If you can stomach caffeine before a run, that might help. A little coffee with heavy cream for me does the trick.

Otherwise, an egg or something light with a little fat and protein in it should be good. If you haven't been on Atkins style dieting for very long, you probably just need more time for your body to utilize the fat better. Generally though, upping the fat/protein just a bit at a time will probably bring up your energy levels.