FAIRMol

NMT-TY0623

Pose ID 3695 Compound 343 Pose 309

DB SELECTIONDocking 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
T06
T. brucei DHFR T. brucei
Ligand NMT-TY0623
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
38.9 kcal/mol
Protein clashes
6
Internal clashes
9
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.25
Burial
98%
Hydrophobic fit
74%
Reason: 9 internal clashes
6 protein-contact clashes 9 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.824 kcal/mol/HA) ✓ Good fit quality (FQ -7.87) ✓ Good H-bonds (5 bonds) ✓ Deep burial (98% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (38.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-23.894
kcal/mol
LE
-0.824
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.54
cLogP
Strain ΔE
38.9 kcal/mol
SASA buried
98%
Lipo contact
74% BSA apolar/total
SASA unbound
651 Ų
Apolar buried
471 Ų

Interaction summary

HB 5 HY 24 PI 4 CLASH 9
Final rank4.287Score-23.894
Inter norm-0.802Intra norm-0.022
Top1000noExcludedno
Contacts20H-bonds5
Artifact reasongeometry warning; 14 clashes; 2 protein clashes; 1 severe cofactor-context clash; high strain Δ 38.6
Residues
ALA34 ARG100 ARG59 ASP54 GLY161 ILE160 ILE47 ILE51 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 THR86 TRP49 TYR166 VAL32 VAL33

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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:NDP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap16Native recall0.76
Jaccard0.64RMSD-
HB strict1Strict recall0.20
HB same residue+role1HB role recall0.25
HB same residue2HB residue recall0.50

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 0.00 - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 0 0.00 0.00 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 0.00 - no Open
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 0.00 - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 0 0.00 0.00 - no Open
424 2.557044498817305 -0.988533 -28.1895 8 17 0 0.00 0.00 - no Open
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 0.00 - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 0.00 - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 0.00 - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 0.00 - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 1 0.05 0.00 - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 0 0.00 0.00 - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 0 0.00 0.00 - no Open
289 3.87862843107247 -0.963867 -29.2468 8 19 1 0.05 0.00 - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 0 0.00 0.00 - no Open
309 4.286815840501966 -0.801912 -23.8944 5 20 16 0.76 0.25 - no Current
269 4.88188196770325 -1.1395 -32.34 11 17 0 0.00 0.00 - no Open
255 5.815034729044303 -0.891682 -22.7371 13 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 -23.894kcal/mol
Ligand efficiency (LE) -0.8239kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.865
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.54
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -63.78kcal/mol
Minimised FF energy -102.71kcal/mol

SASA & burial

✓ computed
SASA (unbound) 650.9Ų
Total solvent-accessible surface area of free ligand
BSA total 638.3Ų
Buried surface area upon binding
BSA apolar 470.7Ų
Hydrophobic contacts buried
BSA polar 167.6Ų
Polar contacts buried
Fraction buried 98.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1708.2Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 583.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)