if custom query present - export to Mol file

**Steps to Reproduce**
1. Open from file: [Custom.zip](https://github.com/epam/ketcher/files/14497993/Custom.zip)
2. Save it to Mol V2000 file format/RXN V2000/SDF V2000
3. Clear canvas
4. Load from Mol V2000 file format

**Actual behavior**
System throws exception: Convert error! struct data not recognized as molecule, query, reaction or reaction query
[rc.test.lifescience.opensource.epam.com-1709654286430.log](https://github.com/epam/ketcher/files/14498035/rc.test.lifescience.opensource.epam.com-1709654286430.log)

**Expected behavior**
No exception.
Should work as intended

**Environment details (please complete the following information):**
- Indigo Toolkit Version 1.18.0-rc.9.0-gc7efb4e71-x86_64-linux-gnu-11.2.1
- Ketcher Version 2.19.0-rc.1 Build at 2024-03-01; 19:35:12
- Chrome Version 122.0.6261.95 (Official Build) (64-bit)
- Win10
- Issue found while testing https://github.com/epam/Indigo/issues/1440

Start by reproducing the round trip with Custom.zip: export the custom-query structure to Mol V2000, RXN V2000, and SDF V2000, then reload the result. Trace the format conversion and parsing entry points for the failing export, and consider the issue done when each exported file reloads without the reported conversion exception.

Written by the indexing model from the issue text.