What else besides nitro cream (side effects not good) can be used to relieve pain from anal sphincter spasms and throbbing pain. Anything natural?

Diltiazem 2% ointmen. 50% of fissures will get better on their own, without any intervention. For the other half, the majority can get treated with these ointments. Unfortunately, there is not a natural remedy that has been investigated that provides cure. If the side effects are bothering you with the nitro ointment, Diltiazem has a lower side effect profile and higher cure rate. I'd suggest that.
Moist heat (sitz) Pain from anal fissures usually comes from sphincter muscle spasm, often relieved naturally by heat (sitz baths), otc creams which contain 'caine compounds (many herbal remedies), and avoidance of hard bms. If pain persists, discuss with your doc as easily fixed with a minor procedure.