What does the "total energy" of a molecule mean for the Chem3D MM2 minimized energy calculation?
General definition of energy

Usually, the total energy of a system is subdivided into kinetic energies of all particles and potential energies of the interactions between them, where the later terms are most often limited to the strongest Coulomb interactions only. In atomic units we get then:

$$
    E
    =
    - \sum\limits_{\alpha=1}^{ν} \frac{1}{2 m_{\alpha}} \nabla_{\alpha}^{2}
    - \sum\limits_{i=1}^{n} \frac{1}{2} \nabla_{i}^{2}
    - \sum\limits_{\alpha=1}^{ν} \sum\limits_{i=1}^{n} \frac{Z_{\alpha}}{r_{\alpha i}}
    + \sum\limits_{\alpha=1}^{ν} \sum\limits_{\beta &gt; \alpha} \frac{Z_{\alpha} Z_{\beta}}{r_{\alpha \beta}} 
    + \sum\limits_{i=1}^{n} \sum\limits_{j &gt; i}^{n} \frac{1}{r_{ij}} \, ,
$$
where $m_{\alpha}$ is the rest mass of nucleus $\alpha$ and $Z_{\alpha}$ is its atomic number, $r_{\alpha i} = |\vec{r}_{\alpha} - \vec{r}_{i}|$ is the distance between nucleus $\alpha$ and electron $i$, $r_{\alpha \beta} = |\vec{r}_{\alpha} - \vec{r}_{\beta}|$ is the distance between two nuclei $\alpha$ and $β$, and $r_{ij} = |\vec{r}_{i} - \vec{r}_{j}|$ is the distance between two electrons $i$ and $j$.

Now, the zero of energy corresponds to the case when all the terms are zero. Kinetic energy is zero when velocity is zero, while the Coulomb interaction energy is zero when particles are infinitely separated from each other. Thus, the zero of energy corresponds to the case when all the particles are infinitely far away from each other and not moving. In accordance with that choice of the zero of energy, the energy of any stable molecular system in the modeled environment (usually, an isolated molecule in the gas phase) has to be negative.

Molecular mechanics definition of energy

Molecular mechanics (MM) operates with a different kind of energy. To start from, usually, it is just the potential energy. Secondly, in MM we think about a molecule in terms of atoms and bonds (rather than nuclei and electrons) and the potential energy is divided into contributions from bond stretching, angle bending, torsional rotations around single bonds, non-bonded interactions, etc.
$$
    E = E_{\mathrm{stretch}} + E_{\mathrm{bend}} + E_{\mathrm{torsion}} + E_{\mathrm{nb}} + \dotsc \, ,
$$
where the first term, for instance, is typically proportional to the sum of the squares of extensions from the equilibrium length for all the bonds:
$$
    E_{\mathrm{stretch}} = \sum\limits_{\mathrm{bonds}} k (r - r_{\mathrm{e}})^2 \, .
$$
Now, we could take the energy corresponding to the equilibrium length $r_{\mathrm{e}}$ as the zero of energy and proceed similarly for the other bonded terms, which would mean that (ignoring usually small non-bonded interactions) the MM potential energy is zero when the molecular system is completely "unstrained" (i.e. when all geometrical parameters have their "natural" equilibrium values). However, different molecules are bonded differently, and thus, the zero of energy would, in general, be defined differently.  Each potential energy will thus be computed relative to a different zero of energy which makes the comparison of energies for any two different molecules meaningless.