HighFold-MeD2, an enhancement of the open-source Boltz-2 structure-prediction model, handles cyclic peptides containing backbone N-methylated and d-amino acids, the modifications that drive cyclic-peptide drug-class metabolic stability and oral bioavailability. The model uses Chemical Component Dictionary representations rather than hard-coded non-canonical amino acid entries, making it extensible without retraining. It outperforms HighFold-MeD, AlphaFold3, and Boltz-2 baseline on cyclic-peptide structure prediction.