Molecules with lone electron pairs:
If a molecule has lone electron pairs, these provide the
basis to set the electron pair geometry, but become invisible
when determining the molecular geometry. The molecular geometry
describes only the orientation of the atoms, and does not
included the lone electron pairs.
See what happens for ammonia shown on the middle left.
Ammonia has three bonded H atoms and one lone electron pair around
the N atom.
The electron pair geometry is a tetrahedral.
The molecular geometry is a trigonal pyramid.