FAIRMol

NMT-TY0623

Pose ID 13886 Compound 343 Pose 328

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-TY0623
PDB3K7O↗

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 medium Native strong SASA done
Strain ΔE
38.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.67
Burial
80%
Hydrophobic fit
68%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.941 kcal/mol/HA) ✓ Good fit quality (FQ -8.98) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (80% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Very high strain energy (38.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-27.277
kcal/mol
LE
-0.941
kcal/mol/HA
Fit Quality
-8.98
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.95
cLogP
Strain ΔE
38.5 kcal/mol
SASA buried
80%
Lipo contact
68% BSA apolar/total
SASA unbound
671 Ų
Apolar buried
366 Ų

Interaction summary

HB 12 HY 13 PI 2 CLASH 3
Final rank4.137Score-27.277
Inter norm-0.976Intra norm0.036
Top1000noExcludedno
Contacts18H-bonds12
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; high strain Δ 38.5
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 ARG113 ASP10 CYS69 GLY70 GLY72 GLY74 HIS11 ILE73 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 overlap14Native recall1.00
Jaccard0.78RMSD-
HB strict7Strict recall0.58
HB same residue+role6HB role recall0.67
HB same residue6HB residue recall0.75

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
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 0.00 - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 0 0.00 0.00 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 0.00 - no Open
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 0.00 - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 0 0.00 0.00 - no Open
424 2.557044498817305 -0.988533 -28.1895 8 17 0 0.00 0.00 - no Open
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 0.00 - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 0.00 - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 0.00 - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 0.00 - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 0 0.00 0.00 - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 0 0.00 0.00 - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 0 0.00 0.00 - no Open
289 3.87862843107247 -0.963867 -29.2468 8 19 0 0.00 0.00 - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 14 1.00 0.67 - no Current
309 4.286815840501966 -0.801912 -23.8944 5 20 0 0.00 0.00 - no Open
269 4.88188196770325 -1.1395 -32.34 11 17 0 0.00 0.00 - no Open
255 5.815034729044303 -0.891682 -22.7371 13 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 -27.277kcal/mol
Ligand efficiency (LE) -0.9406kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.979
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.95
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -38.43kcal/mol
Minimised FF energy -76.91kcal/mol

SASA & burial

✓ computed
SASA (unbound) 671.4Ų
Total solvent-accessible surface area of free ligand
BSA total 533.7Ų
Buried surface area upon binding
BSA apolar 365.5Ų
Hydrophobic contacts buried
BSA polar 168.2Ų
Polar contacts buried
Fraction buried 79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2210.3Ų
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 772.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)