FAIRMol

Z199054106

Pose ID 11490 Compound 4084 Pose 647

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 Z199054106
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
40.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.38, H-bond role recall 1.00
Burial
83%
Hydrophobic fit
93%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.608 kcal/mol/HA) ✓ Good fit quality (FQ -5.87) ✓ Good H-bonds (4 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ Extreme strain energy (40.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (11)
Score
-18.243
kcal/mol
LE
-0.608
kcal/mol/HA
Fit Quality
-5.87
FQ (Leeson)
HAC
30
heavy atoms
MW
393
Da
LogP
6.58
cLogP
Strain ΔE
40.1 kcal/mol
SASA buried
83%
Lipo contact
93% BSA apolar/total
SASA unbound
685 Ų
Apolar buried
533 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 2
Final rank1.534Score-18.243
Inter norm-0.777Intra norm0.168
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 11 clashes; 6 protein contact clashes; high strain Δ 40.1
Residues
ALA284 ALA365 ARG287 ARG331 ASP330 FAD501 GLY197 GLY286 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 PHE230 SER200 VAL366

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 overlap8Native recall0.67
Jaccard0.38RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
631 0.7641378312650706 -0.728918 -20.0211 3 12 0 0.00 0.00 - no Open
647 1.5343132795776104 -0.776554 -18.2427 4 17 8 0.67 1.00 - no Current
644 2.319025147822157 -1.06752 -30.0889 4 20 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 -18.243kcal/mol
Ligand efficiency (LE) -0.6081kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.866
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 392.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.58
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 108.00kcal/mol
Minimised FF energy 67.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 685.2Ų
Total solvent-accessible surface area of free ligand
BSA total 570.4Ų
Buried surface area upon binding
BSA apolar 532.8Ų
Hydrophobic contacts buried
BSA polar 37.6Ų
Polar contacts buried
Fraction buried 83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 93.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6608.2Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2089.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)