Program says the charitable gift annuity code does not usually apply to an IRA.

Correct.  Code F is for distributions made from a Charitable Gift Annuity, not from an IRA.  An IRA is not a Charitable Gift Annuity; a Charitable Gift  Annuity is something entirely different.  If a distribution truly was paid to you from a Charitable Gift Annuity, the Form 1099-R from the payer will have code F in box 7 and the IRA/SEP/SIMPLE not be marked.

If you made a Qualified Charitable Distribution form an IRA, enter the Form 1099-R exactly as received and in the questions that follow indicate the amount that you had transferred to charity.  Note that a QCD can only be made if the one for whom the IRA is maintained is over age 70½ at the time of the distribution.  If you were under age 70½ you'll need to report the charitable contribution on Schedule A.