Yes, if you do not have interest for box 1, you do not enter the amount from box 3 in box 1. Only enter the amount in box 3.
Box 1 is used to show taxable interest paid to you during the Calendar year. If you enter an amount from box 3 in box 1, it will be considered taxable income.
Per the IRS instructions for 1099-INT, "Box 3. Shows interest on U.S. Savings Bonds, Treasury bills, Treasury bonds, and Treasury notes. This may or may not all be taxable. See Pub. 550. This interest is exempt from state and local income taxes. This interest is not included in box 1. See the instructions above for a taxable covered security acquired at a premium."
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