Arrows overlap atoms of chemical elements after save/load to/from RDF or layout actions

[ivanmaslow]

Steps to Reproduce

1. Add reactions with chemical elements containing atoms:
   overlapping-issue.zip
   
2. Make Layout or save/load to/from RDF actions

Actual behavior

• Arrows overlap atoms of chemical elements:
  

Expected behavior

• They are not overlapped, expected indent should be clarified - TBD

Environment details:

• Reproduced on RC SA env;
• Ketcher [Version 2.26.0-rc.6] Build at 2024-10-25; 09:57:12;
• Indigo Version 1.25.0-rc.4.0-g8862ccb7e-wasm32-wasm-clang-19.0.0
• Desktop, Windows 11 Enterprise
• Chrome, Version 130.0.6723.70 (Official Build) (64-bit)

Additional context

• Test case is added to xls and have to be automated after fix
• The defect is detected during retesting of Not correct length of Multi-Tailed Arrow and Single arrow after loading from RDF or Layout action #2555, but initially it's related to Update layout for pathway reaction on canvas #2309