FAIRMol

OHD_TB2020_32

Pose ID 12235 Compound 1604 Pose 34

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
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand OHD_TB2020_32
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
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
24.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.26, Jaccard 0.17, H-bond role recall 0.20
Burial
91%
Hydrophobic fit
90%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.981 kcal/mol/HA) ✓ Good fit quality (FQ -9.36) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ High strain energy (24.2 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Internal clashes (9)
Score
-28.442
kcal/mol
LE
-0.981
kcal/mol/HA
Fit Quality
-9.36
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
4.59
cLogP
Strain ΔE
24.2 kcal/mol
SASA buried
91%
Lipo contact
90% BSA apolar/total
SASA unbound
666 Ų
Apolar buried
547 Ų

Interaction summary

HB 7 HY 23 PI 1 CLASH 5

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 rank1.429Score-28.442
Inter norm-1.075Intra norm0.094
Top1000noExcludedno
Contacts20H-bonds7
Artifact reasongeometry warning; 9 clashes; 9 protein contact clashes; moderate strain Δ 24.2
Residues
ARG287 ASP327 CYS52 CYS57 GLU202 GLY56 ILE199 LEU334 LYS60 LYS61 NDP800 PHE182 PHE203 PHE367 PRO336 SER14 SER178 THR335 THR51 VAL55

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 overlap7Native recall0.26
Jaccard0.17RMSD-
HB strict1Strict recall0.08
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.25

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
30 0.061844617147083565 -1.00649 -28.4867 1 12 0 0.00 0.00 - no Open
53 0.3426622328668827 -1.16149 -31.6116 3 18 0 0.00 0.00 - no Open
34 1.4290823205317824 -1.0748 -28.4422 7 20 7 0.26 0.20 - 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 -28.442kcal/mol
Ligand efficiency (LE) -0.9808kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.362
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 434.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.59
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -1.52kcal/mol
Minimised FF energy -25.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 666.3Ų
Total solvent-accessible surface area of free ligand
BSA total 606.1Ų
Buried surface area upon binding
BSA apolar 546.7Ų
Hydrophobic contacts buried
BSA polar 59.5Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3200.2Ų
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 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1468.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)