FAIRMol

NMT-TY0939

Pose ID 6372 Compound 912 Pose 276

DB fairmolDocking 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-TY0939

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
84.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.82
Burial
73%
Hydrophobic fit
49%
Reason: strain 84.6 kcal/mol
strain ΔE 84.6 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (8/12 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.667 kcal/mol/HA) ✓ Good fit quality (FQ -6.14) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (73% SASA buried) ✗ Extreme strain energy (84.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-17.337
kcal/mol
LE
-0.667
kcal/mol/HA
Fit Quality
-6.14
FQ (Leeson)
HAC
26
heavy atoms
MW
402
Da
LogP
0.13
cLogP
Final rank
5.5461
rank score
Inter norm
-0.990
normalised
Contacts
17
H-bonds 15
Strain ΔE
84.6 kcal/mol
SASA buried
73%
Lipo contact
49% BSA apolar/total
SASA unbound
600 Ų
Apolar buried
214 Ų

Interaction summary

HBD 2 HBA 8 HY 3 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 8.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap17Native recall1.00
Jaccard1.00RMSD-
HB strict11Strict recall0.85
HB same residue+role9HB role recall0.82
HB same residue9HB residue recall0.82

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
347 0.47311557931133086 -0.935109 -19.2367 4 13 0 0.00 0.00 - no Open
322 1.415578661134894 -1.03243 -26.6288 12 15 0 0.00 0.00 - no Open
374 1.7236615503669714 -1.05315 -30.1239 8 13 0 0.00 0.00 - no Open
380 2.2523504511266683 -1.00941 -20.4416 7 16 0 0.00 0.00 - no Open
298 3.331173736035127 -1.11268 -26.9067 10 14 0 0.00 0.00 - no Open
327 3.4700047251715773 -0.87606 -20.3514 3 16 0 0.00 0.00 - no Open
445 3.506483242040409 -0.904121 -22.2104 13 16 0 0.00 0.00 - no Open
276 5.5461368627814105 -0.989799 -17.3373 15 17 17 1.00 0.82 - no Current
339 6.810864659394439 -0.970214 -24.4372 16 15 0 0.00 0.00 - 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 -17.337kcal/mol
Ligand efficiency (LE) -0.6668kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 402.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.13
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 84.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -4.20kcal/mol
Minimised FF energy -88.78kcal/mol

SASA & burial

✓ computed
SASA (unbound) 600.5Ų
Total solvent-accessible surface area of free ligand
BSA total 438.6Ų
Buried surface area upon binding
BSA apolar 213.6Ų
Hydrophobic contacts buried
BSA polar 224.9Ų
Polar contacts buried
Fraction buried 73.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 48.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2070.7Ų
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 653.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)