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
Reject
No SASA yet
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA missing
Strain ΔE
32.7 kcal/mol
Protein clashes
12
Internal clashes
10
Native overlap
contact recall 0.70, Jaccard 0.67, H-bond role recall 0.20
Reason: 12 protein-contact clashes, 10 internal clashes
12 protein-contact clashes
10 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.869 kcal/mol/HA)
✓ Good fit quality (FQ -8.38)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (32.7 kcal/mol)
✗ Geometry warnings
✗ Severe protein-contact clashes (12)
✗ Many internal clashes (10)
ℹ SASA not computed
Score
-26.065
kcal/mol
LE
-0.869
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
30
heavy atoms
MW
457
Da
LogP
4.07
cLogP
Interaction summary
HB 7
HY 24
PI 1
CLASH 0
Interaction summary
HB 7
HY 24
PI 1
CLASH 0
| Final rank | 6.391 | Score | -26.065 |
|---|---|---|---|
| Inter norm | -0.853 | Intra norm | -0.016 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 12 protein contact clashes; high strain Δ 33.1 | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
THR180
TYR162
VAL30
VAL31
| ||
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: permissive.
| 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 | 0.67 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2085 | 3.7455999172086187 | -0.910863 | -24.5258 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2087 | 4.9305657277534 | -0.929606 | -25.0038 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2177 | 5.746147205921879 | -0.914004 | -26.8537 | 3 | 19 | 18 | 0.90 | 0.20 | - | no | Open |
| 2175 | 6.391428284754564 | -0.852881 | -26.065 | 5 | 15 | 14 | 0.70 | 0.20 | - | no | Current |
| 2088 | 7.098387350979841 | -0.867806 | -28.6497 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2176 | 5.320168698013479 | -0.874951 | -24.4856 | 4 | 18 | 17 | 0.85 | 0.20 | - | yes | Open |
| 2178 | 6.444099753091593 | -0.905993 | -28.7764 | 5 | 18 | 17 | 0.85 | 0.20 | - | yes | Open |
| 2086 | 11.452162562313429 | -0.929261 | -26.8997 | 8 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.065kcal/mol
Ligand efficiency (LE)
-0.8688kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.381
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
456.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.07
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
158.10kcal/mol
Minimised FF energy
125.42kcal/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.