FAIRMol

Z56327358

Pose ID 1142 Compound 979 Pose 464

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
T02
Human DHFR Human
Ligand Z56327358
PDB5SD8↗

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
43.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
88%
Reason: strain 43.7 kcal/mol
strain ΔE 43.7 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.824 kcal/mol/HA) ✓ Good fit quality (FQ -8.02) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (88%) ✗ Extreme strain energy (43.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-25.533
kcal/mol
LE
-0.824
kcal/mol/HA
Fit Quality
-8.02
FQ (Leeson)
HAC
31
heavy atoms
MW
418
Da
LogP
1.01
cLogP
Strain ΔE
43.7 kcal/mol
SASA buried
83%
Lipo contact
88% BSA apolar/total
SASA unbound
693 Ų
Apolar buried
510 Ų

Interaction summary

HB 1 HY 24 PI 1 CLASH 1

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
Final rank2.960Score-25.533
Inter norm-0.832Intra norm0.009
Top1000noExcludedno
Contacts15H-bonds1
Artifact reasongeometry warning; 18 clashes; 1 protein clash; high strain Δ 43.7
Residues
ALA10 ARG29 ASN65 GLU31 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 PRO62 TRP25 TYR122 VAL9

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap11Native recall0.52
Jaccard0.44RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

200 residues
Protein targetT02Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
464 2.9598857202487494 -0.832482 -25.5331 1 15 11 0.52 0.00 - no Current
502 3.462750317764966 -0.80471 -21.546 6 15 0 0.00 0.00 - no Open
395 3.478015244539325 -0.975463 -29.171 9 20 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 -25.533kcal/mol
Ligand efficiency (LE) -0.8236kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.024
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.01
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -67.61kcal/mol
Minimised FF energy -111.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.2Ų
Total solvent-accessible surface area of free ligand
BSA total 576.8Ų
Buried surface area upon binding
BSA apolar 510.1Ų
Hydrophobic contacts buried
BSA polar 66.7Ų
Polar contacts buried
Fraction buried 83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 88.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1661.3Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 627.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)