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The solution is very unintuitive: 

1. you must select the selection tool (this is easy, just click on it in the left top corner)
2. you go to some place of the canvas and hold down the left mouse button, than start dragging towards your molecule
3. When everything that you want to select is highlighted as green, release the mouse button
4. At this point your structure is selected, but you don't have any specific thing to use for dragging (unlike other scenarios, like rotate)
5. Now: you have to click on any bond / atom within your selection, and than not just the atom / bond, but the whole selection will be moved 
6. Hold your left mouse button and move the structure where you want it
7. Release the mouse button, and now your structure is replaced