FAIRMol

NMT-TY0601

Pose ID 2351 Compound 15 Pose 318

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
T04
L. major PTR1 L. major
Ligand NMT-TY0601
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
31.0 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.20
Burial
75%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.878 kcal/mol/HA) ✓ Good fit quality (FQ -8.47) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (31.0 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-26.352
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-8.47
FQ (Leeson)
HAC
30
heavy atoms
MW
446
Da
LogP
2.40
cLogP
Final rank
0.5314
rank score
Inter norm
-0.917
normalised
Contacts
14
H-bonds 1
Strain ΔE
31.0 kcal/mol
SASA buried
75%
Lipo contact
74% BSA apolar/total
SASA unbound
680 Ų
Apolar buried
377 Ų

Interaction summary

HB 0 HY 5 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
No hbd/hba · h-bonds (geometric) detected for this pose.

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.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap13Native recall0.68
Jaccard0.65RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
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
363 0.3236686833943817 -0.922656 -24.2954 3 19 0 0.00 0.00 - no Open
318 0.5313914739558929 -0.916521 -26.3515 1 14 13 0.68 0.20 - no Current
296 1.340576599260557 -0.866114 -23.6414 3 20 0 0.00 0.00 - no Open
313 1.395589756323132 -0.754263 -20.827 5 15 0 0.00 0.00 - no Open
284 1.7396787330526 -1.11044 -33.9659 13 23 0 0.00 0.00 - no Open
281 1.85607159171697 -1.14564 -34.7998 11 16 0 0.00 0.00 - no Open
348 2.510631852879237 -0.8762 -24.8059 8 14 0 0.00 0.00 - no Open
258 2.860860253450067 -1.00124 -25.4028 9 16 0 0.00 0.00 - no Open
271 2.8833662991378333 -0.970487 -29.5939 10 15 13 0.68 0.40 - no Open
273 3.372067864906788 -0.984025 -30.8549 11 15 0 0.00 0.00 - no Open
413 3.9499962992021005 -0.803776 -21.0277 6 18 0 0.00 0.00 - no Open
336 3.9850996762335 -0.846144 -23.7714 8 19 0 0.00 0.00 - no Open
296 4.196552406559037 -0.888004 -22.2524 5 13 0 0.00 0.00 - no Open
327 4.734313839890531 -0.780717 -23.4612 7 14 0 0.00 0.00 - no Open
318 5.396631318612632 -0.860345 -25.47 12 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 -26.352kcal/mol
Ligand efficiency (LE) -0.8784kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.473
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 445.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.40
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -72.28kcal/mol
Minimised FF energy -103.27kcal/mol

SASA & burial

✓ computed
SASA (unbound) 680.3Ų
Total solvent-accessible surface area of free ligand
BSA total 512.3Ų
Buried surface area upon binding
BSA apolar 376.8Ų
Hydrophobic contacts buried
BSA polar 135.4Ų
Polar contacts buried
Fraction buried 75.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1631.3Ų
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 1041.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)