lots of chemicals have the same empirical formula but different effects. how those molecules are arranged in three dimensions determines their effects to a greater extent than their formula.
yep, the empirical formula is nothing but a sum of the buildingblocks. However, the arrangement of those building blocks is essential to the identity of the compound.
For instance you and I might be made up of the same sum and quantity of a certain list of atoms, but since we are built in different patterns we are not really alike.