FAIRMol

Z29466261

Pose ID 13551 Compound 5201 Pose 672

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 Z29466261
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
16.9 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.62, Jaccard 0.38, H-bond role recall 0.00
Burial
60%
Hydrophobic fit
85%
Reason: 9 internal clashes
9 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.631 kcal/mol/HA) ✓ Good fit quality (FQ -5.88) ✓ Good H-bonds (4 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (16.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-17.031
kcal/mol
LE
-0.631
kcal/mol/HA
Fit Quality
-5.88
FQ (Leeson)
HAC
27
heavy atoms
MW
423
Da
LogP
3.36
cLogP
Strain ΔE
16.9 kcal/mol
SASA buried
60%
Lipo contact
85% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
333 Ų

Interaction summary

HB 4 HY 17 PI 1 CLASH 0
Final rank2.084Score-17.031
Inter norm-0.724Intra norm0.091
Top1000noExcludedno
Contacts10H-bonds4
Artifact reasongeometry warning; 9 clashes; 1 protein clash
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
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
672 2.0841470065466727 -0.724412 -17.0311 4 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 -17.031kcal/mol
Ligand efficiency (LE) -0.6308kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.885
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 422.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.36
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -35.01kcal/mol
Minimised FF energy -51.95kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.7Ų
Total solvent-accessible surface area of free ligand
BSA total 393.0Ų
Buried surface area upon binding
BSA apolar 332.6Ų
Hydrophobic contacts buried
BSA polar 60.4Ų
Polar contacts buried
Fraction buried 59.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3048.5Ų
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 1510.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)