1992 Bonneville cranks but won't start

I left my dome light on the other day and let the battery go completely
dead. Jumped it the next day. Engine cranked but wouldn't start.
Checked fuses in all three locations and charged battery overnight.
Tried again yesterday. Cranks like a champ but still won't fire. Pulled
a plug and I have no spark but I can smell some fuel in the cylinder
(plus I can hear the fuel pump when I turn the key on). Bought a code
reader and it says code 58 (VATS). Thought maybe the VATS wasn't
working (it has pass-key II), but I have since found out that when the
resistor in the key is bad that the engine won't crank and the security
light flashes. The engine cranks and the security light comes on solid
for 5 seconds and then goes out like it should, so I guess it isn't
that. Must be that some other component went bad because of a low
battery (unlikely?), got fried because I jump started it (any ideas?),
or maybe just coincidently a component died. The car only has about 60K
on it and had no symptom or problems previously.

Suggestions?