Docking pose detail

Molecular metrics status: missing

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T22

L. donovani rab5a L. donovani

Ligand Z30932744

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak Metrics pending

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA pending

Strain ΔE

47.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.86, Jaccard 0.78, H-bond role recall 0.64

Burial

33%

Reason: strain 47.6 kcal/mol

strain ΔE 47.6 kcal/mol 2 protein-contact clashes 67% of hydrophobic surface is solvent-exposed (8/12 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

Interaction summary

HBD 2 HBA 10 HY 1 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 9.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	RAB5A	Contacts	21
Pose	Open native pose	HB	0
IFP residues	ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap	18	Native recall	0.86
Jaccard	0.78	RMSD	-
HB strict	9	Strict recall	0.60
HB same residue+role	7	HB role recall	0.64
HB same residue	7	HB residue recall	0.64

Protein summary

165 residues

Protein target	T22	Atoms	2561
Residues	165	Chains	1
Residue summary	LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
585	6.169459668776651	-1.44765	-29.8797	15	20	18	0.86	0.64	-	yes	Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

⚠ Not yet computed

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