FAIRMol

Z45290023

Pose ID 13321 Compound 3838 Pose 442

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 Z45290023
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
22.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.70, H-bond role recall 0.00
Burial
50%
Hydrophobic fit
67%
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 (-0.827 kcal/mol/HA) ✓ Good fit quality (FQ -7.42) ✓ Good H-bonds (4 bonds) ✓ Good burial (50% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (22.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-19.857
kcal/mol
LE
-0.827
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
24
heavy atoms
MW
359
Da
LogP
3.03
cLogP
Strain ΔE
22.4 kcal/mol
SASA buried
50%
Lipo contact
67% BSA apolar/total
SASA unbound
587 Ų
Apolar buried
199 Ų

Interaction summary

HB 4 HY 13 PI 1 CLASH 2
Final rank1.990Score-19.857
Inter norm-0.820Intra norm-0.008
Top1000noExcludedno
Contacts9H-bonds4
Artifact reasongeometry warning; 8 clashes; 1 protein clash; moderate strain Δ 22.1
Residues
ASN402 GLU467 LEU399 LYS410 PHE396 PRO398 SER394 SER395 THR397

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 overlap7Native recall0.88
Jaccard0.70RMSD-
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
416 0.7977187698621058 -1.25698 -29.8779 11 15 0 0.00 0.00 - no Open
442 1.9904283981561657 -0.819566 -19.857 4 9 7 0.88 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 -19.857kcal/mol
Ligand efficiency (LE) -0.8274kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.415
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 359.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.03
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -44.46kcal/mol
Minimised FF energy -66.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 586.5Ų
Total solvent-accessible surface area of free ligand
BSA total 295.9Ų
Buried surface area upon binding
BSA apolar 199.3Ų
Hydrophobic contacts buried
BSA polar 96.6Ų
Polar contacts buried
Fraction buried 50.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2982.1Ų
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 1502.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)