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
24.1 kcal/mol
Protein clashes
5
Internal clashes
10
Native overlap
contact recall 0.65, Jaccard 0.57, H-bond role recall 0.80
Reason: 10 internal clashes
5 protein-contact clashes
10 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.991 kcal/mol/HA)
✓ Good fit quality (FQ -9.13)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (24.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (10)
ℹ SASA not computed
Score
-25.774
kcal/mol
LE
-0.991
kcal/mol/HA
Fit Quality
-9.13
FQ (Leeson)
HAC
26
heavy atoms
MW
369
Da
LogP
2.83
cLogP
Interaction summary
HB 8
HY 24
PI 1
CLASH 0
Interaction summary
HB 8
HY 24
PI 1
CLASH 0
| Final rank | 3.680 | Score | -25.774 |
|---|---|---|---|
| Inter norm | -1.114 | Intra norm | 0.123 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 10 clashes; 5 protein contact clashes; high strain Δ 27.1 | ||
| Residues |
ALA32
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
TRP47
TYR162
VAL30
VAL31
VAL49
| ||
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 | 13 | Native recall | 0.65 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2761 | 3.679571422655938 | -1.1141 | -25.774 | 8 | 16 | 13 | 0.65 | 0.80 | - | no | Current |
| 2015 | 3.9637882795787753 | -0.708788 | -16.62 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1783 | 4.50899255342546 | -0.950014 | -21.6522 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 3392 | 5.024280167565795 | -0.760226 | -18.4075 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2016 | 5.249917048313938 | -0.868198 | -19.1442 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3393 | 5.836985889792018 | -0.931065 | -21.7495 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1784 | 4.8360261066062575 | -1.03976 | -24.8291 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2762 | 9.507763869675289 | -0.946253 | -22.0577 | 7 | 15 | 11 | 0.55 | 0.40 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.774kcal/mol
Ligand efficiency (LE)
-0.9913kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.133
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
369.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.83
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
34.98kcal/mol
Minimised FF energy
10.92kcal/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.