The MOL V3000 specification allows for atomic charge and mass. It would be nice to have Jmol recognize those values, both go in each atom line (after the coordinates).
The string "CHG=" is followed by the atomic charge (same values as for MOL V2000: 0 = uncharged, 1 = +3, 2 = +2, 3 = +1,
4 = doublet radical, 5 = -1, 6 = -2, 7 = -3)
The string "MASS=" is followed by the atomic mass of the isotope (if not specified, defaults to natural abundant isotope)
The alanine files in SVN Jmol-datafiles/V3000 can be used for testing.