FAIRMol

Z45901653

Pose ID 11500 Compound 12 Pose 657

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z45901653
PDB5S9T↗

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
14.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.32, H-bond role recall 0.00
Burial
75%
Hydrophobic fit
79%
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 (-0.837 kcal/mol/HA) ✓ Good fit quality (FQ -7.81) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Moderate strain (14.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-22.604
kcal/mol
LE
-0.837
kcal/mol/HA
Fit Quality
-7.81
FQ (Leeson)
HAC
27
heavy atoms
MW
489
Da
LogP
3.48
cLogP
Strain ΔE
14.0 kcal/mol
SASA buried
75%
Lipo contact
79% BSA apolar/total
SASA unbound
669 Ų
Apolar buried
395 Ų

Interaction summary

HB 2 HY 17 PI 1 CLASH 3
Final rank2.251Score-22.604
Inter norm-0.865Intra norm0.028
Top1000noExcludedno
Contacts17H-bonds2
Artifact reasongeometry warning; 11 clashes; 1 protein clash
Residues
ARG228 CYS375 GLY196 GLY197 GLY229 GLY376 HIS428 ILE378 LEU227 LEU332 LEU377 PHE198 PHE230 SER364 THR374 TYR221 VAL381

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap7Native recall0.58
Jaccard0.32RMSD-
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
633 0.2609782440549323 -0.981497 -25.4214 1 14 0 0.00 0.00 - no Open
657 2.251143140203868 -0.865442 -22.6044 2 17 7 0.58 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 -22.604kcal/mol
Ligand efficiency (LE) -0.8372kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.811
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 488.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.48
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -47.97kcal/mol
Minimised FF energy -61.96kcal/mol

SASA & burial

✓ computed
SASA (unbound) 669.0Ų
Total solvent-accessible surface area of free ligand
BSA total 501.1Ų
Buried surface area upon binding
BSA apolar 394.6Ų
Hydrophobic contacts buried
BSA polar 106.5Ų
Polar contacts buried
Fraction buried 74.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6511.7Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2101.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)