Not of a complete cell, that would seriously overload even most powerful animation software/hardware you could build, not to mention there are gaps in our understanding of the cell. Understanding a cell purely through chemistry is possible if a bit masochistic, sooner or later you are going to need to approach it from a different direction to get the whole picture. There is so much complexity in a modern cell that sooner or later you have to start looking at the emergent characteristics. Don't believe me check out this chart of just the common metabolic pathways in a human cell, you are looking a 3.5 billions years of kluges, breathtaking elegance, rube goldberg monstrosities, and duck tape solutions all layered and tangled into each other, messy doesn't begin to describe it.
But there is several places creating models of individual processes, modeling each individual atom. These will let you at least understand hte chemistry of the components.
www.dnalc.org is focused on nucleic acids and their interactions.
Their work is related to Harvard's biovisions program which uses XVIVO. which is a much rougher but larger scale approach and may be the closest to what you want.
Cambridge MRC has a more diverse selection with better visualization of the actual chemical interactions.
Swissmodel by the Swiss Institute of bioinformatics focuses on protein modeling and has a free to use program and database.
There is even a wikipedia database Protepedia
Image from www.dnalc.org animation
I'm sure others on the site could list a dozen other such programs/databases.
