Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
No SASA yet
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA missing
Strain ΔE
15.6 kcal/mol
Protein clashes
6
Internal clashes
15
Native overlap
contact recall 0.85, Jaccard 0.77, H-bond role recall 0.20
Reason: 15 internal clashes
6 protein-contact clashes
15 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.808 kcal/mol/HA)
✓ Good fit quality (FQ -7.87)
✓ Good H-bonds (3 bonds)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (15)
ℹ SASA not computed
Score
-25.051
kcal/mol
LE
-0.808
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
31
heavy atoms
MW
413
Da
LogP
3.02
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
| Final rank | 4.356 | Score | -25.051 |
|---|---|---|---|
| Inter norm | -0.849 | Intra norm | 0.041 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 6 protein contact clashes; moderate strain Δ 15.8 | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE55
PHE56
PHE91
PRO88
SER86
THR180
TYR162
TYR178
VAL30
VAL31
VAL87
| ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU: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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 17 | Native recall | 0.85 |
| Jaccard | 0.77 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 355 | 3.57838899383271 | -0.800245 | -20.3634 | 3 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 425 | 3.6448787780462286 | -0.823752 | -24.162 | 1 | 19 | 18 | 0.90 | 0.20 | - | no | Open |
| 423 | 4.355630340910759 | -0.849221 | -25.0512 | 3 | 19 | 17 | 0.85 | 0.20 | - | no | Current |
| 373 | 4.603056154697007 | -0.666846 | -20.2303 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 5.255604267396025 | -0.753426 | -19.7441 | 5 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 371 | 4.365133445288876 | -0.632329 | -19.228 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 372 | 5.533507926318224 | -0.700886 | -19.808 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 353 | 6.517390336928039 | -0.836262 | -25.736 | 5 | 21 | 1 | 0.05 | 0.00 | - | yes | Open |
| 424 | 6.921673466316996 | -0.789527 | -19.5675 | 1 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.051kcal/mol
Ligand efficiency (LE)
-0.8081kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.873
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
412.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.02
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.25kcal/mol
Minimised FF energy
32.69kcal/mol
SASA & burial
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate SASA burial metrics without blocking the page.