Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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
26.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.52, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (14/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.881 kcal/mol/HA)
✓ Good fit quality (FQ -8.74)
✓ Good H-bonds (5 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (26.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-29.076
kcal/mol
LE
-0.881
kcal/mol/HA
Fit Quality
-8.74
FQ (Leeson)
HAC
33
heavy atoms
MW
454
Da
LogP
3.86
cLogP
Final rank
3.3242
rank score
Inter norm
-0.962
normalised
Contacts
17
H-bonds 9
Interaction summary
HBD 3
HBA 2
HY 7
PI 2
CLASH 2
Interaction summary
HBD 3
HBA 2
HY 7
PI 2
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 13 | Native recall | 0.62 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.50 |
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU: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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 252 | 2.3798004038943423 | -1.0212 | -25.285 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 210 | 2.4494532002174654 | -0.823637 | -22.9301 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 310 | 2.552007957651151 | -0.854858 | -22.3807 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 293 | 2.8801978461699402 | -0.695516 | -20.8755 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 225 | 3.3242163212911824 | -0.962012 | -29.0765 | 9 | 17 | 13 | 0.62 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.076kcal/mol
Ligand efficiency (LE)
-0.8811kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.742
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
453.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.54kcal/mol
Minimised FF energy
40.22kcal/mol
SASA & burial
✓ computed
SASA (unbound)
739.0Ų
Total solvent-accessible surface area of free ligand
BSA total
618.7Ų
Buried surface area upon binding
BSA apolar
492.7Ų
Hydrophobic contacts buried
BSA polar
126.0Ų
Polar contacts buried
Fraction buried
83.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3364.8Ų
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
1667.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)