System positions object at long distance on the preview and on the canvas

[AlexeyGirin]

Steps to Reproduce

1. Click Open... button (Ctrl+O)
2. Select open from file
3. Select file: Outlayer.pptx
4. Click Open

Actual behavior

Press Open as New Project button

Expected behavior

Environment details:

• Ketcher Version 2.18.0-rc.5 Build at 2024-02-09; 17:07:18
• Indigo Toolkit Version 1.18.0-rc.6+cdx.0-g99f004a82-x86_64-linux-gnu-11.4.0
• Chrome Version Version 121.0.6167.161 (Official Build) (64-bit)
• Win10
• Issue found while testing Add support for opening structures in CDX format embedded into MS PowerPoint ketcher#3914

[AliaksandrDziarkach]

CDX file contains same log distance.
In CDX this is superatom TFA with coordinates x:511,y:428 and located beside arrow and text.
But atoms inside TFA has coordinates like x:405,y:64546.
In ketcher we have no coordinates field for superatom so it placed according to internal atoms coodinates.

[AlexeyGirin]

Decided to postpone since unclear how to fix (as per @AliaksandrDziarkach )

[AlexeyGirin]

Moved to Refined Backlog since no fix over 2 versions