FAIRMol

Z56833421

Pose ID 1247 Compound 263 Pose 569

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 Z56833421
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
54.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.40
Burial
77%
Hydrophobic fit
75%
Reason: strain 54.9 kcal/mol
strain ΔE 54.9 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.892 kcal/mol/HA) ✓ Good fit quality (FQ -8.22) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (77% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (54.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-23.189
kcal/mol
LE
-0.892
kcal/mol/HA
Fit Quality
-8.22
FQ (Leeson)
HAC
26
heavy atoms
MW
378
Da
LogP
0.79
cLogP
Strain ΔE
54.9 kcal/mol
SASA buried
77%
Lipo contact
75% BSA apolar/total
SASA unbound
639 Ų
Apolar buried
366 Ų

Interaction summary

HB 6 HY 14 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 rank1.772Score-23.189
Inter norm-1.015Intra norm0.124
Top1000noExcludedno
Contacts14H-bonds6
Artifact reasongeometry warning; 7 clashes; 1 protein clash; 1 cofactor-context clash; high strain Δ 54.9
Residues
ALA10 ASP22 ILE8 LEU23 NAP201 PHE35 PRO26 PRO27 SER60 THR57 TRP25 TYR122 VAL116 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
Jaccard0.46RMSD-
HB strict2Strict recall0.40
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
538 1.6890420589433734 -0.876062 -18.5492 5 17 0 0.00 0.00 - no Open
578 1.7455832875701298 -1.04513 -22.1499 6 14 11 0.52 0.40 - no Open
569 1.7724214234298203 -1.01549 -23.1894 6 14 11 0.52 0.40 - no Current
569 1.7783840791674765 -1.0041 -24.7592 6 16 0 0.00 0.00 - no Open
545 2.1801023352322155 -1.14702 -29.589 14 14 0 0.00 0.00 - no Open
578 2.2950088551183443 -0.939152 -19.4559 10 15 0 0.00 0.00 - no Open
572 2.4866872836960074 -1.07884 -24.8429 11 15 0 0.00 0.00 - no Open
573 3.847742802334122 -0.869936 -20.868 10 17 0 0.00 0.00 - no Open
564 4.090578712367698 -0.991863 -19.9768 10 13 0 0.00 0.00 - no Open
595 4.424815777537417 -0.904088 -20.6734 8 14 0 0.00 0.00 - no Open
550 4.437704091940646 -1.08851 -28.813 14 16 0 0.00 0.00 - no Open
548 4.53216170732747 -1.11454 -27.9889 13 18 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 -23.189kcal/mol
Ligand efficiency (LE) -0.8919kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.217
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 378.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.79
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 54.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 144.17kcal/mol
Minimised FF energy 89.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 638.6Ų
Total solvent-accessible surface area of free ligand
BSA total 489.3Ų
Buried surface area upon binding
BSA apolar 365.5Ų
Hydrophobic contacts buried
BSA polar 123.8Ų
Polar contacts buried
Fraction buried 76.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1502.0Ų
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 625.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)