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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA missing
Strain ΔE
30.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.70, Jaccard 0.61, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.693 kcal/mol/HA)
✓ Good fit quality (FQ -7.10)
✗ Very high strain energy (30.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-25.656
kcal/mol
LE
-0.693
kcal/mol/HA
Fit Quality
-7.10
FQ (Leeson)
HAC
37
heavy atoms
MW
517
Da
LogP
5.19
cLogP
Interaction summary
HB 1
HY 24
PI 2
CLASH 1
Interaction summary
HB 1
HY 24
PI 2
CLASH 1
| Final rank | 8.399 | Score | -25.656 |
|---|---|---|---|
| Inter norm | -0.738 | Intra norm | 0.044 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 17 clashes; 2 protein clashes; high strain Δ 30.7 | ||
| Residues |
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR83
TRP47
VAL156
VAL49
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 | 14 | Native recall | 0.70 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1934 | 7.287963904486295 | -0.570791 | -19.1898 | 2 | 14 | 12 | 0.60 | 0.20 | - | no | Open |
| 1935 | 7.695504257605581 | -0.645211 | -23.9468 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1933 | 8.399052943030991 | -0.737716 | -25.6557 | 1 | 17 | 14 | 0.70 | 0.20 | - | yes | Current |
| 1936 | 60.15708035878353 | -0.667604 | -16.5442 | 2 | 15 | 12 | 0.60 | 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
-25.656kcal/mol
Ligand efficiency (LE)
-0.6934kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.099
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
516.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.19
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.58kcal/mol
Minimised FF energy
67.89kcal/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.