FAIRMol

Z1213651839

Pose ID 11453 Compound 536 Pose 610

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 Z1213651839
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
34.5 kcal/mol
Protein clashes
10
Internal clashes
11
Native overlap
contact recall 0.83, Jaccard 0.43, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
86%
Reason: 10 protein-contact clashes, 11 internal clashes
10 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.570 kcal/mol/HA) ✓ Good fit quality (FQ -5.80) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Very high strain energy (34.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-20.531
kcal/mol
LE
-0.570
kcal/mol/HA
Fit Quality
-5.80
FQ (Leeson)
HAC
36
heavy atoms
MW
483
Da
LogP
0.88
cLogP
Final rank
3.9874
rank score
Inter norm
-0.623
normalised
Contacts
21
H-bonds 7
Strain ΔE
34.5 kcal/mol
SASA buried
81%
Lipo contact
86% BSA apolar/total
SASA unbound
790 Ų
Apolar buried
549 Ų

Interaction summary

HBA 2 HY 8 PI 4 CLASH 11

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap10Native recall0.83
Jaccard0.43RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
609 3.0641401779374218 -0.771676 -25.6514 5 16 0 0.00 0.00 - no Open
613 3.706288720740278 -0.792109 -28.0575 6 16 0 0.00 0.00 - no Open
602 3.8525293786513526 -0.867928 -28.7592 6 22 0 0.00 0.00 - no Open
610 3.987352034276114 -0.623204 -20.5309 7 21 10 0.83 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 -20.531kcal/mol
Ligand efficiency (LE) -0.5703kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.796
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 482.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.88
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -77.88kcal/mol
Minimised FF energy -112.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 789.6Ų
Total solvent-accessible surface area of free ligand
BSA total 641.2Ų
Buried surface area upon binding
BSA apolar 549.4Ų
Hydrophobic contacts buried
BSA polar 91.7Ų
Polar contacts buried
Fraction buried 81.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6682.0Ų
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 2075.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)