FAIRMol

Z31703705

Pose ID 10642 Compound 4085 Pose 477

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand Z31703705
PDB6RB5↗

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 mixed SASA done
Strain ΔE
34.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.24
Burial
59%
Hydrophobic fit
75%
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 (-0.854 kcal/mol/HA) ✓ Good fit quality (FQ -8.15) ✓ Good H-bonds (5 bonds) ✓ Good burial (59% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (34.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-24.769
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-8.15
FQ (Leeson)
HAC
29
heavy atoms
MW
487
Da
LogP
5.80
cLogP
Strain ΔE
34.9 kcal/mol
SASA buried
59%
Lipo contact
75% BSA apolar/total
SASA unbound
697 Ų
Apolar buried
305 Ų

Interaction summary

HB 5 HY 9 PI 0 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank3.744Score-24.769
Inter norm-0.821Intra norm-0.037
Top1000noExcludedno
Contacts9H-bonds5
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; high strain Δ 34.9
Residues
ALA209 ALA90 ASN91 GLY214 GLY215 LYS211 LYS89 PRO212 PRO213

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap4Native recall0.33
Jaccard0.24RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT16Atoms7551
Residues493Chains1
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:276; 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
401 0.7741397286888331 -0.849597 -21.1703 3 18 0 0.00 - - no Open
411 1.4911761889571216 -0.645119 -19.8697 3 11 0 0.00 - - no Open
477 3.7439465334665742 -0.820888 -24.7691 5 9 4 0.33 - - 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 -24.769kcal/mol
Ligand efficiency (LE) -0.8541kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.153
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 487.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.80
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 60.53kcal/mol
Minimised FF energy 25.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 696.7Ų
Total solvent-accessible surface area of free ligand
BSA total 408.7Ų
Buried surface area upon binding
BSA apolar 305.3Ų
Hydrophobic contacts buried
BSA polar 103.3Ų
Polar contacts buried
Fraction buried 58.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3064.8Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1575.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)