FAIRMol

NMT-TY0957

Pose ID 2382 Compound 264 Pose 349

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-TY0957
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
25.9 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.00
Burial
78%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
1 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.768 kcal/mol/HA) ✓ Good fit quality (FQ -7.25) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (25.9 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (3) ✗ Internal clashes (9)
Score
-21.515
kcal/mol
LE
-0.768
kcal/mol/HA
Fit Quality
-7.25
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
25.9 kcal/mol
SASA buried
78%
Lipo contact
72% BSA apolar/total
SASA unbound
667 Ų
Apolar buried
374 Ų

Interaction summary

HB 2 HY 20 PI 4 CLASH 4

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 rank0.728Score-21.515
Inter norm-0.881Intra norm0.113
Top1000noExcludedno
Contacts14H-bonds2
Artifact reasongeometry warning; 9 clashes; 3 protein contact clashes; 3 cofactor-context clashes; moderate strain Δ 25.9
Residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 MET233 NDP302 PHE113 SER111 TYR194 VAL230 VAL237 ARG287

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 strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
349 0.7278409086070636 -0.881455 -21.5148 2 14 13 0.68 0.00 - no Current
311 1.3229509224018154 -1.16017 -29.6884 9 15 0 0.00 0.00 - no Open
334 1.51730203346956 -0.851135 -24.9989 8 16 0 0.00 0.00 - no Open
335 1.7260732089299 -0.999198 -26.3291 6 21 0 0.00 0.00 - no Open
403 1.7481430375200544 -0.991243 -27.3069 7 18 0 0.00 0.00 - no Open
347 2.3447902198011827 -0.753436 -19.3121 7 15 0 0.00 0.00 - no Open
389 2.786111419208295 -1.0956 -28.7016 6 16 0 0.00 0.00 - no Open
289 3.0086401503696756 -1.24814 -30.9089 9 21 0 0.00 0.00 - no Open
301 3.1451083125642456 -1.02377 -27.2511 8 23 0 0.00 0.00 - no Open
357 3.2475516904388395 -0.897972 -24.0584 9 11 0 0.00 0.00 - no Open
377 3.304488419434868 -0.914277 -26.47 6 16 0 0.00 0.00 - no Open
379 3.3253823915120413 -1.07446 -31.7967 5 19 0 0.00 0.00 - no Open
414 3.598164167482077 -0.922403 -23.4985 9 14 0 0.00 0.00 - no Open
332 3.624289409705216 -0.937648 -25.3511 7 11 0 0.00 0.00 - no Open
330 4.212597954691834 -0.897031 -24.2894 4 14 0 0.00 0.00 - no Open
451 4.456710646262987 -0.898418 -22.7057 8 16 0 0.00 0.00 - no Open
324 5.157273396991818 -1.11879 -29.0355 13 26 0 0.00 0.00 - no Open
284 5.171548217517241 -0.94018 -23.463 14 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 -21.515kcal/mol
Ligand efficiency (LE) -0.7684kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.254
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -84.83kcal/mol
Minimised FF energy -110.71kcal/mol

SASA & burial

✓ computed
SASA (unbound) 667.3Ų
Total solvent-accessible surface area of free ligand
BSA total 520.3Ų
Buried surface area upon binding
BSA apolar 373.7Ų
Hydrophobic contacts buried
BSA polar 146.6Ų
Polar contacts buried
Fraction buried 78.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1642.6Ų
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 1025.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)