FAIRMol

Z68347496

Pose ID 1921 Compound 1425 Pose 566

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
T03
L. major DHFR L. major
Ligand Z68347496

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
75.8 kcal/mol
Protein clashes
0
Internal clashes
9
Native overlap
contact recall 0.35, Jaccard 0.28, H-bond role recall 0.20
Burial
69%
Hydrophobic fit
66%
Reason: 9 internal clashes, strain 75.8 kcal/mol
strain ΔE 75.8 kcal/mol 9 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.715 kcal/mol/HA) ✓ Good fit quality (FQ -6.90) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Extreme strain energy (75.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-21.457
kcal/mol
LE
-0.715
kcal/mol/HA
Fit Quality
-6.90
FQ (Leeson)
HAC
30
heavy atoms
MW
425
Da
LogP
2.58
cLogP
Strain ΔE
75.8 kcal/mol
SASA buried
69%
Lipo contact
66% BSA apolar/total
SASA unbound
676 Ų
Apolar buried
308 Ų

Interaction summary

HB 10 HY 16 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 rank3.790Score-21.457
Inter norm-0.890Intra norm0.175
Top1000noExcludedno
Contacts12H-bonds10
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; high strain Δ 75.0
Residues
ARG92 ARG97 LEU94 LYS57 LYS90 LYS95 MET53 PHE56 PHE91 PRO50 PRO93 THR54

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 overlap7Native recall0.35
Jaccard0.28RMSD-
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
551 0.7863990384040856 -1.0689 -34.3256 10 13 0 0.00 0.00 - no Open
540 2.01639219542086 -0.846568 -22.4366 9 19 1 0.05 0.00 - no Open
597 2.6257543792701297 -0.791858 -27.3268 6 16 0 0.00 0.00 - no Open
552 2.841916052752017 -1.32572 -41.1595 11 19 0 0.00 0.00 - no Open
543 2.925843509730519 -1.38782 -43.7879 9 19 0 0.00 0.00 - no Open
577 3.073966426611157 -0.901 -28.5624 12 17 0 0.00 0.00 - no Open
554 3.391884301661245 -0.86851 -30.1896 8 19 1 0.05 0.00 - no Open
566 3.7897586704157433 -0.890481 -21.4571 10 12 7 0.35 0.20 - no Current
571 4.379321273351954 -0.866284 -27.1145 5 17 0 0.00 0.00 - no Open
577 4.446355622158319 -0.795751 -23.7085 6 19 0 0.00 0.00 - no Open
556 4.761776816752896 -0.850102 -27.284 9 14 0 0.00 0.00 - no Open
566 4.827703850716491 -1.36608 -35.1918 12 19 0 0.00 0.00 - no Open
581 5.166757877468878 -0.708586 -24.5919 8 14 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 -21.457kcal/mol
Ligand efficiency (LE) -0.7152kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.899
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 425.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.58
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 75.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 140.67kcal/mol
Minimised FF energy 64.83kcal/mol

SASA & burial

✓ computed
SASA (unbound) 676.3Ų
Total solvent-accessible surface area of free ligand
BSA total 469.6Ų
Buried surface area upon binding
BSA apolar 307.8Ų
Hydrophobic contacts buried
BSA polar 161.8Ų
Polar contacts buried
Fraction buried 69.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1441.7Ų
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 865.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)