FAIRMol

OHD_TB2021_76

Pose ID 12944 Compound 4107 Pose 65

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_TB2021_76
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
12.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.31, H-bond role recall 0.00
Burial
56%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes 56% of hydrophobic surface appears solvent-exposed (10/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.849 kcal/mol/HA) ✓ Good fit quality (FQ -7.49) ✓ Good H-bonds (3 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (12.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-19.522
kcal/mol
LE
-0.849
kcal/mol/HA
Fit Quality
-7.49
FQ (Leeson)
HAC
23
heavy atoms
MW
303
Da
LogP
2.51
cLogP
Final rank
2.9768
rank score
Inter norm
-0.845
normalised
Contacts
9
H-bonds 5
Strain ΔE
12.2 kcal/mol
SASA buried
56%
Lipo contact
74% BSA apolar/total
SASA unbound
551 Ų
Apolar buried
229 Ų

Interaction summary

HBA 3 HY 3 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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 overlap4Native recall0.50
Jaccard0.31RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
70 1.736716694845178 -0.948783 -22.6203 4 11 0 0.00 0.00 - no Open
65 2.976826282107063 -0.845128 -19.5223 5 9 4 0.50 0.00 - no Current
36 3.3707797679056615 -1.3162 -25.7605 6 17 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 -19.522kcal/mol
Ligand efficiency (LE) -0.8488kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.491
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 303.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.51
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 147.25kcal/mol
Minimised FF energy 135.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 550.6Ų
Total solvent-accessible surface area of free ligand
BSA total 307.6Ų
Buried surface area upon binding
BSA apolar 228.7Ų
Hydrophobic contacts buried
BSA polar 78.9Ų
Polar contacts buried
Fraction buried 55.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3007.0Ų
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 1513.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)