FAIRMol

3CL9

Pose ID 2033 Compound 1459

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
T03
L. major DHFR L. major
Ligand 3CL9

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding weak Geometry low Native strong SASA done
Strain ΔE
51.0 kcal/mol
Protein clashes
0
Internal clashes
0
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 1.00
Burial
91%
Hydrophobic fit
65%
Reason: strain 51.0 kcal/mol
strain ΔE 51.0 kcal/mol
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Strong H-bond network (9 bonds) ✓ Deep burial (91% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Extreme strain energy (51.0 kcal/mol)
HAC
33
heavy atoms
MW
453
Da
LogP
-1.18
cLogP
Strain ΔE
51.0 kcal/mol
SASA buried
91%
Lipo contact
65% BSA apolar/total
SASA unbound
744 Ų
Apolar buried
445 Ų

Interaction summary

HB 9 HY 22 PI 1 CLASH 0

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
No clash · clashes detected for this pose.
Final rank-Score-
Inter norm-Intra norm-
Top1000noExcludedno
Contacts20H-bonds9
Artifact reasonNative reference ligand
Residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap20Native recall1.00
Jaccard1.00RMSD0.00 Å
HB strict7Strict recall1.00
HB same residue+role5HB role recall1.00
HB same residue5HB residue recall1.00

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
- ★ Native - - - 9 20 20 1.00 1.00 0.00 Å no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Heavy atom count 33HA

Physicochemical properties
Molecular weight 453.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.18
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 51.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 111.77kcal/mol
Minimised FF energy 60.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 743.8Ų
Total solvent-accessible surface area of free ligand
BSA total 680.1Ų
Buried surface area upon binding
BSA apolar 445.1Ų
Hydrophobic contacts buried
BSA polar 235.0Ų
Polar contacts buried
Fraction buried 91.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1506.2Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 780.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)