Then some of the electron clouds are non-bonding. CH4, NH3, H2O all have 4 electron clouds around the central atom, but they have different molecular structures due to what's at the end of each cloud.
CH4 ---> 4 atoms at ends of clouds
NH3 ---> 3 atoms at end, one NB pair
H2O ---> 2 atoms at end, two NB pair
All have same electron geometry, ut different molecular structures.