FAIRMol

NMT-TY0623

Pose ID 6351 Compound 343 Pose 255

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-TY0623

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
35.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.64
Burial
74%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 42% of hydrophobic surface appears solvent-exposed (8/19 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 (-0.784 kcal/mol/HA) ✓ Good fit quality (FQ -7.48) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Very high strain energy (35.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-22.737
kcal/mol
LE
-0.784
kcal/mol/HA
Fit Quality
-7.48
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.78
cLogP
Strain ΔE
35.3 kcal/mol
SASA buried
74%
Lipo contact
73% BSA apolar/total
SASA unbound
656 Ų
Apolar buried
352 Ų

Interaction summary

HB 13 HY 10 PI 1 CLASH 4 ⚠ Exposure 42%
⚠️Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 11 Exposed 8 LogP 2.78 H-bonds 13
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank5.815Score-22.737
Inter norm-0.892Intra norm0.108
Top1000noExcludedno
Contacts16H-bonds13
Artifact reasongeometry warning; 14 clashes; 3 protein clashes; high strain Δ 35.3
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY77 HIS105 HIS14 HIS141 LEU101 THR117 THR74 TYR49

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 overlap15Native recall0.88
Jaccard0.83RMSD-
HB strict9Strict recall0.69
HB same residue+role7HB role recall0.64
HB same residue7HB residue recall0.64

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
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 0.00 - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 0 0.00 0.00 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 0.00 - no Open
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 0.00 - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 0 0.00 0.00 - no Open
424 2.557044498817305 -0.988533 -28.1895 8 17 0 0.00 0.00 - no Open
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 0.00 - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 0.00 - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 0.00 - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 0.00 - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 0 0.00 0.00 - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 0 0.00 0.00 - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 0 0.00 0.00 - no Open
289 3.87862843107247 -0.963867 -29.2468 8 19 0 0.00 0.00 - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 0 0.00 0.00 - no Open
309 4.286815840501966 -0.801912 -23.8944 5 20 0 0.00 0.00 - no Open
269 4.88188196770325 -1.1395 -32.34 11 17 5 0.29 0.27 - no Open
255 5.815034729044303 -0.891682 -22.7371 13 16 15 0.88 0.64 - 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 -22.737kcal/mol
Ligand efficiency (LE) -0.7840kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.484
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -45.52kcal/mol
Minimised FF energy -80.84kcal/mol

SASA & burial

✓ computed
SASA (unbound) 655.5Ų
Total solvent-accessible surface area of free ligand
BSA total 484.1Ų
Buried surface area upon binding
BSA apolar 352.0Ų
Hydrophobic contacts buried
BSA polar 132.1Ų
Polar contacts buried
Fraction buried 73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2264.4Ų
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 656.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)