FAIRMol

Z56773006

Pose ID 4021 Compound 2511 Pose 635

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
T06
T. brucei DHFR T. brucei
Ligand Z56773006
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native strong SASA done
Strain ΔE
14.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.76, H-bond role recall 0.00
Burial
100%
Hydrophobic fit
97%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.385 kcal/mol/HA) ✓ Good fit quality (FQ -11.10) ✓ Good H-bonds (4 bonds) ✓ Deep burial (100% SASA buried) ✓ Lipophilic contacts well-matched (97%) ✗ Moderate strain (14.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-24.935
kcal/mol
LE
-1.385
kcal/mol/HA
Fit Quality
-11.10
FQ (Leeson)
HAC
18
heavy atoms
MW
259
Da
LogP
2.74
cLogP
Strain ΔE
14.3 kcal/mol
SASA buried
100%
Lipo contact
97% BSA apolar/total
SASA unbound
466 Ų
Apolar buried
452 Ų

Interaction summary

HB 4 HY 24 PI 1 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 rank1.255Score-24.935
Inter norm-1.388Intra norm0.002
Top1000noExcludedno
Contacts16H-bonds4
Artifact reasongeometry warning; 6 clashes; 1 protein clash; 1 severe cofactor-context clash
Residues
ALA34 ASP54 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 THR184 THR86 TYR166 TYR57 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 overlap16Native recall0.76
Jaccard0.76RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
635 1.2550995898910275 -1.38773 -24.9346 4 16 16 0.76 0.00 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.935kcal/mol
Ligand efficiency (LE) -1.3853kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.102
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 258.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.74
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -89.49kcal/mol
Minimised FF energy -103.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 465.6Ų
Total solvent-accessible surface area of free ligand
BSA total 465.3Ų
Buried surface area upon binding
BSA apolar 451.8Ų
Hydrophobic contacts buried
BSA polar 13.5Ų
Polar contacts buried
Fraction buried 99.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 97.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1666.8Ų
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 594.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)