The most frequently met causes for such a large
.eps are: a) there are really many of atoms in the picture, b) the
.eps includes the complete definition of those atoms and bonds behind other objects, thus invisible (equally known as the painter’s problem), or c) the
.eps is used as a container for bitmap data.
If it has to be this very visual representation, the import into Inkscape (or other programs) as a
.pdf instead of a
.(e)ps may be an option; by volume, it is a less large file.
ps2pdf (e.g., in Linux) or epspdf (for Windows, from CTAN) are examples to offer such a conversion.
An alternative may be to use e.g., molekel for the image generation. In addition to
.png snap shoots,
.pdf may be exported as true vector images. I.e., you may remove and alter the background in Inkscape because it is in a different layer than the molecules which consists of polygons, remove guide lines seen in the preview, etc.
For this, the small Windows XP 32-bit engine often is sufficient (download approx. 80 MB) which, e.g. in Linux Xubuntu 18.04 LTS, is supported well by wine. But the program is cross-platform and the source code public.
(Sadly, the current settings of the discussion interface do not allow to upload an example .pdf, or .zip.)