"Convert error! metalayout: average bond length is too small" error appears when loading from RDF and RXN V2000/V3000 reactions with molecules with 0 coordinates

**Steps to Reproduce Case 1 - Reactions**
1. Add to Canvas a reaction:
2. Save reaction to RXN V2000 or V3000
3. Open RXN document and manually change coordinates to 0.0000:
Example of files with changed coordinates for RXN V2000, V3000:
[!rxn-v2000-0-coordinates.zip](https://github.com/user-attachments/files/17148035/rxn-v2000-0-coordinates.zip)
[!rxn-v3000-0-coordinates.zip](https://github.com/user-attachments/files/17148039/rxn-v3000-0-coordinates.zip)
4. Add RXN files to Canvas

**Actual behavior**
- Error "Convert error! metalayout: average bond length is too small" appears for RXN V2000/V3000:

**Expected behavior**
- 1:1 reaction is added to Canvas without errors;

**Environment details**
- Tested on RC SA env
- Ketcher [Version 2.25.0-rc.5] Build at 2024-09-24; 18:17:25
- Indigo Version Version 1.24.0-rc.4.0-gdf51dc428-wasm32-wasm-clang-19.0.0
- Desktop Windows 11 Enterprise
- Chrome Version 129.0.6668.70 (Official Build) (64-bit)

**Notes**
- The fix also should be tested for RDF - to load as RDF, add $RDFILE to the top line of RXN document with reaction;
- Issue can be related to this defect - https://github.com/epam/Indigo/issues/2432
- Issue is detected during exploratory testing of Load from RDF feature, but it's an existing issue and not related to new changes - https://github.com/epam/Indigo/issues/2102

Start by loading the provided RXN V2000 and V3000 files with all coordinates set to 0.0000, then repeat the check with the same reaction marked as RDF using $RDFILE. Done means both formats load as the expected 1:1 reaction without the "metalayout: average bond length is too small" error.

Written by the indexing model from the issue text.