Box 2 and 3 being empty means the plan administrator didn't calculate the earnings portion of the distribution. Somewhere on the 1099-Q is the fair market value of the account. Using that and your total basis (($4000), you have to calculate the earnings portion of the distribution. TT will do that for you, with the proper entries.
The fact that your total basis is more than the distribution does not mean the distribution is not taxable. You don't get to remove your contributions (basis) first. Every distribution is part basis and part earnings (unless the account lost money).
Q. Regarding the early withdrawal penalty would you have to file if the Gross distribution is less than $1100 too?
A. Yes. The penalty is due regardless of how small the taxable amount is. So, you have to file.
