you can request first time abatement
see this link
write to address on notice requesting first time abatement. sign and date include notice and send by method where you get proof of delivery. you could point out that you weren't required to file it
from IRS 1065 instructions
Except as provided below, every domestic
partnership must file Form 1065, unless it
neither receives income nor incurs any
expenditures treated as deductions or
credits for federal income tax purposes.
Entities formed as LLCs that are
classified as partnerships for federal income
tax purposes have the same filing
requirements as domestic partnerships.
The IRS messed up the last couple of years due to the change in the filing deadline for form 1065 & 1120S ... on the acceptance notice of the EIN the letter clearly states the deadline for the filing as 4/15 not 3/15 ... if this is your case send a copy of the notice with a request for abatement of the penalty due to the IRS error.