Some Hbonds not detected while ChimeraX detects them

[CLG68]

Hi

PLIP does not detect all the Hbonds, see the attached complex and screenshots from ChimeraX

PLIP should report 2 Hbond between the ligand and Asp189 but it does not neither using CLI nor from the server: https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index

Positives-Cmpd8_HA45-15_complex-minimized-hydrated.zip

Also, your tool does not report metal-ion interactions as it seems to only detect bonds with the receptor. Have a look at the complex I uploaded, this complex shows:

from my analysis tool:
Ligand as LEWIS BASE to CA333(B) via O1x(S:4810) (Metal-Coordination) (Strong): Dist(M-D)=2.55A

This is a significant interaction... I think it should also be reported by your tool.

[CLG68]

As PLIP and ChimeraX did not see the same thing, I had ChatGPT analyze the pdb file.

from ChatGPT:

What PLIP actually outputs (server XML):

In your uploaded report.xml, PLIP reports only 2 H-bonds:

GLU100(A) (ligand as donor)

SER188(A) (ligand as donor)

There is no hydrogen bond entry at all for ASP189(A) in the <hydrogen_bonds> section.

But ChimeraX is not hallucinating — the geometry really looks like an H-bond

I checked the actual coordinates in your PDB:

📌 ASP189(A) has OD1 / OD2 very close to ligand N2x (serial 4797):

N2x → ASP189 OD2: 2.68 Å

N2x → ASP189 OD1: 2.86 Å

And since your ligand has explicit hydrogens, we can even compute the real H-bond geometry:

✅ H15x (on N2x) → ASP189 OD2

H-A = 1.79 Å

Angle(D-H-A) = 141.4°

D-A = 2.68 Å

✅ H15x (on N2x) → ASP189 OD1

H-A = 1.94 Å

Angle = 147.2°

D-A = 2.86 Å

These are absolutely “legit” hydrogen-bond geometries.