FAIRMol

NMT-TY0824

Pose ID 6361 Compound 1750 Pose 265

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-TY0824

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
18.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.56, H-bond role recall 0.27
Burial
75%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
2 protein-contact clashes 40% of hydrophobic surface appears solvent-exposed (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.289 kcal/mol/HA) ✓ Good fit quality (FQ -10.33) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Moderate strain (18.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-23.194
kcal/mol
LE
-1.289
kcal/mol/HA
Fit Quality
-10.33
FQ (Leeson)
HAC
18
heavy atoms
MW
266
Da
LogP
0.15
cLogP
Strain ΔE
18.4 kcal/mol
SASA buried
75%
Lipo contact
71% BSA apolar/total
SASA unbound
448 Ų
Apolar buried
237 Ų

Interaction summary

HB 14 HY 2 PI 1 CLASH 2 ⚠ Exposure 40%
⚠️Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (4/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 10 Buried (contacted) 6 Exposed 4 LogP 0.15 H-bonds 14
Exposed fragments: phenyl (4/6 atoms exposed)
Final rank3.805Score-23.194
Inter norm-1.364Intra norm0.076
Top1000noExcludedno
Contacts11H-bonds14
Artifact reasongeometry warning; 6 clashes; 3 protein clashes
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 strict4Strict recall0.31
HB same residue+role3HB role recall0.27
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
340 1.015571438451004 -1.5344 -25.1285 5 11 0 0.00 0.00 - no Open
306 3.435362664430664 -1.6822 -27.6233 14 18 0 0.00 0.00 - no Open
265 3.804863587511328 -1.36447 -23.1944 14 11 10 0.59 0.27 - 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 -23.194kcal/mol
Ligand efficiency (LE) -1.2886kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.327
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 266.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.15
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -86.70kcal/mol
Minimised FF energy -105.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 447.8Ų
Total solvent-accessible surface area of free ligand
BSA total 335.0Ų
Buried surface area upon binding
BSA apolar 236.5Ų
Hydrophobic contacts buried
BSA polar 98.5Ų
Polar contacts buried
Fraction buried 74.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2084.2Ų
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 653.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)