Error while trying to convert 2d structure to 3d using gfn-ff

[Gvein]

Describe the bug Hi, I encountered a problem when trying to use gfn-ff to convert a two-dimensional molecular structure into 3D. For some reason, xtb is unable to read the connectivity information of atoms from the file. The molecule file is valid and opens with other programs (ketcher, marvin sketch, ...). I am attaching the molecule file and xtb output to the email.Different file formats cause xtb to behave differently. When using the .mol format, the program crashes with an error, but if the same structure is converted to .sdf, the program runs and optimization results in all atoms flying apart at huge distances from each other. Could this be a bug, or am I preparing the data incorrectly for processing?

To Reproduce Steps to reproduce the behaviour: xtb C(C)(P(S)(=S)C(C)CCCCCC)CCCCCC_ketcher.sdf --gfn 2 --sp mol_file.txt

Output files xtb_output_mol.txt xtb_output_sdf.txt

All calculations were carried out on laptop with Arch Linux using xtb 6.7.0

Expected behaviour Valid transformation of 2D coords to 3D

[mcbennet]

Attaching another example using a .sdf that hits the reported issue.

Command line invocation: xtb test.sdf &> test.log

Input SDF:
test.sdf.txt

Output XYZ: out.xyz.txt