I am taking a molecular modeling course and we are using a Software called Spartan. I don't have too much trouble with the software, but I don't understand some general concepts.

For example, say I build methane in the software. Then I use some method that is an approximation of the Shrodinger equation, say Hartree Fock equation. OK. I will end up getting some energy, usually really high, that says relE, relative Energy. My question is, what is this energy exactly? What does it represent? What does this value mean? I know energy is PE + KE, so does this value truly represent that? I mean, I know there are errors in calculations thats not what I'm asking, I'm just beweildered on what it actually means.

I know that from taking all these energies I can find deltaH(rxn) and deltaH(form) of different molecules, but that's about it. I know how to do those things but not why its happening

The reason I ask is because when the situation is appropriate I can use Molecular Mechanics instead of Quantum Mechanics to get some energy, but that energy value

E = stretchingE + bendingE + torsionE + non-bondinginteractionsE

so I am really confused. I know you only use the molecular mechanics energies as comparisons (like compare the energy of cis v. trans).

PLEASE HELP ME FROM GETTING A D, THANKS!!

BTW I am a math major... can someone please kick me in the head for taking this course??