FAIRMol

GemmaOHDUnisi_41

Pose ID 13239 Compound 1416 Pose 360

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 GemmaOHDUnisi_41
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
13.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 0.00
Burial
57%
Hydrophobic fit
78%
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 (-0.644 kcal/mol/HA) ✓ Good fit quality (FQ -6.50) ✓ Good H-bonds (4 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Moderate strain (13.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (14)
Score
-22.538
kcal/mol
LE
-0.644
kcal/mol/HA
Fit Quality
-6.50
FQ (Leeson)
HAC
35
heavy atoms
MW
462
Da
LogP
6.37
cLogP
Final rank
1.9859
rank score
Inter norm
-0.606
normalised
Contacts
15
H-bonds 8
Strain ΔE
13.7 kcal/mol
SASA buried
57%
Lipo contact
78% BSA apolar/total
SASA unbound
772 Ų
Apolar buried
345 Ų

Interaction summary

HBD 1 HBA 3 HY 3 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.35RMSD-
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
360 1.9858794448475394 -0.60587 -22.5384 8 15 6 0.75 0.00 - no Current
310 2.215876786266132 -0.810312 -26.2423 7 20 0 0.00 0.00 - no Open
296 2.3735761215630813 -0.974129 -31.9318 5 22 0 0.00 0.00 - no Open
304 2.4109016880892273 -0.837854 -29.8668 7 13 0 0.00 0.00 - no Open
350 2.5106836985505296 -0.819328 -29.6374 5 17 0 0.00 0.00 - no Open
350 2.9414702362290113 -0.751309 -27.9819 5 17 0 0.00 0.00 - no Open
358 3.175808622050242 -0.595751 -15.5491 3 17 0 0.00 0.00 - no Open
421 3.3117905327030788 -0.65678 -23.4933 3 16 0 0.00 0.00 - no Open
340 3.408980607340969 -0.695149 -24.1764 7 10 0 0.00 0.00 - no Open
387 3.5593066442778185 -0.749818 -29.818 7 21 0 0.00 0.00 - no Open
384 3.6360066859245648 -0.841444 -26.102 8 16 0 0.00 0.00 - no Open
458 3.684952783737684 -0.836742 -25.2904 4 18 0 0.00 0.00 - no Open
341 4.458291848249892 -0.632747 -19.3542 9 19 0 0.00 0.00 - no Open
340 4.6006376252543095 -0.940685 -33.7094 11 24 0 0.00 0.00 - no Open
312 5.204738389636102 -0.790161 -23.6613 11 20 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 -22.538kcal/mol
Ligand efficiency (LE) -0.6440kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.495
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.37
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 95.39kcal/mol
Minimised FF energy 81.71kcal/mol

SASA & burial

✓ computed
SASA (unbound) 771.9Ų
Total solvent-accessible surface area of free ligand
BSA total 443.5Ų
Buried surface area upon binding
BSA apolar 345.2Ų
Hydrophobic contacts buried
BSA polar 98.3Ų
Polar contacts buried
Fraction buried 57.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3151.4Ų
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 1572.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)