FAIRMol

Z56902329

Pose ID 13277 Compound 1435 Pose 398

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 Z56902329
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 1.00
Burial
59%
Hydrophobic fit
80%
Reason: strain 43.3 kcal/mol
strain ΔE 43.3 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.663 kcal/mol/HA) ✓ Good fit quality (FQ -6.11) ✓ Strong H-bond network (8 bonds) ✓ Good burial (59% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (43.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-17.251
kcal/mol
LE
-0.663
kcal/mol/HA
Fit Quality
-6.11
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Strain ΔE
43.3 kcal/mol
SASA buried
59%
Lipo contact
80% BSA apolar/total
SASA unbound
602 Ų
Apolar buried
282 Ų

Interaction summary

HB 8 HY 17 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 rank2.061Score-17.251
Inter norm-0.798Intra norm0.135
Top1000noExcludedno
Contacts11H-bonds8
Artifact reasongeometry warning; 10 clashes; 1 protein clash; high strain Δ 43.2
Residues
ASN402 GLU466 GLU467 LEU399 PHE396 PRO398 PRO462 SER394 SER464 THR397 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 overlap7Native recall0.88
Jaccard0.58RMSD-
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
336 0.10214502245811838 -1.26749 -33.2096 7 13 0 0.00 0.00 - no Open
398 2.060629453322421 -0.798133 -17.2509 8 11 7 0.88 1.00 - no Current
419 4.090345340807407 -1.05369 -22.2147 10 19 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 -17.251kcal/mol
Ligand efficiency (LE) -0.6635kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.113
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.98
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.39kcal/mol
Minimised FF energy 55.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 602.4Ų
Total solvent-accessible surface area of free ligand
BSA total 354.2Ų
Buried surface area upon binding
BSA apolar 281.8Ų
Hydrophobic contacts buried
BSA polar 72.4Ų
Polar contacts buried
Fraction buried 58.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3024.6Ų
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 1536.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)