The movements of the structures without bonds after Clean Up action

Affected Version: Release/2.1+

Steps to reproduce:

**Scenario I**

1. Execute /convert endpoint with the following params:
[request_convert2.txt](https://github.com/epam/Indigo/files/7527368/request_convert2.txt)
[request_convert1.txt](https://github.com/epam/Indigo/files/7527369/request_convert1.txt)
2. Execute /clean endpoint with the following params:

[clean_request.txt](https://github.com/epam/Indigo/files/7527373/clean_request.txt)
**Actual result**

[clean_response.txt](https://github.com/epam/Indigo/files/7527413/clean_response.txt)

The benzene structure has become undistorted and has not changed the position. _**The NH3 structure has moved to the left upper corner of the canvas.**_

**Expected result**

The benzene structure should become undistorted. The positions of the structures should not be changed.
Note: Similar behavior is observed for any case when any structure without bonds and any other structure with bonds take place on the canvas.

**Scenario II**

1. Execute /clean endpoint with the following params:

[clean_request.txt](https://github.com/epam/Indigo/files/7527429/clean_request.txt)

**Actual result**
[clean_response.txt](https://github.com/epam/Indigo/files/7527435/clean_response.txt)

_**All structures without bonds have overlapped**_ each other in the left upper corner of the canvas.

**Expected result**

The positions of the structures should not be changed.