FAIRMol

NMT-TY0249

Pose ID 6319 Compound 3378 Pose 223

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
T10
L. infantum R5P L. infantum
Ligand NMT-TY0249

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
27.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.36
Burial
88%
Hydrophobic fit
78%
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 (-1.599 kcal/mol/HA) ✓ Good fit quality (FQ -11.82) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (27.3 kcal/mol) ✗ Geometry warnings
Score
-23.991
kcal/mol
LE
-1.599
kcal/mol/HA
Fit Quality
-11.82
FQ (Leeson)
HAC
15
heavy atoms
MW
248
Da
LogP
0.61
cLogP
Strain ΔE
27.3 kcal/mol
SASA buried
88%
Lipo contact
78% BSA apolar/total
SASA unbound
427 Ų
Apolar buried
293 Ų

Interaction summary

HB 12 HY 5 PI 1 CLASH 3

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
Final rank1.748Score-23.991
Inter norm-1.592Intra norm-0.007
Top1000noExcludedno
Contacts13H-bonds12
Artifact reasongeometry warning; 4 clashes; 1 protein clash; moderate strain Δ 27.3
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 HIS105 HIS14 HIS141 SER46 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap12Native recall0.71
Jaccard0.67RMSD-
HB strict6Strict recall0.46
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

Protein summary

155 residues
Protein targetT10Atoms4590
Residues155Chains1
Residue summaryILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
223 1.7482793182141037 -1.59199 -23.9911 12 13 12 0.71 0.36 - 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 -23.991kcal/mol
Ligand efficiency (LE) -1.5994kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.818
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 15HA

Physicochemical properties
Molecular weight 247.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.61
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -66.28kcal/mol
Minimised FF energy -93.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 427.0Ų
Total solvent-accessible surface area of free ligand
BSA total 377.7Ų
Buried surface area upon binding
BSA apolar 293.1Ų
Hydrophobic contacts buried
BSA polar 84.5Ų
Polar contacts buried
Fraction buried 88.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2100.7Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 640.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)