FAIRMol

NMT-TY0614

Pose ID 13881 Compound 444 Pose 323

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
T21
T. cruzi R5P T. cruzi
Ligand NMT-TY0614
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
46.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.56
Burial
77%
Hydrophobic fit
68%
Reason: strain 46.3 kcal/mol
strain ΔE 46.3 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 (-0.686 kcal/mol/HA) ✓ Good fit quality (FQ -6.75) ✓ Good H-bonds (5 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Extreme strain energy (46.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-21.955
kcal/mol
LE
-0.686
kcal/mol/HA
Fit Quality
-6.75
FQ (Leeson)
HAC
32
heavy atoms
MW
474
Da
LogP
2.84
cLogP
Final rank
5.6611
rank score
Inter norm
-0.801
normalised
Contacts
18
H-bonds 9
Strain ΔE
46.3 kcal/mol
SASA buried
77%
Lipo contact
68% BSA apolar/total
SASA unbound
702 Ų
Apolar buried
369 Ų

Interaction summary

HBD 1 HBA 4 HY 5 PI 3 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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: permissive.
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 strict6Strict recall0.50
HB same residue+role5HB role recall0.56
HB same residue5HB residue recall0.62

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
341 1.1339898602829128 -0.748485 -23.9309 5 20 0 0.00 0.00 - no Open
303 1.3372398954075264 -0.804404 -24.1855 3 21 0 0.00 0.00 - no Open
283 2.139474337523808 -0.817859 -25.2468 5 15 0 0.00 0.00 - no Open
371 2.559480306330345 -0.816062 -23.2325 7 17 0 0.00 0.00 - no Open
354 2.6386474714478307 -0.812846 -23.9788 3 17 0 0.00 0.00 - no Open
301 2.8439180620978584 -0.787716 -20.8602 8 16 0 0.00 0.00 - no Open
321 2.895404379539044 -0.670765 -19.5853 8 15 0 0.00 0.00 - no Open
275 3.0839455449061752 -0.895097 -27.2356 6 16 0 0.00 0.00 - no Open
263 3.997061431046954 -0.87282 -25.9359 11 18 0 0.00 0.00 - no Open
323 5.661054598843183 -0.800961 -21.9554 9 18 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 -21.955kcal/mol
Ligand efficiency (LE) -0.6861kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.747
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 473.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.84
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 46.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -56.24kcal/mol
Minimised FF energy -102.51kcal/mol

SASA & burial

✓ computed
SASA (unbound) 702.3Ų
Total solvent-accessible surface area of free ligand
BSA total 542.7Ų
Buried surface area upon binding
BSA apolar 368.8Ų
Hydrophobic contacts buried
BSA polar 174.0Ų
Polar contacts buried
Fraction buried 77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2233.8Ų
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 766.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)