Why does Chem3D minimize nitrogen dioxide (radical) so badly? I build from text O-N+O (the SMILES of this is O=[N+][O-]), I delete the hydrogen atom added automatically on N, then I start MM2 Minimization. Both the bond length and the angle differ from what I see in the top right image here: https://en.wikipedia.org/wiki/Nitrogen_dioxide
By the looks of it, Chem3D uses generalised classical force fields to describe the molecular interactions.

Such force fields are optimised to provide a reasonable fit to multiple properties for lots of different molecules. For example, they reproduce reasonable bond lengths not only for $\ce{NO2}$ but also for the various bonds in organic molecules.

They are also constructed to reasonably reproduce solvation properties which depend on the molecule-specific partial charges, which in turn alter bond lengths and angles.

So it is unlikely that you have done anything wrong.

If you require a more accurate model, either apply more accurate force fields (e.g. those fitted specifically to $\ce{}$) or switch to quantum chemistry methods such as DFT.