FAIRMol

Z49565795

Pose ID 635 Compound 563 Pose 635

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
T01
Human DHFR Human
Ligand Z49565795
PDB5SD8↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
14.2 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.48, Jaccard 0.40, H-bond role recall 0.00
Burial
84%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
3 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.966 kcal/mol/HA) ✓ Good fit quality (FQ -9.01) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (14.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-26.088
kcal/mol
LE
-0.966
kcal/mol/HA
Fit Quality
-9.01
FQ (Leeson)
HAC
27
heavy atoms
MW
355
Da
LogP
3.37
cLogP
Strain ΔE
14.2 kcal/mol
SASA buried
84%
Lipo contact
84% BSA apolar/total
SASA unbound
597 Ų
Apolar buried
421 Ų

Interaction summary

HB 2 HY 24 PI 4 CLASH 4
Final rank3.325Score-26.088
Inter norm-0.986Intra norm0.020
Top1000noExcludedno
Contacts14H-bonds2
Artifact reasongeometry warning; 13 clashes; 2 protein clashes; 1 cofactor-context clash
Residues
ALA10 ARG29 GLU31 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 TRP25 TYR122 VAL116 VAL9

Protein summary

200 residues
Protein targetT01Atoms3128
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

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 overlap10Native recall0.48
Jaccard0.40RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
668 2.219769786585919 -1.13327 -31.1956 5 21 0 0.00 0.00 - no Open
649 3.083294048470608 -1.01992 -27.9507 6 17 0 0.00 0.00 - no Open
635 3.324688483197734 -0.985934 -26.0878 2 14 10 0.48 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 -26.088kcal/mol
Ligand efficiency (LE) -0.9662kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.014
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.37
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 126.92kcal/mol
Minimised FF energy 112.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 597.3Ų
Total solvent-accessible surface area of free ligand
BSA total 502.8Ų
Buried surface area upon binding
BSA apolar 420.7Ų
Hydrophobic contacts buried
BSA polar 82.0Ų
Polar contacts buried
Fraction buried 84.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1560.0Ų
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 626.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)