FAIRMol

Z56964630

Pose ID 4033 Compound 295 Pose 647

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 Z56964630
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
Weak or marginal quality
Binding strong Geometry high Native strong SASA done
Strain ΔE
21.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.59, H-bond role recall 0.00
Burial
96%
Hydrophobic fit
96%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.780 kcal/mol/HA) ✓ Good fit quality (FQ -7.18) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (96%) ✗ High strain energy (21.8 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Many internal clashes (14)
Score
-20.272
kcal/mol
LE
-0.780
kcal/mol/HA
Fit Quality
-7.18
FQ (Leeson)
HAC
26
heavy atoms
MW
362
Da
LogP
4.69
cLogP
Strain ΔE
21.8 kcal/mol
SASA buried
96%
Lipo contact
96% BSA apolar/total
SASA unbound
603 Ų
Apolar buried
556 Ų

Interaction summary

HB 1 HY 24 PI 3 CLASH 2
Final rank0.879Score-20.272
Inter norm-0.942Intra norm0.156
Top1000noExcludedno
Contacts14H-bonds1
Artifact reasongeometry warning; 14 clashes; 2 protein contact clashes; moderate strain Δ 21.8
Residues
ALA34 ARG59 ASP54 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 THR86 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 overlap13Native recall0.62
Jaccard0.59RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
647 0.8794012212348199 -0.942021 -20.2719 1 14 13 0.62 0.00 - no Current
640 1.8925450849930585 -1.12804 -27.9377 3 18 0 0.00 0.00 - no Open
657 2.352878492528774 -0.984211 -25.938 2 13 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 -20.272kcal/mol
Ligand efficiency (LE) -0.7797kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.184
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 361.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.69
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 107.92kcal/mol
Minimised FF energy 86.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 603.4Ų
Total solvent-accessible surface area of free ligand
BSA total 576.5Ų
Buried surface area upon binding
BSA apolar 555.6Ų
Hydrophobic contacts buried
BSA polar 21.0Ų
Polar contacts buried
Fraction buried 95.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 96.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1813.5Ų
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 577.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)