FAIRMol

Z56787095

Pose ID 10674 Compound 820 Pose 509

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand Z56787095
PDB6RB5↗

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
66.0 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.58, Jaccard 0.39
Burial
61%
Hydrophobic fit
70%
Reason: 15 internal clashes, strain 66.0 kcal/mol
strain ΔE 66.0 kcal/mol 15 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.697 kcal/mol/HA) ✓ Good fit quality (FQ -7.24) ✓ Good H-bonds (4 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Extreme strain energy (66.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-27.197
kcal/mol
LE
-0.697
kcal/mol/HA
Fit Quality
-7.24
FQ (Leeson)
HAC
39
heavy atoms
MW
570
Da
LogP
4.15
cLogP
Final rank
3.9217
rank score
Inter norm
-0.685
normalised
Contacts
13
H-bonds 5
Strain ΔE
66.0 kcal/mol
SASA buried
61%
Lipo contact
70% BSA apolar/total
SASA unbound
837 Ų
Apolar buried
358 Ų

Interaction summary

HBD 2 HBA 2 HY 6 PI 0 CLASH 0

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap7Native recall0.58
Jaccard0.39RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

493 residues
Protein targetT16Atoms7551
Residues493Chains1
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:276; 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
488 1.672200773331258 -0.719774 -22.9505 3 19 0 0.00 - - no Open
447 1.9322741281478826 -0.717572 -28.5262 3 21 0 0.00 - - no Open
480 1.992766089379955 -0.587649 -23.5693 5 21 0 0.00 - - no Open
462 3.0789642120118357 -0.8542 -33.1254 4 21 1 0.08 - - no Open
440 3.7496370630942577 -0.624881 -21.4116 9 14 0 0.00 - - no Open
509 3.921737239173272 -0.684945 -27.1972 5 13 7 0.58 - - no Current
423 4.448396986697342 -0.829802 -27.9931 13 23 1 0.08 - - no Open
450 4.44869914518263 -0.509693 -17.2386 7 12 0 0.00 - - no Open
443 4.693852668046735 -0.811438 -26.2177 12 24 0 0.00 - - no Open
420 5.195508061932922 -0.713708 -25.239 7 16 0 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 -27.197kcal/mol
Ligand efficiency (LE) -0.6974kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.237
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 39HA

Physicochemical properties
Molecular weight 569.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.15
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 66.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 19.46kcal/mol
Minimised FF energy -46.58kcal/mol

SASA & burial

✓ computed
SASA (unbound) 837.2Ų
Total solvent-accessible surface area of free ligand
BSA total 512.2Ų
Buried surface area upon binding
BSA apolar 357.6Ų
Hydrophobic contacts buried
BSA polar 154.6Ų
Polar contacts buried
Fraction buried 61.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3197.4Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1483.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)