FAIRMol

Z56899981

Pose ID 6030 Compound 2609 Pose 612

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
T09
L. major DHFR-TS L. major
Ligand Z56899981

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
20.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.00
Burial
89%
Hydrophobic fit
82%
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 (-1.083 kcal/mol/HA) ✓ Good fit quality (FQ -9.98) ✓ Good H-bonds (4 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ High strain energy (20.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-28.152
kcal/mol
LE
-1.083
kcal/mol/HA
Fit Quality
-9.98
FQ (Leeson)
HAC
26
heavy atoms
MW
353
Da
LogP
4.06
cLogP
Strain ΔE
20.4 kcal/mol
SASA buried
89%
Lipo contact
82% BSA apolar/total
SASA unbound
607 Ų
Apolar buried
446 Ų

Interaction summary

HB 4 HY 24 PI 1 CLASH 2
Final rank3.529Score-28.152
Inter norm-1.034Intra norm-0.049
Top1000noExcludedno
Contacts17H-bonds4
Artifact reasongeometry warning; 14 clashes; 2 protein clashes; moderate strain Δ 20.4
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 MET53 PHE56 PRO88 SER44 SER86 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49 VAL87

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap13Native recall0.62
Jaccard0.52RMSD-
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
622 1.7531350104233334 -1.17674 -31.2262 5 15 0 0.00 0.00 - no Open
614 2.2055198786948744 -0.88061 -15.0542 3 19 1 0.05 0.00 - no Open
612 3.5293553397063118 -1.03384 -28.1524 4 17 13 0.62 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 -28.152kcal/mol
Ligand efficiency (LE) -1.0828kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.976
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.06
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 92.14kcal/mol
Minimised FF energy 71.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 607.0Ų
Total solvent-accessible surface area of free ligand
BSA total 539.8Ų
Buried surface area upon binding
BSA apolar 445.5Ų
Hydrophobic contacts buried
BSA polar 94.3Ų
Polar contacts buried
Fraction buried 88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3229.1Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1692.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)