FAIRMol

Z49606031

Pose ID 11456 Compound 988 Pose 613

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z49606031
PDB5S9T↗

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
26.8 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 0.67, Jaccard 0.40, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
72%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.259 kcal/mol/HA) ✓ Good fit quality (FQ -11.88) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (26.8 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (12) ✗ Many internal clashes (11)
Score
-35.251
kcal/mol
LE
-1.259
kcal/mol/HA
Fit Quality
-11.88
FQ (Leeson)
HAC
28
heavy atoms
MW
403
Da
LogP
2.61
cLogP
Strain ΔE
26.8 kcal/mol
SASA buried
83%
Lipo contact
72% BSA apolar/total
SASA unbound
623 Ų
Apolar buried
373 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 7

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 rank2.203Score-35.251
Inter norm-0.983Intra norm-0.285
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 11 clashes; 12 protein contact clashes; moderate strain Δ 26.8
Residues
ALA284 ARG228 ARG287 GLY195 GLY197 GLY229 GLY286 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER200 VAL366

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 overlap8Native recall0.67
Jaccard0.40RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
608 0.28198169869884865 -0.85723 -23.1601 3 14 0 0.00 0.00 - no Open
591 0.9259440503290726 -1.08371 -28.7108 8 13 0 0.00 0.00 - no Open
606 1.8192507548808121 -1.04528 -29.0925 3 14 0 0.00 0.00 - no Open
613 2.2033316024264695 -0.9827 -35.251 7 16 8 0.67 0.00 - no Current
620 2.654583110640994 -0.867156 -29.8358 9 12 0 0.00 0.00 - no Open
610 2.660120191338177 -0.718352 -19.3503 8 10 0 0.00 0.00 - no Open
598 3.0805438009331887 -0.909389 -29.8286 6 18 0 0.00 0.00 - no Open
612 3.2185474535416136 -1.04492 -28.0502 8 17 0 0.00 0.00 - no Open
607 3.5827660316033643 -0.811178 -22.4444 7 13 0 0.00 0.00 - no Open
590 4.255366215778278 -1.056 -34.8672 6 13 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 -35.251kcal/mol
Ligand efficiency (LE) -1.2590kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.885
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.61
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 26.67kcal/mol
Minimised FF energy -0.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 622.7Ų
Total solvent-accessible surface area of free ligand
BSA total 515.9Ų
Buried surface area upon binding
BSA apolar 372.7Ų
Hydrophobic contacts buried
BSA polar 143.2Ų
Polar contacts buried
Fraction buried 82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6479.4Ų
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 2048.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)