FAIRMol

KB_chagas_16

Pose ID 13049 Compound 2192 Pose 170

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 KB_chagas_16
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
20.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 1.00
Burial
57%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.649 kcal/mol/HA) ✓ Good fit quality (FQ -5.90) ✓ Good H-bonds (5 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (20.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-16.235
kcal/mol
LE
-0.649
kcal/mol/HA
Fit Quality
-5.90
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
1.35
cLogP
Strain ΔE
20.0 kcal/mol
SASA buried
57%
Lipo contact
82% BSA apolar/total
SASA unbound
596 Ų
Apolar buried
279 Ų

Interaction summary

HB 5 HY 10 PI 1 CLASH 2
Final rank3.992Score-16.235
Inter norm-0.760Intra norm0.110
Top1000noExcludedno
Contacts10H-bonds5
Artifact reasongeometry warning; 14 clashes; 2 protein clashes
Residues
ASN402 GLU466 GLU467 LEU399 MET400 PHE396 PRO398 SER464 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 overlap6Native recall0.75
Jaccard0.50RMSD-
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
112 2.6746012614280077 -1.18978 -22.4905 7 19 0 0.00 0.00 - no Open
148 3.4341378847043953 -0.931263 -22.6396 7 14 0 0.00 0.00 - no Open
170 3.991942354883419 -0.759639 -16.2355 5 10 6 0.75 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 -16.235kcal/mol
Ligand efficiency (LE) -0.6494kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.904
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.35
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -133.80kcal/mol
Minimised FF energy -153.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 596.0Ų
Total solvent-accessible surface area of free ligand
BSA total 338.3Ų
Buried surface area upon binding
BSA apolar 278.9Ų
Hydrophobic contacts buried
BSA polar 59.5Ų
Polar contacts buried
Fraction buried 56.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3051.4Ų
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 1528.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)