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 strong
SASA missing
Strain ΔE
19.8 kcal/mol
Protein clashes
0
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.50, H-bond role recall 0.40
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.607 kcal/mol/HA)
✓ Good fit quality (FQ -6.08)
✓ Good H-bonds (4 bonds)
✗ Moderate strain (19.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-20.652
kcal/mol
LE
-0.607
kcal/mol/HA
Fit Quality
-6.08
FQ (Leeson)
HAC
34
heavy atoms
MW
469
Da
LogP
6.09
cLogP
Interaction summary
HB 4
HY 24
PI 0
CLASH 2
Interaction summary
HB 4
HY 24
PI 0
CLASH 2
| Final rank | 59.088 | Score | -20.652 |
|---|---|---|---|
| Inter norm | -0.665 | Intra norm | 0.058 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 11 clashes; 2 protein clashes | ||
| Residues |
ARG97
GLY157
ILE45
LEU94
LYS57
LYS90
LYS95
MET53
NDP301
PHE56
PHE91
PRO88
PRO93
THR83
VAL156
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 | 12 | Native recall | 0.60 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
HB · H-bonds
Mode: permissive. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 149 | 4.047887373005908 | -0.516486 | -11.8157 | 3 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 139 | 4.6906090570936625 | -0.536831 | -20.3994 | 1 | 13 | 12 | 0.60 | 0.00 | - | no | Open |
| 138 | 4.905994859984899 | -0.670494 | -25.3015 | 3 | 14 | 13 | 0.65 | 0.00 | - | no | Open |
| 146 | 55.934610089911295 | -0.692774 | -28.1437 | 2 | 15 | 12 | 0.60 | 0.40 | - | yes | Open |
| 147 | 56.34771883473068 | -0.662448 | -25.4322 | 6 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 162 | 56.62391442875628 | -0.717188 | -23.2962 | 2 | 15 | 12 | 0.60 | 0.40 | - | yes | Open |
| 165 | 56.83816213032371 | -0.423343 | -13.6193 | 1 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 164 | 56.91895318372833 | -0.478031 | -16.6032 | 4 | 14 | 10 | 0.50 | 0.00 | - | yes | Open |
| 154 | 57.49057397971445 | -0.529726 | -15.5765 | 1 | 12 | 11 | 0.55 | 0.20 | - | yes | Open |
| 156 | 58.08227678003993 | -0.603221 | -18.1906 | 3 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 153 | 58.1636401838264 | -0.663917 | -19.2432 | 3 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 136 | 58.16980378343325 | -0.541617 | -17.9995 | 2 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 148 | 58.49369130164978 | -0.668917 | -16.4172 | 5 | 15 | 11 | 0.55 | 0.00 | - | yes | Open |
| 143 | 58.660006986060054 | -0.570562 | -16.5023 | 3 | 10 | 7 | 0.35 | 0.00 | - | yes | Open |
| 163 | 59.0878907084202 | -0.664975 | -20.652 | 2 | 16 | 12 | 0.60 | 0.40 | - | yes | Current |
| 142 | 59.094678165216415 | -0.565546 | -17.9421 | 5 | 15 | 13 | 0.65 | 0.40 | - | yes | Open |
| 152 | 59.3801101008321 | -0.435136 | -11.2897 | 1 | 13 | 12 | 0.60 | 0.20 | - | yes | Open |
| 157 | 59.52489744825776 | -0.641126 | -19.7267 | 4 | 15 | 12 | 0.60 | 0.20 | - | yes | Open |
| 134 | 59.52538836541424 | -0.60988 | -18.0373 | 2 | 15 | 10 | 0.50 | 0.20 | - | yes | Open |
| 144 | 59.54156759009728 | -0.714736 | -24.7405 | 2 | 18 | 16 | 0.80 | 0.40 | - | yes | Open |
| 145 | 59.648307015439585 | -0.850289 | -29.6049 | 6 | 18 | 16 | 0.80 | 0.60 | - | yes | Open |
| 161 | 59.9493871750495 | -0.599115 | -22.7478 | 3 | 11 | 7 | 0.35 | 0.00 | - | yes | Open |
| 158 | 60.096423249525046 | -0.669938 | -22.0738 | 4 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 155 | 60.94206863996566 | -0.506885 | -15.7875 | 3 | 12 | 10 | 0.50 | 0.00 | - | yes | Open |
| 141 | 61.112863273097126 | -0.638477 | -17.772 | 5 | 15 | 9 | 0.45 | 0.20 | - | yes | Open |
| 140 | 61.1613288437999 | -0.6849 | -20.9883 | 3 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 150 | 61.54574321719964 | -0.558044 | -16.2437 | 2 | 15 | 9 | 0.45 | 0.20 | - | yes | Open |
| 160 | 61.91170107784806 | -0.587773 | -19.4037 | 7 | 18 | 16 | 0.80 | 0.40 | - | yes | Open |
| 135 | 62.57019389964971 | -0.643455 | -22.1742 | 6 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 159 | 63.879713236990455 | -0.653579 | -22.5869 | 6 | 14 | 12 | 0.60 | 0.00 | - | yes | Open |
| 137 | 64.04549139782667 | -0.518843 | -18.6066 | 7 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 151 | 64.20454014191088 | -0.573451 | -18.4287 | 4 | 13 | 11 | 0.55 | 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
-20.652kcal/mol
Ligand efficiency (LE)
-0.6074kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
468.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.09
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.32kcal/mol
Minimised FF energy
36.51kcal/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.