FAIRMol

Z46078134

Pose ID 12814 Compound 3201 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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand Z46078134
PDB2WOV↗

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
28.3 kcal/mol
Protein clashes
0
Internal clashes
13
Native overlap
contact recall 0.30, Jaccard 0.20, H-bond role recall 0.00
Burial
92%
Hydrophobic fit
83%
Reason: 13 internal clashes
13 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.264 kcal/mol/HA) ✓ Good fit quality (FQ -12.06) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (28.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-36.655
kcal/mol
LE
-1.264
kcal/mol/HA
Fit Quality
-12.06
FQ (Leeson)
HAC
29
heavy atoms
MW
417
Da
LogP
6.21
cLogP
Final rank
1.3510
rank score
Inter norm
-1.243
normalised
Contacts
22
H-bonds 2
Strain ΔE
28.3 kcal/mol
SASA buried
92%
Lipo contact
83% BSA apolar/total
SASA unbound
669 Ų
Apolar buried
516 Ų

Interaction summary

HBA 1 PC 1 HY 10 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap8Native recall0.30
Jaccard0.20RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
C:NDP800

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
619 1.0357649891295575 -0.712271 -20.5399 2 9 0 0.00 0.00 - no Open
598 1.1609293363911366 -0.916148 -28.6471 4 14 0 0.00 0.00 - no Open
613 1.3510130234537063 -1.24287 -36.6547 2 22 8 0.30 0.00 - no Current
604 3.739881015500972 -0.895706 -25.0102 4 11 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 -36.655kcal/mol
Ligand efficiency (LE) -1.2640kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.065
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.21
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 106.00kcal/mol
Minimised FF energy 77.69kcal/mol

SASA & burial

✓ computed
SASA (unbound) 668.9Ų
Total solvent-accessible surface area of free ligand
BSA total 618.3Ų
Buried surface area upon binding
BSA apolar 515.9Ų
Hydrophobic contacts buried
BSA polar 102.4Ų
Polar contacts buried
Fraction buried 92.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3145.1Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1471.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)