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The electrons in the atoms shape the molecule. The 'outermost' electrons in the atoms are the most important because they are shared between atoms in the bonds.

Electrons repel each other because they have the same negative electrical charge, so the bonds tend to repel each other too. If you have a central atom bonded to each of three identical other atoms, the three atoms will form an equilateral triangle because each of the three bonds is trying to get as far away as possible from the others (by repulsion). If the central atom has a fourth bond orbital that has electrons in it, even without another atom, those electrons will push the equilateral triangle of bonds away (and a little closer to each other), making the molecule pyramidal. Without the fourth bond orbital's electrons, the molecule should be triangular and flat.

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