VAT and self assessment.

Dear Sir Madam

Last year HMRC VAT department contacted me to inform me that I should be VAT registered business as I went over the threshold four years ago, I was not aware about it I was clueless I thought VAT is for big businesses I am just a sole trader I never heard about the threshold.I had to pay £30000 plus penalties to HMRC to cover what I owed of VAT, unfortunately I made a loss paying this amount as I was in deficit.
As far as I know 20% tax and 9 % class 4 NIC are applied only on net profit after deducting all costs (Tax allowance, stock and all business expenses)
My questions is the £30000 payed to VAT should not be included in my self assessment as profit ? unfortunately I did include this amount. Could you please advise me how to recover the amount that I should not include as profit. Your help is very appreciated