FAIRMol

NMT-TY0833

Pose ID 2996 Compound 1878 Pose 286

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
T05
L. major PTR1 L. major
Ligand NMT-TY0833
PDB7PXX↗

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
28.6 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.65, Jaccard 0.55, H-bond role recall 0.50
Burial
86%
Hydrophobic fit
58%
Reason: no major geometry red flags detected
4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.290 kcal/mol/HA) ✓ Good fit quality (FQ -11.38) ✓ Good H-bonds (4 bonds) ✓ Deep burial (86% SASA buried) ✗ High strain energy (28.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.665
kcal/mol
LE
-1.290
kcal/mol/HA
Fit Quality
-11.38
FQ (Leeson)
HAC
23
heavy atoms
MW
340
Da
LogP
-0.47
cLogP
Final rank
2.4901
rank score
Inter norm
-1.357
normalised
Contacts
14
H-bonds 8
Strain ΔE
28.6 kcal/mol
SASA buried
86%
Lipo contact
58% BSA apolar/total
SASA unbound
541 Ų
Apolar buried
273 Ų

Interaction summary

HBD 1 HBA 3 PC 1 HY 2 PI 2 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.65
Jaccard0.55RMSD-
HB strict2Strict recall0.29
HB same residue+role3HB role recall0.50
HB same residue3HB residue recall0.60

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
341 2.039766586176745 -1.05172 -21.9472 9 13 13 0.76 0.33 - no Open
286 2.4900543654672744 -1.35688 -29.6651 8 14 11 0.65 0.50 - no Current
308 3.626665037784344 -1.39624 -32.8678 16 16 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 -29.665kcal/mol
Ligand efficiency (LE) -1.2898kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.383
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 340.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.47
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -119.40kcal/mol
Minimised FF energy -148.04kcal/mol

SASA & burial

✓ computed
SASA (unbound) 540.8Ų
Total solvent-accessible surface area of free ligand
BSA total 466.4Ų
Buried surface area upon binding
BSA apolar 272.7Ų
Hydrophobic contacts buried
BSA polar 193.7Ų
Polar contacts buried
Fraction buried 86.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 58.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1476.5Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1026.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)