FAIRMol

3CL9

Pose ID 6096 Compound 3361

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
T09
L. major DHFR-TS 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
Weak SASA cached
Weak or marginal quality
Binding weak Geometry high Native strong SASA done
Strain ΔE
23.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 1.00
Burial
86%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Strong H-bond network (9 bonds) ✓ Deep burial (86% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ High strain energy (23.0 kcal/mol)
HAC
33
heavy atoms
MW
452
Da
LogP
0.01
cLogP
Strain ΔE
23.0 kcal/mol
SASA buried
86%
Lipo contact
65% BSA apolar/total
SASA unbound
738 Ų
Apolar buried
411 Ų

Interaction summary

HB 9 HY 23 PI 2 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 rank-Score-
Inter norm-Intra norm-
Top1000noExcludedno
Contacts21H-bonds9
Artifact reasonNative reference ligand
Residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 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.
Name3CL9Contacts21
PoseOpen native poseHB0
IFP residues
NDP301 ALA32 ARG97 ASP52 GLY157 ILE45 LEU94 LYS57 MET53 PHE55 PHE56 PHE91 PRO88 SER86 THR180 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap21Native recall1.00
Jaccard1.00RMSD0.00 Å
HB strict7Strict recall1.00
HB same residue+role6HB role recall1.00
HB same residue6HB residue recall1.00

Protein summary

511 residues
Protein targetT09Atoms8170
Residues511Chains2
Residue summaryLEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

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 21 21 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 452.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.01
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 138.88kcal/mol
Minimised FF energy 115.90kcal/mol

SASA & burial

✓ computed
SASA (unbound) 738.5Ų
Total solvent-accessible surface area of free ligand
BSA total 635.2Ų
Buried surface area upon binding
BSA apolar 410.9Ų
Hydrophobic contacts buried
BSA polar 224.3Ų
Polar contacts buried
Fraction buried 86.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3231.4Ų
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 4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1645.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)