FAIRMol

OHD_Leishmania_61

Pose ID 12882 Compound 5198 Pose 3

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_61
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
57.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.62, H-bond role recall 0.00
Burial
44%
Hydrophobic fit
87%
Reason: strain 57.4 kcal/mol
strain ΔE 57.4 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.398 kcal/mol/HA) ✓ Good fit quality (FQ -4.44) ✓ Good H-bonds (4 bonds) ✓ Good burial (44% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Extreme strain energy (57.4 kcal/mol)
Score
-21.483
kcal/mol
LE
-0.398
kcal/mol/HA
Fit Quality
-4.44
FQ (Leeson)
HAC
54
heavy atoms
MW
773
Da
LogP
7.32
cLogP
Strain ΔE
57.4 kcal/mol
SASA buried
44%
Lipo contact
87% BSA apolar/total
SASA unbound
1106 Ų
Apolar buried
426 Ų

Interaction summary

HB 4 HY 11 PI 0 CLASH 1

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
Final rank1.776Score-21.483
Inter norm-0.436Intra norm0.032
Top1000noExcludedno
Contacts13H-bonds4
Artifact reason1 protein clash; high strain Δ 52.5
Residues
ARG472 ASN402 GLU466 GLU467 LEU399 MET471 PHE396 PRO398 SER394 SER470 THR397 THR473 TYR455

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 overlap8Native recall1.00
Jaccard0.62RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
3 1.7759421737848078 -0.435684 -21.4829 4 13 8 1.00 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 -21.483kcal/mol
Ligand efficiency (LE) -0.3978kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.440
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 54HA

Physicochemical properties
Molecular weight 773.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 7.32
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 57.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 97.96kcal/mol
Minimised FF energy 40.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1106.4Ų
Total solvent-accessible surface area of free ligand
BSA total 487.7Ų
Buried surface area upon binding
BSA apolar 425.8Ų
Hydrophobic contacts buried
BSA polar 61.9Ų
Polar contacts buried
Fraction buried 44.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3533.1Ų
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 1466.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)