Isoelectric Point calculation should take into account occupied leaving groups (exclude them)

[AlexeyGirin]

Steps to Reproduce

1. Go to Macromolecules mode - Flex canvas (empty)
2. Load from HELM: PEPTIDE1{C}|PEPTIDE2{C}|PEPTIDE3{C}|PEPTIDE4{C}|PEPTIDE5{C.C}|PEPTIDE6{C}|PEPTIDE7{C}$PEPTIDE2,PEPTIDE1,1:R3-1:R3|PEPTIDE4,PEPTIDE3,1:R2-1:R2|PEPTIDE6,PEPTIDE7,1:pair-1:pair$$$V2.0
   
3. Open Calculate properties (press Alt+C)
4. Select each chain

Actual behavior
They all have the same Isoelectric Point - 4.01

Expected behavior
Each chain should have it's own Isoelectric Point value

As per requirement:

1. pKa values for all ionizable groups of all monomers should be determined, ignoring the leaving group atoms if an attachment point is occupied.

Environment details:

• Ketcher Version 3.4.0-rc.3 Build at 2025-05-15; 19:51:50
• Indigo Version 1.32.0-rc.2.0-g94ab270bd-wasm32-wasm-clang-19.0.0
• Chrome Version 136.0.7103.93 (Official Build) (64-bit)
• Win10

Found while testing: epam/ketcher#5727