FAIRMol

OHD_Leishmania_143

Pose ID 12894 Compound 3409 Pose 15

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_143
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
40.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.33, H-bond role recall 1.00
Burial
70%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.829 kcal/mol/HA) ✓ Good fit quality (FQ -7.20) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Extreme strain energy (40.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-18.240
kcal/mol
LE
-0.829
kcal/mol/HA
Fit Quality
-7.20
FQ (Leeson)
HAC
22
heavy atoms
MW
302
Da
LogP
-0.56
cLogP
Strain ΔE
40.7 kcal/mol
SASA buried
70%
Lipo contact
82% BSA apolar/total
SASA unbound
538 Ų
Apolar buried
307 Ų

Interaction summary

HB 6 HY 2 PI 0 CLASH 3
Final rank3.990Score-18.240
Inter norm-0.869Intra norm0.040
Top1000noExcludedno
Contacts12H-bonds6
Artifact reasongeometry warning; 8 clashes; 3 protein clashes; high strain Δ 40.7
Residues
CYS469 GLU466 GLU467 GLY459 HIS461 LEU399 PHE396 PRO398 PRO462 SER464 SER470 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
Jaccard0.33RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
2 2.3539715887632098 -1.10839 -24.1552 12 15 0 0.00 0.00 - no Open
15 3.9901505307463285 -0.869231 -18.2403 6 12 5 0.62 1.00 - 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 -18.240kcal/mol
Ligand efficiency (LE) -0.8291kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.198
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 302.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.56
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 26.97kcal/mol
Minimised FF energy -13.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 537.8Ų
Total solvent-accessible surface area of free ligand
BSA total 374.1Ų
Buried surface area upon binding
BSA apolar 306.9Ų
Hydrophobic contacts buried
BSA polar 67.2Ų
Polar contacts buried
Fraction buried 69.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3030.9Ų
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 1476.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)