Hanging a new shed door on a frame that is not level
Almost any door should be hung plumb on both axes, level, and square. Not doing so results in undesirable movement due to gravity along with other adverse functional issues. 

In this case, I'd hang the door roughly centered in the opening using shims, then I'd apply casing on the outside to cover the uneven gaps. Optionally case the inside as well. I'd then construct a threshold in an appropriate shape to mate to the door edges and the floor. 

The ideal gap between a door jamb and the rough framing is one that's large enough to accommodate out-of-plumb and out-of-level conditions, along with room to shim. More is not helpful, but may also not be a problem if the casing is large enough. 



In response to the new information provided... You have a small, lightweight shed. Level the floor by any convenient means and the door opening should return to something approaching plumb/level/square. Then you can hang the door parallel to the opening and expect it to work well.