How does ChemBio3D calculate "Total Energy" for enantiomeric molecules in a non-chiral environment, such as crystals of (1S,2R,8R,8aR)-octahydroindolizine-1,2,8-triol versus its enantiomer, (1R,2S,8S,8aS)-octahydroindolizine-1,2,8-triol?

How does ChemBio3D calculate "Total Energy" for enantiomeric molecules in a non-chiral environment, such as crystals of (1S,2R,8R,8aR)-octahydroindolizine-1,2,8-triol versus its enantiomer, (1R,2S,8S,8aS)-octahydroindolizine-1,2,8-triol?

The Total Energy for the two enantiomers should be the same when an energy minimization is completed. The Total Energy for the MM2 calculation differs by about 10% for the two molecules, but differs by a bit under 1% for a GAMESS calculation. The question is why they differ at all. The answer is that the energy minimization routines are iterative approximations, where you have some control over the number of iterations and their termination point. First the concept; then the methods to change them.

In concept, the Total Energy for two enantiomers should be identical, but any computation package will stop calculating at a point where it considers the energy at a reasonable minimum, in order to balance computation time versus accuracy. Furthermore, the starting point partly determines the end point -- how one draws the two enantiomers as the starting point may lead to different end-point configurations, especially in MM2. To get a best-matched Total Energy for an enantiomer pair, start with the molecules in a similar configuration, and let the computations run for longer than the default time settings.

In practice, the means to accomplish that is as follows:
In MM2 the following parameters are relevant; here are the default settings:
-On the "Job Type" tab:
Minimum RMS Gradient = 0.100
-On the "Dynamics" tab:
Step interval = 2.0 fs
Frame interval = 10 fs
Terminate after 10,000 steps
Changing any of those would alter the end-point and would potentially make the two enatiomers have a closer Total Energy.

The equivalent parameters in GAMESS are:
-On the "Advanced-1" tab:
Convergence Tolerance = 0.001000 Hartree/Bohr
-On the "General" tab:
"MAXIT=50" means "maximum iterations".

The equiavlent for MOPAC:
-On "Job & Theory" tab:
Minimum RMS Gradient = 0.100

In summary, to investigate convergence of enantiomeric Total Energy, look into the energy minimization parameters for each computation chemistry package.