The results ligand is different from SMILES I have entered

[MinsikBae]

I am experiencing a discrepancy between the ligand structure I expect based on my input SMILES and the 3D structure generated by Boltz. My SMILES string specifies an alkane chain (CCCCCCCN) as a linker, but the output structure has an alkene (C=C) in that linker(1 to 3 alkene generated), and the molecule forms an unexpected macrocycle.

I have already attempted the following troubleshooting steps:

Used the MMFF94 force field instead of UFF.
Modified the compute_3d_conformer function in schema.py to check for and convert unexpected double bonds to single bonds.
Verified that useRandomCoords is effectively disabled.
Checked input SMILES string
Adjust recycling_steps , sampling_steps, step_scale