FAIRMol

NMT-TY0929

Pose ID 3003 Compound 484 Pose 293

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-TY0929
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
40.1 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.61, H-bond role recall 0.67
Burial
79%
Hydrophobic fit
69%
Reason: no major geometry red flags detected
3 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.058 kcal/mol/HA) ✓ Good fit quality (FQ -9.87) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Extreme strain energy (40.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (5) ✗ Many internal clashes (12)
Score
-28.572
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-9.87
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
40.1 kcal/mol
SASA buried
79%
Lipo contact
69% BSA apolar/total
SASA unbound
627 Ų
Apolar buried
340 Ų

Interaction summary

HB 7 HY 23 PI 4 CLASH 5

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
Final rank1.275Score-28.572
Inter norm-1.036Intra norm-0.022
Top1000noExcludedno
Contacts12H-bonds7
Artifact reasongeometry warning; 12 clashes; 5 protein contact clashes; 7 cofactor-context clashes; high strain Δ 40.1
Residues
ARG17 HIS241 LEU188 LEU226 LEU229 NDP302 PHE113 SER111 SER112 TYR191 TYR194 VAL230

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
Jaccard0.61RMSD-
HB strict3Strict recall0.43
HB same residue+role4HB role recall0.67
HB same residue4HB residue recall0.80

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
346 0.35538722495997677 -0.978913 -25.6036 2 13 12 0.71 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 11 0.65 0.67 - no Current
323 1.3627403067812827 -0.906394 -18.7308 3 16 0 0.00 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 0 0.00 0.00 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 0 0.00 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 0 0.00 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 0 0.00 0.00 - no Open
392 2.7685730244744846 -1.12247 -31.1016 6 15 0 0.00 0.00 - no Open
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 0 0.00 0.00 - no Open
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 0 0.00 0.00 - no Open
287 4.830955251729373 -1.16188 -25.6924 10 15 0 0.00 0.00 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 0 0.00 0.00 - no Open
409 5.703467463727863 -0.909529 -26.8524 10 16 0 0.00 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 17 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 -28.572kcal/mol
Ligand efficiency (LE) -1.0582kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.873
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -23.39kcal/mol
Minimised FF energy -63.49kcal/mol

SASA & burial

✓ computed
SASA (unbound) 627.1Ų
Total solvent-accessible surface area of free ligand
BSA total 495.7Ų
Buried surface area upon binding
BSA apolar 340.1Ų
Hydrophobic contacts buried
BSA polar 155.5Ų
Polar contacts buried
Fraction buried 79.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1609.0Ų
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 1041.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)