FAIRMol

OHD_TB2021_63

Pose ID 10907 Compound 565 Pose 64

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 OHD_TB2021_63
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
39.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.27, H-bond role recall 0.00
Burial
75%
Hydrophobic fit
93%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.467 kcal/mol/HA) ✓ Good fit quality (FQ -4.78) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ Very high strain energy (39.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (20)
Score
-17.283
kcal/mol
LE
-0.467
kcal/mol/HA
Fit Quality
-4.78
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
3.06
cLogP
Strain ΔE
39.1 kcal/mol
SASA buried
75%
Lipo contact
93% BSA apolar/total
SASA unbound
868 Ų
Apolar buried
600 Ų

Interaction summary

HB 7 HY 24 PI 1 CLASH 1
Final rank5.550Score-17.283
Inter norm-0.647Intra norm0.180
Top1000noExcludedno
Contacts21H-bonds7
Artifact reasongeometry warning; 20 clashes; 3 protein clashes; high strain Δ 38.7
Residues
ALA284 ALA363 ARG287 ARG331 ASP330 CYS375 GLY197 GLY229 GLY286 GLY376 HIS359 HIS428 ILE199 ILE378 LEU332 MET333 PHE198 SER200 SER364 THR374 VAL362

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 overlap7Native recall0.58
Jaccard0.27RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
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
72 3.32829075269889 -0.710959 -18.7974 6 23 0 0.00 0.00 - no Open
65 4.892844926649685 -0.908225 -23.8089 10 17 0 0.00 0.00 - no Open
64 5.549861096531534 -0.64742 -17.2834 7 21 7 0.58 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 -17.283kcal/mol
Ligand efficiency (LE) -0.4671kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.782
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 37HA

Physicochemical properties
Molecular weight 494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.06
Lipinski: ≤ 5
Rotatable bonds 12

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 90.11kcal/mol
Minimised FF energy 51.01kcal/mol

SASA & burial

✓ computed
SASA (unbound) 867.5Ų
Total solvent-accessible surface area of free ligand
BSA total 646.9Ų
Buried surface area upon binding
BSA apolar 599.7Ų
Hydrophobic contacts buried
BSA polar 47.2Ų
Polar contacts buried
Fraction buried 74.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6747.9Ų
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 2106.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)