FAIRMol

OHD_Leishmania_402

Pose ID 12907 Compound 3791 Pose 28

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_Leishmania_402
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
23.8 kcal/mol
Protein clashes
0
Internal clashes
7
Native overlap
contact recall 0.62, Jaccard 0.38, H-bond role recall 0.00
Burial
51%
Hydrophobic fit
79%
Reason: 7 internal clashes
7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.681 kcal/mol/HA) ✓ Good fit quality (FQ -6.81) ✓ Good H-bonds (5 bonds) ✓ Good burial (51% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (23.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.143
kcal/mol
LE
-0.681
kcal/mol/HA
Fit Quality
-6.81
FQ (Leeson)
HAC
34
heavy atoms
MW
469
Da
LogP
6.09
cLogP
Strain ΔE
23.8 kcal/mol
SASA buried
51%
Lipo contact
79% BSA apolar/total
SASA unbound
723 Ų
Apolar buried
293 Ų

Interaction summary

HB 5 HY 14 PI 0 CLASH 0
Final rank3.862Score-23.143
Inter norm-0.602Intra norm-0.079
Top1000noExcludedno
Contacts10H-bonds5
Artifact reasongeometry warning; 7 clashes; 3 protein clashes; moderate strain Δ 23.8
Residues
ASN402 LEU399 LYS410 MET400 PHE396 PRO398 PRO462 SER395 THR397 THR463

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.38RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
26 3.5443738984448103 -0.743691 -27.3876 8 13 0 0.00 0.00 - no Open
28 3.861925915799633 -0.602062 -23.1426 5 10 5 0.62 0.00 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -23.143kcal/mol
Ligand efficiency (LE) -0.6807kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.811
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 468.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.09
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 53.19kcal/mol
Minimised FF energy 29.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 723.1Ų
Total solvent-accessible surface area of free ligand
BSA total 369.8Ų
Buried surface area upon binding
BSA apolar 292.9Ų
Hydrophobic contacts buried
BSA polar 76.9Ų
Polar contacts buried
Fraction buried 51.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3224.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1487.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)