FAIRMol

Z18797806

Pose ID 642 Compound 272 Pose 642

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 Z18797806
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 high Native strong SASA done
Strain ΔE
13.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.00
Burial
85%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.917 kcal/mol/HA) ✓ Good fit quality (FQ -8.85) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Moderate strain (13.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-27.509
kcal/mol
LE
-0.917
kcal/mol/HA
Fit Quality
-8.85
FQ (Leeson)
HAC
30
heavy atoms
MW
421
Da
LogP
4.62
cLogP
Strain ΔE
13.4 kcal/mol
SASA buried
85%
Lipo contact
84% BSA apolar/total
SASA unbound
692 Ų
Apolar buried
498 Ų

Interaction summary

HB 2 HY 24 PI 3 CLASH 1
Final rank1.795Score-27.509
Inter norm-0.860Intra norm-0.057
Top1000noExcludedno
Contacts17H-bonds2
Artifact reasongeometry warning; 12 clashes; 1 protein clash
Residues
ARG29 ASN65 GLU31 ILE61 ILE8 LEU23 LEU28 LEU68 NAP201 PHE32 PHE35 PRO27 PRO62 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 overlap13Native recall0.62
Jaccard0.52RMSD-
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
648 1.0067689689367874 -0.853561 -28.7274 1 18 14 0.67 0.00 - no Open
642 1.7947821590494437 -0.859943 -27.5094 2 17 13 0.62 0.00 - no Current
667 3.6844563727899438 -0.691562 -23.0759 4 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 -27.509kcal/mol
Ligand efficiency (LE) -0.9170kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.845
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 420.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.62
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 36.28kcal/mol
Minimised FF energy 22.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 691.8Ų
Total solvent-accessible surface area of free ligand
BSA total 589.4Ų
Buried surface area upon binding
BSA apolar 498.1Ų
Hydrophobic contacts buried
BSA polar 91.3Ų
Polar contacts buried
Fraction buried 85.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1618.0Ų
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 653.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)