In this display I have chosen to move the origin of the coordinate axes to the x, y, and z coordinates of one of atoms. We of course are free to place coordinate axes at any convenient location and this location makes it easier to see the angular relationships. The second atom could lie anywhere on a sphere whose radius is the fixed distance between atoms. A click on the Action button frees the second atom to wander on this sphere.
Click on the Action button second time to fix the distance from the second atom to the z-axis and notice how the possible configurations are restricted by the additional constraint. The constraint is represented by the line in the axes color. Click the Action button a third time to fix the distance to the y-axis. Now the second atom has only one point where it may reside. So five numbers have fixed the position of this two atom lump.