FAIRMol

NMT-TY0622

Pose ID 13885 Compound 524 Pose 327

DB SELECTIONDocking 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
T21
T. cruzi R5P T. cruzi
Ligand NMT-TY0622
PDB3K7O↗

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
43.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.93, Jaccard 0.72, H-bond role recall 0.56
Burial
81%
Hydrophobic fit
67%
Reason: strain 43.7 kcal/mol
strain ΔE 43.7 kcal/mol 5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.993 kcal/mol/HA) ✓ Good fit quality (FQ -9.03) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Extreme strain energy (43.7 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-24.826
kcal/mol
LE
-0.993
kcal/mol/HA
Fit Quality
-9.03
FQ (Leeson)
HAC
25
heavy atoms
MW
381
Da
LogP
2.18
cLogP
Strain ΔE
43.7 kcal/mol
SASA buried
81%
Lipo contact
67% BSA apolar/total
SASA unbound
580 Ų
Apolar buried
317 Ų

Interaction summary

HB 12 HY 2 PI 2 CLASH 5
Final rank3.725Score-24.826
Inter norm-1.022Intra norm0.029
Top1000noExcludedno
Contacts17H-bonds12
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; high strain Δ 43.7
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 ARG113 ASP10 CYS69 GLY70 GLY72 GLY74 HIS11 PRO12 SER71 TYR46

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap13Native recall0.93
Jaccard0.72RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.56
HB same residue5HB residue recall0.62

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
308 0.3842150656616825 -0.951549 -25.0395 4 17 0 0.00 0.00 - no Open
276 1.2600618081157402 -1.12204 -28.7499 9 15 0 0.00 0.00 - no Open
288 1.7018393222780244 -1.13668 -28.6792 9 14 0 0.00 0.00 - no Open
352 1.9271195694416656 -1.10716 -29.8519 6 13 0 0.00 0.00 - no Open
341 1.927730112535267 -0.859185 -22.1976 9 12 0 0.00 0.00 - no Open
273 1.9961552376915304 -1.35584 -31.5197 14 17 0 0.00 0.00 - no Open
327 2.0961391154894002 -0.86609 -19.9983 5 13 0 0.00 0.00 - no Open
392 2.3248094781583672 -0.940735 -21.0428 11 16 0 0.00 0.00 - no Open
308 2.8353655663354234 -1.13363 -28.9578 5 19 0 0.00 0.00 - no Open
378 2.966730885309019 -1.23963 -28.1056 8 15 0 0.00 0.00 - no Open
423 3.5162080347453757 -1.16596 -29.4186 9 16 0 0.00 0.00 - no Open
361 3.58426702200673 -1.22019 -28.4754 6 15 0 0.00 0.00 - no Open
268 3.6431928517433407 -1.15199 -28.179 10 14 0 0.00 0.00 - no Open
327 3.7246234846293826 -1.02174 -24.8257 12 17 13 0.93 0.56 - no Current
347 3.9186485478235458 -1.05383 -26.5042 6 19 0 0.00 0.00 - no Open
269 4.208957465627367 -1.25064 -26.887 9 18 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 -24.826kcal/mol
Ligand efficiency (LE) -0.9930kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.028
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 381.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.18
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -35.57kcal/mol
Minimised FF energy -79.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 580.5Ų
Total solvent-accessible surface area of free ligand
BSA total 469.3Ų
Buried surface area upon binding
BSA apolar 316.5Ų
Hydrophobic contacts buried
BSA polar 152.8Ų
Polar contacts buried
Fraction buried 80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2172.7Ų
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 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 731.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)