FAIRMol

NMT-TY1002

Pose ID 6386 Compound 861 Pose 290

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-TY1002

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
25.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.27
Burial
64%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 57% of hydrophobic surface appears solvent-exposed (8/14 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 (-0.959 kcal/mol/HA) ✓ Good fit quality (FQ -8.46) ✓ Strong H-bond network (14 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (25.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-22.046
kcal/mol
LE
-0.959
kcal/mol/HA
Fit Quality
-8.46
FQ (Leeson)
HAC
23
heavy atoms
MW
354
Da
LogP
2.04
cLogP
Strain ΔE
25.2 kcal/mol
SASA buried
64%
Lipo contact
72% BSA apolar/total
SASA unbound
599 Ų
Apolar buried
276 Ų

Interaction summary

HB 14 HY 3 PI 1 CLASH 3 ⚠ Exposure 57%
⚠️Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (8/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 14 Buried (contacted) 6 Exposed 8 LogP 2.04 H-bonds 14
Exposed fragments: phenyl (4/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank4.192Score-22.046
Inter norm-1.043Intra norm0.085
Top1000noExcludedno
Contacts13H-bonds14
Artifact reasongeometry warning; 6 clashes; 3 protein clashes; moderate strain Δ 25.2
Residues
ALA15 ARG116 ARG140 ARG144 ASP13 CYS72 GLU138 GLY73 HIS105 HIS14 HIS141 SER46 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 overlap11Native recall0.65
Jaccard0.58RMSD-
HB strict4Strict recall0.31
HB same residue+role3HB role recall0.27
HB same residue4HB residue recall0.36

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
400 1.9174733193957332 -1.17093 -25.6369 5 13 0 0.00 0.00 - no Open
335 4.010221975268383 -1.31658 -28.8486 9 21 0 0.00 0.00 - no Open
290 4.192024057328294 -1.04312 -22.0455 14 13 11 0.65 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 -22.046kcal/mol
Ligand efficiency (LE) -0.9585kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.460
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 354.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.04
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -106.42kcal/mol
Minimised FF energy -131.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 599.4Ų
Total solvent-accessible surface area of free ligand
BSA total 385.4Ų
Buried surface area upon binding
BSA apolar 275.6Ų
Hydrophobic contacts buried
BSA polar 109.7Ų
Polar contacts buried
Fraction buried 64.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2214.5Ų
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 654.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)