FAIRMol

NMT-TY0625

Pose ID 13888 Compound 587 Pose 330

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-TY0625
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
38.8 kcal/mol
Protein clashes
7
Internal clashes
7
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.56
Burial
77%
Hydrophobic fit
63%
Reason: 7 internal clashes
7 protein-contact clashes 7 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.753 kcal/mol/HA) ✓ Good fit quality (FQ -7.03) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (63%) ✗ Very high strain energy (38.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-20.337
kcal/mol
LE
-0.753
kcal/mol/HA
Fit Quality
-7.03
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
38.8 kcal/mol
SASA buried
77%
Lipo contact
63% BSA apolar/total
SASA unbound
619 Ų
Apolar buried
299 Ų

Interaction summary

HB 11 HY 11 PI 3 CLASH 7
Final rank5.564Score-20.337
Inter norm-0.904Intra norm0.151
Top1000noExcludedno
Contacts17H-bonds11
Artifact reasongeometry warning; 12 clashes; 3 protein clashes; high strain Δ 38.8
Residues
ARG137 ARG141 ASN103 HIS102 HIS138 MET98 TYR94 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
Jaccard0.82RMSD-
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
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 0.00 - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 0.00 - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 0.00 - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 0.00 - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 0.00 - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 0.00 - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 0.00 - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 0.00 - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 0.00 - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 0.00 - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 0 0.00 0.00 - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 0.00 - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 0.00 - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 0.00 - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 0.00 - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 0.00 - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 0.00 - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 0.00 - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 0.00 - no Open
330 5.564206722433145 -0.904232 -20.3369 11 17 14 1.00 0.56 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -20.337kcal/mol
Ligand efficiency (LE) -0.7532kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.027
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -8.65kcal/mol
Minimised FF energy -47.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 619.1Ų
Total solvent-accessible surface area of free ligand
BSA total 476.8Ų
Buried surface area upon binding
BSA apolar 298.8Ų
Hydrophobic contacts buried
BSA polar 178.0Ų
Polar contacts buried
Fraction buried 77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2162.3Ų
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 759.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)