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 high
Native mixed
SASA missing
Strain ΔE
18.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.45, Jaccard 0.39, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.762 kcal/mol/HA)
✓ Good fit quality (FQ -7.42)
✓ Strong H-bond network (9 bonds)
✗ Moderate strain (18.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-23.618
kcal/mol
LE
-0.762
kcal/mol/HA
Fit Quality
-7.42
FQ (Leeson)
HAC
31
heavy atoms
MW
451
Da
LogP
4.37
cLogP
Interaction summary
HB 9
HY 24
PI 2
CLASH 2
Interaction summary
HB 9
HY 24
PI 2
CLASH 2
| Final rank | 8.249 | Score | -23.618 |
|---|---|---|---|
| Inter norm | -0.815 | Intra norm | 0.053 |
| Top1000 | no | Excluded | yes |
| Contacts | 12 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 10 clashes; 2 protein clashes; high strain Δ 21.1 | ||
| Residues |
ARG97
ILE45
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO93
THR54
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: 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 | 9 | Native recall | 0.45 |
| Jaccard | 0.39 | 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: 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3004 | 3.9668595301518597 | -1.02439 | -27.3199 | 2 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 2253 | 5.327401996336064 | -0.746834 | -18.085 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3002 | 6.351191444178622 | -0.787944 | -20.8633 | 0 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 2251 | 6.513145329437519 | -0.653949 | -16.9668 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3003 | 8.248678926211404 | -0.815038 | -23.6177 | 3 | 12 | 9 | 0.45 | 0.20 | - | yes | Current |
| 2252 | 8.620171025639754 | -0.797963 | -29.2064 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2254 | 58.268724196618294 | -0.910914 | -25.7999 | 12 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3005 | 58.59849774154099 | -0.78957 | -17.4738 | 3 | 11 | 8 | 0.40 | 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
-23.618kcal/mol
Ligand efficiency (LE)
-0.7619kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.422
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
450.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
83.75kcal/mol
Minimised FF energy
64.95kcal/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.