Using dummy atoms

Dummy ("Xx") atoms are treated a little different when used in structures. A dummy atom will not replace an existing atom when it is defined as the 'replacing atom'. Instead, the double-clicked atom will remain and will accept the bonds that the dummy atom had in the structure.

Build a methane molecule
Replace the carbon atom by a nitrogen atom
Select one of the hydrogens and replace it by a dummy atom
Select the dummy atom and choose the 'Set Origin' command from the Edit menu
Save the structure in (a subdirectory of) your $SCM_STRUCTURES directory

Now you can select the structure from the structures menu and directly use it.

Select your new structure from the structures menu
Double-click on one of the hydrogens

Notice that the hydrogen atom is not removed and that the NH3 group is attached to it. Similar behavior has been demonstrated with the bidentate ligands, where the dummy atoms are also used.