FAIRMol

Z18551701

Pose ID 13544 Compound 345 Pose 665

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 Z18551701
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
23.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.50, H-bond role recall 0.00
Burial
60%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.539 kcal/mol/HA) ✓ Good fit quality (FQ -5.26) ✓ Strong H-bond network (6 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (23.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-16.725
kcal/mol
LE
-0.539
kcal/mol/HA
Fit Quality
-5.26
FQ (Leeson)
HAC
31
heavy atoms
MW
498
Da
LogP
4.09
cLogP
Strain ΔE
23.4 kcal/mol
SASA buried
60%
Lipo contact
70% BSA apolar/total
SASA unbound
704 Ų
Apolar buried
297 Ų

Interaction summary

HB 6 HY 16 PI 2 CLASH 2

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
Final rank2.354Score-16.725
Inter norm-0.636Intra norm0.097
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 11 clashes; 1 protein clash; moderate strain Δ 23.4
Residues
ASN402 GLU466 GLU467 GLY459 HIS461 LEU399 PHE396 PRO398 PRO462 SER464 SER470 THR397 THR463

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 strict0Strict recall0.00
HB same residue+role0HB role recall0.00
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
660 0.5295804964357603 -0.996473 -27.6652 2 20 0 0.00 0.00 - no Open
650 1.0837521999406954 -0.860182 -25.7656 1 18 0 0.00 0.00 - no Open
647 1.1057279554427575 -0.82458 -22.7668 3 18 0 0.00 0.00 - no Open
670 1.9655946151535648 -0.997941 -23.1066 5 19 0 0.00 0.00 - no Open
641 2.067400124768355 -0.847561 -27.4139 1 19 0 0.00 0.00 - no Open
665 2.3541405331674663 -0.636352 -16.7251 6 13 7 0.88 0.00 - no Current
659 2.467759077605822 -0.750771 -19.8725 6 12 0 0.00 0.00 - no Open
671 3.368417260105743 -0.961077 -24.6186 9 19 0 0.00 0.00 - no Open
659 5.142259304440157 -0.87636 -24.9893 10 16 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 -16.725kcal/mol
Ligand efficiency (LE) -0.5395kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.256
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 498.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.09
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 25.10kcal/mol
Minimised FF energy 1.72kcal/mol

SASA & burial

✓ computed
SASA (unbound) 703.8Ų
Total solvent-accessible surface area of free ligand
BSA total 422.1Ų
Buried surface area upon binding
BSA apolar 296.7Ų
Hydrophobic contacts buried
BSA polar 125.5Ų
Polar contacts buried
Fraction buried 60.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3086.1Ų
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 1508.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)