Clean Up action does not work with selected structures in distorted reactions

**Steps to Reproduce**
1. Launch Ketcher
2. Open reaction [reaction_3 (2).zip](https://github.com/epam/ketcher/files/6853319/reaction_3.2.zip)
3. Distort the structures.
4. Select distorted structure(s).
5. Click the 'Clean Up' button.

**Expected behavior**
'Clean Up' works for selected structures.

**Actual behavior**
'Clean Up' does not work for selected structures. No changes on the canvas.

**Desktop:**
- OS: W10

**Additional context**
The same issue, if reaction components were mapped (AutoMap Tool) after distortion

Reproduce the issue in Ketcher using the attached reaction_3 (2).zip: distort structures, select them, and click Clean Up. Start by tracing how Clean Up handles selected structures in distorted reactions, including components mapped with AutoMap Tool. Done means Clean Up changes the selected structures on the canvas in both cases.

Written by the indexing model from the issue text.