FAIRMol

OHD_TbNat_124

Pose ID 12962 Compound 5257 Pose 83

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_TbNat_124
PDB9IFH↗

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 high Native strong SASA done
Strain ΔE
19.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.50, H-bond role recall 1.00
Burial
56%
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 (-0.456 kcal/mol/HA) ✓ Good fit quality (FQ -4.84) ✓ Good H-bonds (3 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ Moderate strain (19.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-19.602
kcal/mol
LE
-0.456
kcal/mol/HA
Fit Quality
-4.84
FQ (Leeson)
HAC
43
heavy atoms
MW
581
Da
LogP
4.02
cLogP
Final rank
3.2850
rank score
Inter norm
-0.460
normalised
Contacts
13
H-bonds 5
Strain ΔE
19.1 kcal/mol
SASA buried
56%
Lipo contact
93% BSA apolar/total
SASA unbound
799 Ų
Apolar buried
414 Ų

Interaction summary

HBD 1 HBA 2 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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 overlap7Native recall0.88
Jaccard0.50RMSD-
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
83 3.285018139243498 -0.460284 -19.602 5 13 7 0.88 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 -19.602kcal/mol
Ligand efficiency (LE) -0.4559kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.845
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 43HA

Physicochemical properties
Molecular weight 580.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.02
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 210.47kcal/mol
Minimised FF energy 191.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 799.4Ų
Total solvent-accessible surface area of free ligand
BSA total 445.7Ų
Buried surface area upon binding
BSA apolar 413.6Ų
Hydrophobic contacts buried
BSA polar 32.2Ų
Polar contacts buried
Fraction buried 55.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3326.8Ų
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 1495.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)