FAIRMol

Z49691086

Pose ID 1165 Compound 138 Pose 487

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 Z49691086
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 strong SASA done
Strain ΔE
44.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.86, Jaccard 0.72, H-bond role recall 0.00
Burial
85%
Hydrophobic fit
87%
Reason: strain 44.2 kcal/mol
strain ΔE 44.2 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.584 kcal/mol/HA) ✓ Good fit quality (FQ -6.14) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Extreme strain energy (44.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-23.961
kcal/mol
LE
-0.584
kcal/mol/HA
Fit Quality
-6.14
FQ (Leeson)
HAC
41
heavy atoms
MW
589
Da
LogP
6.42
cLogP
Strain ΔE
44.2 kcal/mol
SASA buried
85%
Lipo contact
87% BSA apolar/total
SASA unbound
847 Ų
Apolar buried
628 Ų

Interaction summary

HB 1 HY 24 PI 3 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 rank2.792Score-23.961
Inter norm-0.628Intra norm0.044
Top1000noExcludedno
Contacts22H-bonds1
Artifact reasongeometry warning; 17 clashes; 1 protein clash; high strain Δ 44.0
Residues
ALA10 ARG29 ASN65 ASP22 GLU31 GLY21 ILE61 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 PRO27 PRO62 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 overlap18Native recall0.86
Jaccard0.72RMSD-
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
494 1.1779785607197466 -0.63534 -23.9924 4 19 15 0.71 0.20 - no Open
445 2.297742431915645 -0.478985 -17.4837 6 12 0 0.00 0.00 - no Open
487 2.791937129485576 -0.628302 -23.9607 1 22 18 0.86 0.00 - 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 -23.961kcal/mol
Ligand efficiency (LE) -0.5844kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.141
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 41HA

Physicochemical properties
Molecular weight 589.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.42
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 44.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 17.24kcal/mol
Minimised FF energy -26.91kcal/mol

SASA & burial

✓ computed
SASA (unbound) 846.7Ų
Total solvent-accessible surface area of free ligand
BSA total 723.4Ų
Buried surface area upon binding
BSA apolar 628.0Ų
Hydrophobic contacts buried
BSA polar 95.4Ų
Polar contacts buried
Fraction buried 85.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1798.3Ų
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 599.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)