Well if she had regular periods and regular menstrual cycle before then there are great chances of pregnancy being the cause of her missed period.You had unprotected sex so the chances are further enhanced of being pregnant. But since it is just 4 days above her due date then urine test for pregnancy might not detect such an early pregnancy and you might get false negative results. I will advise you to wait for few more days that will clear the ambiguity,either she will have her periods or you will get time to get credible pregnancy test result(Home check via urine). Otherwise blood test called Beta HCG can detect very early pregnancy,even before urine test becomes positive. Hope it helps you. Thanks