Are you using the Online software or the CD/desktop software? Please see this thread where several experts discuss how to do what you want to do. The first suggestion is to take the missed RMD immediately so that you can mention that in the waiver request. Now that the IRS is not eager to assess the 50% penalty if you provide any sort of halfway decent explanation (Heaven knows that the last couple of years have provide a sackful of reasons).
Then - if your administrator is quick - you can maybe get the 1099-R online (not wait for the mail) and enter the info into TurboTax. I mention this because I don't think you can generate a stand-alone 5329 in the Online product without a 1099-R (but read that thread closely). And I don't think that a 1099-R with zeros will do what you want, either.
So read the thread and see if you have any questions.
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