I have created a complex chemical structure (Covalent-Organic framework) in Avogadro 1.2.0n. After optimizing the geometry, and applying ‘Auto Optimization’ tool, a final well defined structure has emerged. However, some of the individual structure (like Benzene) were twisted in other direction. This makes my structure to go out of the xy (or yz or zx) plane. I want my structure to be in only one plane, without any twisting. Is it possible?
EDIT-1: Please find below the screenshot of the structure
As you can see, the benzene is twisted into another plane, while other structures are in other direction. I look for a plain structure. Since it is a complex structure it is very difficult to edit the coordinates. Can some one suggest the correct method to solve it?