FAIRMol

Z49633576

Pose ID 11457 Compound 992 Pose 614

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand Z49633576
PDB5S9T↗

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
70.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.58, Jaccard 0.32, H-bond role recall 0.00
Burial
84%
Hydrophobic fit
58%
Reason: strain 70.0 kcal/mol
strain ΔE 70.0 kcal/mol 4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.729 kcal/mol/HA) ✓ Good fit quality (FQ -7.03) ✓ Good H-bonds (5 bonds) ✓ Deep burial (84% SASA buried) ✗ Extreme strain energy (70.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (14)
Score
-21.854
kcal/mol
LE
-0.729
kcal/mol/HA
Fit Quality
-7.03
FQ (Leeson)
HAC
30
heavy atoms
MW
439
Da
LogP
1.07
cLogP
Final rank
2.3486
rank score
Inter norm
-0.756
normalised
Contacts
17
H-bonds 8
Strain ΔE
70.0 kcal/mol
SASA buried
84%
Lipo contact
58% BSA apolar/total
SASA unbound
619 Ų
Apolar buried
305 Ų

Interaction summary

HBD 3 HBA 2 HY 5 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap7Native recall0.58
Jaccard0.32RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
592 1.088467834021099 -1.21638 -35.5119 11 17 0 0.00 0.00 - no Open
591 1.279920394623608 -0.958585 -27.9306 8 14 0 0.00 0.00 - no Open
614 2.169494058727323 -0.722846 -19.1394 4 9 0 0.00 0.00 - no Open
614 2.3485621669480374 -0.756077 -21.8538 8 17 7 0.58 0.00 - no Current
608 2.3978756382173834 -0.914409 -20.3444 11 15 0 0.00 0.00 - no Open
607 2.7193451061352016 -1.01606 -22.4387 11 12 0 0.00 0.00 - no Open
599 3.151702278102694 -0.858251 -17.4184 6 18 0 0.00 0.00 - no Open
605 4.43482713094104 -1.22494 -33.3039 11 22 0 0.00 0.00 - no Open
602 4.713471072673453 -1.10206 -23.637 16 19 0 0.00 0.00 - no Open
613 5.4625540130581856 -1.04999 -29.3846 12 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 -21.854kcal/mol
Ligand efficiency (LE) -0.7285kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.027
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 439.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.07
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 70.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 103.42kcal/mol
Minimised FF energy 33.41kcal/mol

SASA & burial

✓ computed
SASA (unbound) 619.5Ų
Total solvent-accessible surface area of free ligand
BSA total 520.5Ų
Buried surface area upon binding
BSA apolar 304.6Ų
Hydrophobic contacts buried
BSA polar 215.8Ų
Polar contacts buried
Fraction buried 84.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6397.1Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2051.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)