covalent bond violation in predicted RNA structures

[sahakyanhk]

I noticed a problem with phosphodiester bonds in artificial protein-RNA structures when the RNA forms a hairpin.

Here is the structure predicted with esmfold2-2026-05 for:

protein
YNQHRRLQDQLN
rna
GAGACGACCGGUCGUUGC

But then, I noticed that this is a general problem for structures with strong complementarity in the hairpin loops; if you predict any sequence with a GCGC or GGCC in the loop, the phosphodiester bond will be broken.

e.g., here is GCGCGCGCGCGCGCGCGCGC

Interestingly, that AUAUAUAUAUAUAUAUAUAU is fine, but if there are GC pairs in the loop (i.e. AUAUAUAUGCGCAUAUAUAU ), it will cause the same problem