FAIRMol

NMT-TY0980

Pose ID 6385 Compound 3329 Pose 289

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-TY0980

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
32.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.56, H-bond role recall 0.18
Burial
68%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
2 protein-contact clashes 50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.318 kcal/mol/HA) ✓ Good fit quality (FQ -11.24) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (32.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-27.674
kcal/mol
LE
-1.318
kcal/mol/HA
Fit Quality
-11.24
FQ (Leeson)
HAC
21
heavy atoms
MW
326
Da
LogP
1.51
cLogP
Strain ΔE
32.9 kcal/mol
SASA buried
68%
Lipo contact
76% BSA apolar/total
SASA unbound
532 Ų
Apolar buried
273 Ų

Interaction summary

HB 12 HY 3 PI 1 CLASH 2 ⚠ Exposure 50%
⚠️Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12 Buried (contacted) 6 Exposed 6 LogP 1.51 H-bonds 12
Exposed fragments: phenyl (4/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.898Score-27.674
Inter norm-1.206Intra norm-0.112
Top1000noExcludedno
Contacts11H-bonds12
Artifact reasongeometry warning; 6 clashes; 3 protein clashes; high strain Δ 32.9
Residues
ALA15 ARG116 ARG140 ARG144 ASP13 CYS72 GLY73 HIS105 HIS14 HIS141 SER46

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

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 overlap10Native recall0.59
Jaccard0.56RMSD-
HB strict3Strict recall0.23
HB same residue+role2HB role recall0.18
HB same residue3HB residue recall0.27

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
341 3.1491404705212647 -1.22745 -28.5635 8 12 0 0.00 0.00 - no Open
289 3.8977759112906605 -1.20629 -27.6738 12 11 10 0.59 0.18 - no Current
306 4.327463775817033 -1.28947 -26.3805 11 12 4 0.24 0.27 - 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 -27.674kcal/mol
Ligand efficiency (LE) -1.3178kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.240
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.51
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 32.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -76.77kcal/mol
Minimised FF energy -109.65kcal/mol

SASA & burial

✓ computed
SASA (unbound) 531.6Ų
Total solvent-accessible surface area of free ligand
BSA total 359.2Ų
Buried surface area upon binding
BSA apolar 272.7Ų
Hydrophobic contacts buried
BSA polar 86.5Ų
Polar contacts buried
Fraction buried 67.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2133.8Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 655.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)