The Edit → Align command contains commands to align your molecule to the indicated axes or plane.
If you are aligning to an axes, you need to select which atoms to align. If you select one atom, the molecule is rotated around the origin such that the selected atom is on the specified axes. If you select two atoms, first the molecule is translated such that one of the selected atoms is on the origin. Next, the molecule will be rotated such that the other selected atom is on the specified axes.
If you are aligning to a plane, you need to select a plane to align. If you select two atoms, these will define the normal of the plane to be aligned. If you select three atoms, these define the plane to be aligned.
This Align command does change the coordinates of your atoms, unlike the Align Screen command in the View menu.
Typically the Align command will change your origin. You can always set the origin as you like after-wards.
