FAIRMol

OHD_TbNat_126

Pose ID 12963 Compound 432 Pose 84

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_TbNat_126
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
27.3 kcal/mol
Protein clashes
3
Internal clashes
20
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Burial
50%
Hydrophobic fit
88%
Reason: 20 internal clashes
3 protein-contact clashes 20 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.407 kcal/mol/HA) ✓ Good fit quality (FQ -4.39) ✓ Good H-bonds (3 bonds) ✓ Good burial (50% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ High strain energy (27.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Many internal clashes (20)
Score
-18.731
kcal/mol
LE
-0.407
kcal/mol/HA
Fit Quality
-4.39
FQ (Leeson)
HAC
46
heavy atoms
MW
623
Da
LogP
4.24
cLogP
Strain ΔE
27.3 kcal/mol
SASA buried
50%
Lipo contact
88% BSA apolar/total
SASA unbound
846 Ų
Apolar buried
369 Ų

Interaction summary

HB 3 HY 13 PI 1 CLASH 0
Final rank2.332Score-18.731
Inter norm-0.415Intra norm0.008
Top1000noExcludedno
Contacts12H-bonds3
Artifact reasongeometry warning; 20 clashes; 3 protein contact clashes; moderate strain Δ 27.3
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 PHE396 PRO398 SER394 SER464 SER470 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 overlap8Native recall1.00
Jaccard0.67RMSD-
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
Native π–π recall is disabled because no explicit native π–π reference was stored.

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
88 2.107196163600904 -0.570982 -14.5556 0 18 0 0.00 0.00 - no Open
84 2.3322273296990996 -0.415063 -18.7308 3 12 8 1.00 1.00 - no Current
96 2.4902473371946754 -0.560498 -23.8982 3 20 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -18.731kcal/mol
Ligand efficiency (LE) -0.4072kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.395
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 46HA

Physicochemical properties
Molecular weight 622.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.24
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 225.30kcal/mol
Minimised FF energy 198.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 846.0Ų
Total solvent-accessible surface area of free ligand
BSA total 419.6Ų
Buried surface area upon binding
BSA apolar 368.8Ų
Hydrophobic contacts buried
BSA polar 50.8Ų
Polar contacts buried
Fraction buried 49.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 87.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3342.0Ų
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 1503.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)