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If you look at the equipment summary output in the EnergyPlus results, you should see the nominal efficiency (in the "cooling coils" table) listed as the high speed COP, and the standard rated net COP (in the "DX cooling coils" table) as the lower value. From what I understand from the EngineeringReference, the standard rated net COP is calculated from the standard rating cooling capacity which adjusts the rated capacity to a specific temperature and flow fraction.
I don't think these values are actually used in your simulation, they are just outputted for your information (anyone feel free to correct me if I am wrong).
If you are concerned with complying with LEED, you should be removing your fan energy from your EER or COP before inputting it into your model. Refer to ASHRAE 90.1-2013 or later for an updated version of Appendix G which includes the equations to use.