FAIRMol

OHD_TB2020_3

Pose ID 12928 Compound 545 Pose 49

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_TB2020_3
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
52.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.38, H-bond role recall 1.00
Burial
52%
Hydrophobic fit
83%
Reason: strain 52.2 kcal/mol
strain ΔE 52.2 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.357 kcal/mol/HA) ✓ Good fit quality (FQ -3.87) ✓ Good H-bonds (5 bonds) ✓ Good burial (52% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (52.2 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (15)
Score
-16.785
kcal/mol
LE
-0.357
kcal/mol/HA
Fit Quality
-3.87
FQ (Leeson)
HAC
47
heavy atoms
MW
651
Da
LogP
4.10
cLogP
Strain ΔE
52.2 kcal/mol
SASA buried
52%
Lipo contact
83% BSA apolar/total
SASA unbound
866 Ų
Apolar buried
376 Ų

Interaction summary

HB 5 HY 23 PI 2 CLASH 1
Final rank2.071Score-16.785
Inter norm-0.405Intra norm0.048
Top1000noExcludedno
Contacts14H-bonds5
Artifact reasongeometry warning; 15 clashes; 4 protein contact clashes; high strain Δ 52.2
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 MET393 MET400 PHE396 PRO398 PRO462 SER394 SER395 SER464 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 overlap6Native recall0.75
Jaccard0.38RMSD-
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
49 2.070719971733801 -0.404834 -16.7854 5 14 6 0.75 1.00 - no Current
61 3.1433524629369596 -0.598467 -28.4911 2 20 0 0.00 0.00 - no Open
51 3.768285019266341 -0.632942 -29.3174 3 19 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 -16.785kcal/mol
Ligand efficiency (LE) -0.3571kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -3.873
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 47HA

Physicochemical properties
Molecular weight 650.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.10
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 52.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 186.47kcal/mol
Minimised FF energy 134.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 866.0Ų
Total solvent-accessible surface area of free ligand
BSA total 454.3Ų
Buried surface area upon binding
BSA apolar 375.6Ų
Hydrophobic contacts buried
BSA polar 78.6Ų
Polar contacts buried
Fraction buried 52.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3270.2Ų
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 1567.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)