Depends if you deducted it or not. If deducted then it was deducted twice, once on your W-2 form and once as an IRA.
You don't calculate the interest and penalty if you owe additional tax, the IRS bills you for it separately. Often the IRS waives the penalty and only charges interest. Put your explanation on the 1040X in the reason form amending box.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
