Chain not sliding into casette perfectly I have a RD 7900 derailleur and a standard 105 28t casette.

After replacing my wheelset I observed after I put my bike on the workstand that the chain is not sliding in perfectly into the casette cogs in the lowest (28t) gear, all other gears are fine. 

It makes some sort of grinding noies because, spoiler alert, the casette teeth are grinding on the chain rings and "forcing them" into place.

The derailleur is indexed and high low screws are properly set. I also dont think the derailleurs bent but I cant make that judgement with my bare eye.

How do I adjust my derailleur so that the teeth on the casette will fit perfectly in the chain ?
By definition, if the chain is not running on all cassette sprockets properly, the indexing and/or limits are not properly adjusted. Low limit setting being off would be my guess.

Run through the full indexing adjustment procedure. Park Tool Company has the best instruction video. 

You can check the derailleur hanger by lifting up the rear wheel and looking down a line from the derailleur cage to the chainrings. The cage should look parallel to the rings.