Poses don't make physical sense

[TheLegalist]

I'm currently trying to dock a ligand with a guanidino group to a target, and the top pose doesn't make physical sense. The guanidino group's hydrogens aren't planar with respect to the rest of the moiety, and this shouldn't happen. Why is that? Did I set certain parameters incorrectly? Please advise on this issue. I'll attach a couple of screenshots of top poses to illustrate what's going on. The ligand is in cyan/light blue.

[xbarril]

Looks like the chemical description is incorrect. Can you convert the input SDF into SMILES and share?

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On 9 Mar 2026, at 15:18, TheLegalist ***@***.***> wrote: TheLegalist created an issue (CBDD/rDock#158) <#158> I'm currently trying to dock a ligand with a guanidino group to a target, and the top pose doesn't make physical sense. The guanidino group's hydrogens aren't planar with respect to the rest of the moiety, and this shouldn't happen. Why is that? Did I set certain parameters incorrectly? Please advise on this issue. I'll attach a couple of screenshots of top poses to illustrate what's going on. The ligand is in cyan/light blue. 1.png (view on web) <https://github.com/user-attachments/assets/6020399e-89c9-4331-9a25-fd1ed56b9b1d> 2.png (view on web) <https://github.com/user-attachments/assets/a1511f7f-7380-424c-87b1-27d6de152b93> — Reply to this email directly, view it on GitHub <#158>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACH7XJTJZLPBQKACM5ZIGZ34P3HCVAVCNFSM6AAAAACWL5WX3GVHI2DSMVQWIX3LMV43ASLTON2WKOZUGA2DKOBXGY4DKMI>. You are receiving this because you are subscribed to this thread.

[TheLegalist]

C(=O)(C)N[ C@H ](C(=O)N[ C@H ] (C(=O)OC)Cc1c[nH]c2ccccc12)CCCNC(=[NH2+])N

Here's the corrected one - sorry for the mistake earlier.

[xbarril]

Except for the white spaces, this second SMILES appears correct. The first one was incorrect. Please share the SD file used as input and I will check if it works on my end.

[ggutierrez-sunbright]

Hi @TheLegalist,
is there any update on this issue?
(thanks for the help on this one @xbarril)

I'll give a bit more time and after that I'll close the issue if there's no new information.

Thanks for using rdock, and regards

[TheLegalist]

Except for the white spaces, this second SMILES appears correct. The first one was incorrect. Please share the SD file used as input and I will check if it works on my end.

It seems like the issue was with the energy minimization that I did with Avogadro as opposed to an issue with rDock. I had used UFF instead of MMFF94, the latter of which resolved the issue of the guanidino geometry.