Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
Viewer legend
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
38.0 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.75, Jaccard 0.68, H-bond role recall 0.00
Reason: 15 internal clashes
15 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.492 kcal/mol/HA)
✓ Good fit quality (FQ -4.88)
✗ Very high strain energy (38.0 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Many internal clashes (15)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-16.227
kcal/mol
LE
-0.492
kcal/mol/HA
Fit Quality
-4.88
FQ (Leeson)
HAC
33
heavy atoms
MW
450
Da
LogP
-0.28
cLogP
Interaction summary
HB 0
HY 24
PI 0
CLASH 0
Interaction summary
HB 0
HY 24
PI 0
CLASH 0
| Final rank | 55.745 | Score | -16.227 |
|---|---|---|---|
| Inter norm | -0.685 | Intra norm | 0.193 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 0 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
PHE56
PHE91
PRO50
PRO88
SER86
THR54
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 | 15 | Native recall | 0.75 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
HB · H-bonds
No hb · h-bonds detected for this pose.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2161 | 4.3782230484754265 | -0.567269 | -19.0306 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1644 | 4.62721433170881 | -0.634089 | -21.4944 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1638 | 4.655002588446546 | -0.673674 | -22.011 | 1 | 14 | 10 | 0.50 | 0.00 | - | no | Open |
| 1637 | 4.7070361837340275 | -0.639717 | -14.2427 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1633 | 4.729953295512503 | -0.85085 | -23.9835 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 2156 | 4.7754537615867685 | -0.585347 | -15.5436 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1642 | 4.818702465343748 | -0.60818 | -19.4837 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 2158 | 5.502538791575042 | -0.625466 | -19.4358 | 1 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 1639 | 53.670220236953455 | -0.655876 | -22.5279 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1634 | 53.809682699443286 | -0.743176 | -21.6774 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 1636 | 53.9453954568506 | -0.660946 | -20.7646 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 2159 | 54.163381058124116 | -0.588296 | -19.5859 | 2 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 2163 | 54.16789142741234 | -0.679053 | -20.5486 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1635 | 54.1984144159069 | -0.674292 | -21.5338 | 2 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 2157 | 54.45603665938433 | -0.582515 | -16.3419 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2162 | 54.84033681809107 | -0.564509 | -17.7505 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2160 | 54.840572484676954 | -0.521303 | -13.7567 | 3 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 1641 | 5.514855704594468 | -0.801783 | -24.2184 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1640 | 55.74529969784381 | -0.68451 | -16.227 | 0 | 17 | 15 | 0.75 | 0.00 | - | yes | Current |
| 1643 | 56.5408976991009 | -0.751697 | -20.6951 | 0 | 16 | 13 | 0.65 | 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
-16.227kcal/mol
Ligand efficiency (LE)
-0.4917kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.879
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
449.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.28
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
327.09kcal/mol
Minimised FF energy
289.11kcal/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.