FAIRMol

Z49891479

Pose ID 3813 Compound 2357 Pose 427

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 Z49891479
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 mixed SASA done
Strain ΔE
24.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.00
Burial
95%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.749 kcal/mol/HA) ✓ Good fit quality (FQ -6.71) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (24.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (2) ✗ Internal clashes (6)
Score
-17.972
kcal/mol
LE
-0.749
kcal/mol/HA
Fit Quality
-6.71
FQ (Leeson)
HAC
24
heavy atoms
MW
340
Da
LogP
3.34
cLogP
Strain ΔE
24.3 kcal/mol
SASA buried
95%
Lipo contact
75% BSA apolar/total
SASA unbound
581 Ų
Apolar buried
412 Ų

Interaction summary

HB 1 HY 24 PI 3 CLASH 1

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 rank0.164Score-17.972
Inter norm-0.972Intra norm0.166
Top1000noExcludedno
Contacts14H-bonds1
Artifact reasongeometry warning; 6 clashes; 2 protein contact clashes; moderate strain Δ 24.3
Residues
ALA34 ARG100 ARG59 ASP54 ILE160 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 SER98 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 overlap11Native recall0.52
Jaccard0.46RMSD-
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
427 0.1637210485937671 -0.972095 -17.9721 1 14 11 0.52 0.00 - no Current
448 2.1011499600434522 -1.32189 -26.4874 6 16 0 0.00 0.00 - no Open
432 3.481521830671832 -1.14179 -26.8947 7 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 -17.972kcal/mol
Ligand efficiency (LE) -0.7488kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.711
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.34
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 24.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 71.20kcal/mol
Minimised FF energy 46.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 580.7Ų
Total solvent-accessible surface area of free ligand
BSA total 549.4Ų
Buried surface area upon binding
BSA apolar 411.9Ų
Hydrophobic contacts buried
BSA polar 137.6Ų
Polar contacts buried
Fraction buried 94.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1671.8Ų
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 573.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)