FAIRMol

Z49891479

Pose ID 11332 Compound 818 Pose 489

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 Z49891479
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 mixed SASA done
Strain ΔE
25.5 kcal/mol
Protein clashes
0
Internal clashes
6
Native overlap
contact recall 0.33, Jaccard 0.20, H-bond role recall 0.00
Burial
77%
Hydrophobic fit
73%
Reason: 6 internal clashes
6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.863 kcal/mol/HA) ✓ Good fit quality (FQ -7.73) ✓ Good H-bonds (3 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ High strain energy (25.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-20.704
kcal/mol
LE
-0.863
kcal/mol/HA
Fit Quality
-7.73
FQ (Leeson)
HAC
24
heavy atoms
MW
340
Da
LogP
3.34
cLogP
Final rank
1.3936
rank score
Inter norm
-0.999
normalised
Contacts
12
H-bonds 3
Strain ΔE
25.5 kcal/mol
SASA buried
77%
Lipo contact
73% BSA apolar/total
SASA unbound
581 Ų
Apolar buried
326 Ų

Interaction summary

HBA 3 HY 7 PI 1 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
No clash · clashes detected for this pose.

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 overlap4Native recall0.33
Jaccard0.20RMSD-
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
459 0.9834178066983842 -1.01619 -22.8206 8 15 0 0.00 0.00 - no Open
489 1.3935518030020047 -0.99865 -20.7043 3 12 4 0.33 0.00 - no Current
494 1.654975662962992 -1.07605 -28.4398 4 15 0 0.00 0.00 - no Open
450 1.8221991932961779 -0.948948 -19.4208 7 12 0 0.00 0.00 - no Open
432 2.0626620653116463 -1.06385 -22.0827 10 14 0 0.00 0.00 - no Open
415 2.2651134184818567 -1.3172 -31.1352 5 15 0 0.00 0.00 - no Open
515 2.8696934123764937 -0.963412 -19.4317 4 10 0 0.00 0.00 - no Open
406 3.633375166152976 -1.19736 -29.6559 6 14 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 -20.704kcal/mol
Ligand efficiency (LE) -0.8627kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.731
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.34
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 85.64kcal/mol
Minimised FF energy 60.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 581.4Ų
Total solvent-accessible surface area of free ligand
BSA total 448.1Ų
Buried surface area upon binding
BSA apolar 326.2Ų
Hydrophobic contacts buried
BSA polar 122.0Ų
Polar contacts buried
Fraction buried 77.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6420.5Ų
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 2080.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)