The instruction on line 55 of Form 5329 say to include the amount on line 6 of Schedule 2, not line 6 of Form 1040.
If there is no other need to include Schedule 2 in your tax return, you could probably omit Schedule 2, but for completeness you might consider downloading Schedule 2 from the IRS website, putting $0 on line 6, filling in the taxpayer name and SSN, and including it with your mailed tax return along with the Form 5329.
