FAIRMol

OHD_TbNat_148

Pose ID 12968 Compound 4256 Pose 89

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_TbNat_148
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
55.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 1.00
Burial
42%
Hydrophobic fit
85%
Reason: strain 55.5 kcal/mol
strain ΔE 55.5 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 41% of hydrophobic surface appears solvent-exposed (19/46 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.375 kcal/mol/HA) ✓ Good fit quality (FQ -4.18) ✓ Strong H-bond network (8 bonds) ✓ Good burial (42% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Extreme strain energy (55.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (31)
Score
-20.235
kcal/mol
LE
-0.375
kcal/mol/HA
Fit Quality
-4.18
FQ (Leeson)
HAC
54
heavy atoms
MW
727
Da
LogP
7.59
cLogP
Strain ΔE
55.5 kcal/mol
SASA buried
42%
Lipo contact
85% BSA apolar/total
SASA unbound
1075 Ų
Apolar buried
379 Ų

Interaction summary

HB 8 HY 17 PI 1 CLASH 3 ⚠ Exposure 41%
⚠️Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (19/46 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 46 Buried (contacted) 27 Exposed 19 LogP 7.59 H-bonds 8
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank5.013Score-20.235
Inter norm-0.358Intra norm-0.035
Top1000noExcludedno
Contacts11H-bonds8
Artifact reasongeometry warning; 31 clashes; 1 protein clash; high strain Δ 55.5
Residues
ASN402 GLU467 ILE403 LEU399 MET400 PHE396 PRO398 SER394 SER470 THR397 THR463

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

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
Jaccard0.73RMSD-
HB strict2Strict recall1.00
HB same residue+role1HB role recall1.00
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
55 3.3497979919415495 -0.464673 -26.1912 3 17 0 0.00 0.00 - no Open
53 3.3758863606086744 -0.464402 -25.8528 4 17 0 0.00 0.00 - no Open
54 3.577924600809405 -0.451894 -28.7976 3 17 0 0.00 0.00 - no Open
87 4.13827499297359 -0.389581 -24.1811 5 12 6 0.75 0.00 - no Open
56 4.18770120335156 -0.462654 -28.0377 3 17 0 0.00 0.00 - no Open
52 4.322987441457952 -0.456955 -29.3071 3 16 0 0.00 0.00 - no Open
74 4.64585637414439 -0.460571 -29.366 4 20 0 0.00 0.00 - no Open
89 5.0128806381886335 -0.357608 -20.2348 8 11 8 1.00 1.00 - no Current
72 5.3307022059735445 -0.507201 -27.1817 4 21 0 0.00 0.00 - no Open
91 5.437408225175003 -0.441797 -29.9598 7 15 0 0.00 0.00 - no Open
92 5.444837849737617 -0.444097 -28.2973 7 17 0 0.00 0.00 - no Open
73 5.678919712128663 -0.491703 -25.9507 2 20 0 0.00 0.00 - no Open
75 5.700971264321272 -0.478973 -28.9123 3 19 0 0.00 0.00 - no Open
76 5.778532105396608 -0.481828 -25.7334 2 19 0 0.00 0.00 - no Open
88 5.871724657289681 -0.39485 -22.2877 5 10 6 0.75 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 -20.235kcal/mol
Ligand efficiency (LE) -0.3747kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.182
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 54HA

Physicochemical properties
Molecular weight 726.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 7.59
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 55.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 243.28kcal/mol
Minimised FF energy 187.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 1074.8Ų
Total solvent-accessible surface area of free ligand
BSA total 447.1Ų
Buried surface area upon binding
BSA apolar 379.4Ų
Hydrophobic contacts buried
BSA polar 67.7Ų
Polar contacts buried
Fraction buried 41.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3534.5Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1540.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)