How to make invoice to service tax expemted companies!

We are private limited company located in mumbai. We want to raise invoice for software selling to our mumbai located customer (pvt ltd company), but customer has given us SEZ service tax expemtion certificate and customer asked us to give invoice without service tax. Our billing amountis Rs.3600 including Service Tax 14% SBcess 0.5% and Vat 5.5 %. Now how should I bill to to customer? Can I raise invoice including 5.5% VAt only. Should I to change rate of my qty i.e. the final amount should not be Rs.3600 if I not charging service tax. In short should I raise customer invoice with Rs.3000 basic rate and 5.5% Vat on it, i.e. 3165.