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A full answer would be very long and complicated and essentially useless to most people, so I'm going to give some hints. If the long answer would have made any sense to you, the hints ought to be enough.

Atoms are typically on the order of 1-2 Angstroms in diameter.

Covalent bonds are about 1 Angstrom for bonds to hydrogen, 1.5 Angstroms between non-hydrogen atoms.

VSEPR theory works pretty well.

If you need to figure out the sizes of a lot of molecules, you should get a molecular modelling program; I'm not really in that field anymore, so I can't make good recommendations, but I've put a link to a list of packages in the related links section. (I personally favor CHARMM, but it's not free, particularly if you want the Momany-Rone force field parameter set which is excellent for small molecules.)

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Q: How do you calculate the molecular size any molecule?
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