I Have Had Protected Sex Twice. I Am Not On

I have had protected sex twice. I am not on the contraceptive pill. I got a sore throat about a week and a half after having sex for the first time and then had sex the second time on the second day of being sick. Since then I have become more fatigued and flemming up a lot more and due to my sore throat I had a loss of appetite which just made my fatigue worse. I was scared I may be pregnant even though the condom did not break and my boyfriend did not ejaculate in me. I have done a store bought pregnancy test and it said negative. I also took the morning after pill within 72 hours of sex. I went to the doctor today and she told me I wasn't pregnant and that the morning after pill will muck up my periods and my period is meant to be due now and I think that is why I feel a bit sick and cramped up because I should be having my period now but my body has been confused. I am still worried that I may be pregnant and I have to wait around until my period comes which could be late due to taking the morning after pill. What are your thoughts or advice? I really do not think I am pregnant as I was safe and I also went and got contraceptive pills to start when my period comes to be extra protected but I cannot stop stressing about being pregnant and it is affecting me physically and mentally.. :(