FAIRMol

Z246803428

Pose ID 5869 Compound 2703 Pose 451

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 Z246803428

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
27.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.57, Jaccard 0.50, H-bond role recall 0.17
Burial
89%
Hydrophobic fit
83%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.961 kcal/mol/HA) ✓ Good fit quality (FQ -8.48) ✓ Good H-bonds (4 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (27.3 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (10)
Score
-22.108
kcal/mol
LE
-0.961
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
23
heavy atoms
MW
328
Da
LogP
3.35
cLogP
Strain ΔE
27.3 kcal/mol
SASA buried
89%
Lipo contact
83% BSA apolar/total
SASA unbound
563 Ų
Apolar buried
417 Ų

Interaction summary

HB 4 HY 24 PI 2 CLASH 3
Final rank0.993Score-22.108
Inter norm-1.122Intra norm0.161
Top1000noExcludedno
Contacts15H-bonds4
Artifact reasongeometry warning; 10 clashes; 6 protein contact clashes; moderate strain Δ 27.3
Residues
NDP301 ALA32 ARG48 ASP52 ILE45 MET53 PHE55 PHE56 THR180 TRP47 TYR162 VAL156 VAL30 VAL31 VAL49

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 overlap12Native recall0.57
Jaccard0.50RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.17
HB same residue1HB residue recall0.17

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
416 0.026635046374333067 -1.35456 -25.6301 3 16 0 0.00 0.00 - no Open
451 0.9928778871593091 -1.1221 -22.1084 4 15 12 0.57 0.17 - no Current
420 3.582389504247814 -1.03685 -21.0643 8 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 -22.108kcal/mol
Ligand efficiency (LE) -0.9612kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.484
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.35
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 70.96kcal/mol
Minimised FF energy 43.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 563.2Ų
Total solvent-accessible surface area of free ligand
BSA total 503.3Ų
Buried surface area upon binding
BSA apolar 417.1Ų
Hydrophobic contacts buried
BSA polar 86.2Ų
Polar contacts buried
Fraction buried 89.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3222.3Ų
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 1683.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)