FAIRMol

Z25474946

Pose ID 2021 Compound 94 Pose 666

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
T03
L. major DHFR L. major
Ligand Z25474946

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
35.8 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.60, Jaccard 0.57, H-bond role recall 0.20
Burial
87%
Hydrophobic fit
86%
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.623 kcal/mol/HA) ✓ Good fit quality (FQ -6.23) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Very high strain energy (35.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-21.164
kcal/mol
LE
-0.623
kcal/mol/HA
Fit Quality
-6.23
FQ (Leeson)
HAC
34
heavy atoms
MW
485
Da
LogP
3.99
cLogP
Strain ΔE
35.8 kcal/mol
SASA buried
87%
Lipo contact
86% BSA apolar/total
SASA unbound
770 Ų
Apolar buried
576 Ų

Interaction summary

HB 2 HY 24 PI 2 CLASH 0

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
No clash · clashes detected for this pose.
Final rank2.552Score-21.164
Inter norm-0.791Intra norm0.168
Top1000noExcludedno
Contacts13H-bonds2
Artifact reasongeometry warning; 15 clashes; 1 protein clash; high strain Δ 35.8
Residues
ARG97 ILE45 LEU94 LYS57 LYS95 MET53 NDP301 PHE56 PHE91 SER86 THR83 VAL156 VAL87

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap12Native recall0.60
Jaccard0.57RMSD-
HB strict2Strict recall0.29
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; 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
645 0.9228072349760513 -0.768534 -12.466 1 20 0 0.00 0.00 - no Open
666 2.5517046449615286 -0.790521 -21.1642 2 13 12 0.60 0.20 - no Current
670 3.801458424038044 -0.578231 -12.1198 4 12 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 -21.164kcal/mol
Ligand efficiency (LE) -0.6225kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.228
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 484.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.99
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -6.04kcal/mol
Minimised FF energy -41.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 770.2Ų
Total solvent-accessible surface area of free ligand
BSA total 673.0Ų
Buried surface area upon binding
BSA apolar 575.9Ų
Hydrophobic contacts buried
BSA polar 97.1Ų
Polar contacts buried
Fraction buried 87.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1681.6Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 794.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)