FAIRMol

Z56778002

Pose ID 13292 Compound 4677 Pose 413

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 Z56778002
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 medium Native strong SASA done
Strain ΔE
29.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 1.00
Burial
62%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.523 kcal/mol/HA) ✓ Good fit quality (FQ -5.40) ✓ Good H-bonds (4 bonds) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (29.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-19.892
kcal/mol
LE
-0.523
kcal/mol/HA
Fit Quality
-5.40
FQ (Leeson)
HAC
38
heavy atoms
MW
562
Da
LogP
3.55
cLogP
Strain ΔE
29.4 kcal/mol
SASA buried
62%
Lipo contact
80% BSA apolar/total
SASA unbound
840 Ų
Apolar buried
413 Ų

Interaction summary

HB 4 HY 17 PI 2 CLASH 3

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 rank2.981Score-19.892
Inter norm-0.526Intra norm0.002
Top1000noExcludedno
Contacts15H-bonds4
Artifact reasongeometry warning; 11 clashes; 1 protein clash; moderate strain Δ 29.4
Residues
GLU466 GLU467 HIS461 LEU399 MET393 MET400 MET471 PHE396 PRO398 PRO462 SER394 SER395 SER470 SER475 THR463

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
Jaccard0.35RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
449 2.7946875374172264 -0.63601 -18.9238 8 20 0 0.00 0.00 - no Open
413 2.9810047788499694 -0.525751 -19.8922 4 15 6 0.75 1.00 - no Current
483 4.175862271338297 -0.625381 -18.0133 5 15 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 -19.892kcal/mol
Ligand efficiency (LE) -0.5235kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.397
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 38HA

Physicochemical properties
Molecular weight 561.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.55
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -16.56kcal/mol
Minimised FF energy -45.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 840.2Ų
Total solvent-accessible surface area of free ligand
BSA total 518.3Ų
Buried surface area upon binding
BSA apolar 413.0Ų
Hydrophobic contacts buried
BSA polar 105.3Ų
Polar contacts buried
Fraction buried 61.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3234.2Ų
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 1487.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)