Didn’t they take any tax withholding out of the IRA withdrawal? The 1040ES is to make an Estimated payment, it’s not the actual tax.
You still have to enter the whole gross amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding and estimated payments are subtracted from the total tax to figure your refund or tax due. The Gross amount shows up on 1040 line 4a or 5a and the taxable amount on 4b/5b. You will get credit for the withholding on 1040 line 25b.
