FAIRMol

Z87656593

Pose ID 5841 Compound 3314 Pose 423

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 Z87656593

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
16.9 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.61, H-bond role recall 0.67
Burial
91%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
2 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.831 kcal/mol/HA) ✓ Good fit quality (FQ -7.85) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Moderate strain (16.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-23.275
kcal/mol
LE
-0.831
kcal/mol/HA
Fit Quality
-7.85
FQ (Leeson)
HAC
28
heavy atoms
MW
422
Da
LogP
2.13
cLogP
Strain ΔE
16.9 kcal/mol
SASA buried
91%
Lipo contact
72% BSA apolar/total
SASA unbound
689 Ų
Apolar buried
450 Ų

Interaction summary

HB 7 HY 24 PI 2 CLASH 3
Final rank2.931Score-23.275
Inter norm-0.927Intra norm0.096
Top1000noExcludedno
Contacts16H-bonds7
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; 1 cofactor-context clash
Residues
NDP301 ALA32 ARG97 GLY157 LEU94 LYS57 LYS95 MET53 PHE56 PHE91 PRO93 TYR162 VAL156 VAL30 VAL31 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 overlap14Native recall0.67
Jaccard0.61RMSD-
HB strict5Strict recall0.71
HB same residue+role4HB role recall0.67
HB same residue4HB residue recall0.67

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
492 2.083198329752847 -0.934815 -24.5022 5 13 0 0.00 0.00 - no Open
400 2.1761425878127802 -0.879661 -21.9787 6 18 0 0.00 0.00 - no Open
423 2.931087130603096 -0.926792 -23.2748 7 16 14 0.67 0.67 - 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 -23.275kcal/mol
Ligand efficiency (LE) -0.8312kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.847
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 421.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.13
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -108.33kcal/mol
Minimised FF energy -125.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 688.6Ų
Total solvent-accessible surface area of free ligand
BSA total 626.8Ų
Buried surface area upon binding
BSA apolar 450.2Ų
Hydrophobic contacts buried
BSA polar 176.6Ų
Polar contacts buried
Fraction buried 91.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3272.5Ų
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 1646.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)