FAIRMol

OHD_TB2022_27

Pose ID 12947 Compound 1429 Pose 68

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_TB2022_27
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
53.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.53, H-bond role recall 1.00
Burial
56%
Hydrophobic fit
83%
Reason: strain 53.3 kcal/mol
strain ΔE 53.3 kcal/mol 1 protein-contact clashes 44% of hydrophobic surface appears solvent-exposed (11/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.547 kcal/mol/HA) ✓ Good fit quality (FQ -5.56) ✓ Strong H-bond network (6 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (53.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-19.698
kcal/mol
LE
-0.547
kcal/mol/HA
Fit Quality
-5.56
FQ (Leeson)
HAC
36
heavy atoms
MW
511
Da
LogP
-0.77
cLogP
Final rank
5.2226
rank score
Inter norm
-0.607
normalised
Contacts
15
H-bonds 10
Strain ΔE
53.3 kcal/mol
SASA buried
56%
Lipo contact
83% BSA apolar/total
SASA unbound
782 Ų
Apolar buried
363 Ų

Interaction summary

HBD 5 HBA 1 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap8Native recall1.00
Jaccard0.53RMSD-
HB strict2Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:319; 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
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
72 3.8594501751747776 -0.827056 -23.8656 4 22 0 0.00 0.00 - no Open
40 4.135873877091396 -0.880898 -31.6966 12 14 0 0.00 0.00 - no Open
57 4.246759468271501 -0.595939 -22.8076 6 16 0 0.00 0.00 - no Open
68 5.222560969371158 -0.606925 -19.6983 10 15 8 1.00 1.00 - 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 -19.698kcal/mol
Ligand efficiency (LE) -0.5472kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.561
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 510.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.77
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 53.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 32.62kcal/mol
Minimised FF energy -20.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 781.6Ų
Total solvent-accessible surface area of free ligand
BSA total 437.1Ų
Buried surface area upon binding
BSA apolar 363.2Ų
Hydrophobic contacts buried
BSA polar 74.0Ų
Polar contacts buried
Fraction buried 55.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3191.4Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1524.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)