FAIRMol

NMT-TY0625

Pose ID 3696 Compound 587 Pose 310

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-TY0625
PDB8RHT↗

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
37.0 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.67, Jaccard 0.58, H-bond role recall 0.75
Burial
94%
Hydrophobic fit
73%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.848 kcal/mol/HA) ✓ Good fit quality (FQ -7.91) ✓ Good H-bonds (4 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Very high strain energy (37.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (11)
Score
-22.895
kcal/mol
LE
-0.848
kcal/mol/HA
Fit Quality
-7.91
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
37.0 kcal/mol
SASA buried
94%
Lipo contact
73% BSA apolar/total
SASA unbound
635 Ų
Apolar buried
435 Ų

Interaction summary

HB 4 HY 24 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 rank1.512Score-22.895
Inter norm-0.902Intra norm0.053
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 11 clashes; 7 protein contact clashes; high strain Δ 37.0
Residues
ALA34 ARG100 ARG59 ASP54 GLN56 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 THR184 VAL32 VAL33

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 overlap14Native recall0.67
Jaccard0.58RMSD-
HB strict3Strict recall0.60
HB same residue+role3HB role recall0.75
HB same residue3HB residue recall0.75

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
324 0.20723889343453514 -0.951386 -23.6661 1 14 0 0.00 0.00 - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 0.00 - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 0.00 - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 1 0.05 0.00 - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 14 0.67 0.75 - no Current
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 0.00 - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 0.00 - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 0.00 - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 0 0.00 0.00 - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 0.00 - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 1 0.05 0.00 - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 0 0.00 0.00 - no Open
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 0.00 - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 0.00 - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 0.00 - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 0.00 - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 0.00 - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 0.00 - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 0.00 - no Open
330 5.564206722433145 -0.904232 -20.3369 11 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 -22.895kcal/mol
Ligand efficiency (LE) -0.8480kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.911
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) 36.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -55.41kcal/mol
Minimised FF energy -92.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 635.0Ų
Total solvent-accessible surface area of free ligand
BSA total 598.7Ų
Buried surface area upon binding
BSA apolar 434.7Ų
Hydrophobic contacts buried
BSA polar 164.0Ų
Polar contacts buried
Fraction buried 94.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 72.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1689.0Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 588.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)