Clean Up and Layout ignore atom hydrogens and indexes

[AlexeyGirin]

Environment details (please complete the following information):

• Ketcher Version 2.18.0-rc.4 Build at 2024-02-06; 13:45:28
• Indigo Toolkit Version 1.18.0-rc.6.0-g98bf384e0-x86_64-linux-gnu-11.2.1
• Chrome Version 121.0.6167.161 (Official Build) (64-bit)
• Win10
• Issue found while testing Support selection entity selection flag in KET format ketcher#3934

Steps to Reproduce

1. Create reaction as shown on the screen
   
   OR
2. Open from file as a New Project: Clean Up causes internal sever error if atom(s) with mapping tool selected.zip
3. Spread atoms as on the picture (it is needed because atoms position are not restored correct because of the bug)
   
4. Remove selection from atoms if any (it required workaround for issues Clean Up causes internal sever error if atom(s) with mapping tool selected #1670)
5. Press Ctrl+L (Layout)
   OR
6. Press Ctrl+Shift+L (Clean Up)

Actual behavior

Layout: System shrinks arrow length, put plus and arrow over H atom index and O atom hydrogens
Clean Up: Works slightly different but problems are the same

Expected behavior
System takes into account indexes and hyrdogens and adds extra space between atom, plus and arrow in the same manner as it does for big molecules

Size of arrow remains the same