FAIRMol

KB_Leish_81

Pose ID 13038 Compound 5016 Pose 159

DB fairmolDocking 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_Leish_81
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
13.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 0.00
Burial
53%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.722 kcal/mol/HA) ✓ Good fit quality (FQ -6.73) ✓ Strong H-bond network (7 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (13.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-19.480
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
27
heavy atoms
MW
357
Da
LogP
2.91
cLogP
Strain ΔE
13.3 kcal/mol
SASA buried
53%
Lipo contact
86% BSA apolar/total
SASA unbound
641 Ų
Apolar buried
295 Ų

Interaction summary

HB 7 HY 11 PI 1 CLASH 1

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
Final rank3.526Score-19.480
Inter norm-0.705Intra norm-0.019
Top1000noExcludedno
Contacts9H-bonds7
Artifact reasongeometry warning; 11 clashes; 2 protein clashes
Residues
ASN402 GLU467 LEU399 LYS407 LYS410 PHE396 PRO398 SER395 THR397

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
Jaccard0.55RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
114 1.2766960703478525 -1.16364 -32.1369 6 17 0 0.00 0.00 - no Open
159 3.5257496922105673 -0.704504 -19.4801 7 9 6 0.75 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 -19.480kcal/mol
Ligand efficiency (LE) -0.7215kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.731
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 357.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.91
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -12.81kcal/mol
Minimised FF energy -26.11kcal/mol

SASA & burial

✓ computed
SASA (unbound) 640.7Ų
Total solvent-accessible surface area of free ligand
BSA total 341.6Ų
Buried surface area upon binding
BSA apolar 294.6Ų
Hydrophobic contacts buried
BSA polar 47.0Ų
Polar contacts buried
Fraction buried 53.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3108.3Ų
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 1533.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)