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 medium
Native strong
SASA missing
Strain ΔE
25.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.75, Jaccard 0.62, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.525 kcal/mol/HA)
✓ Good fit quality (FQ -5.38)
✗ High strain energy (25.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (21)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-19.426
kcal/mol
LE
-0.525
kcal/mol/HA
Fit Quality
-5.38
FQ (Leeson)
HAC
37
heavy atoms
MW
536
Da
LogP
5.36
cLogP
Interaction summary
HB 1
HY 24
PI 3
CLASH 5
Interaction summary
HB 1
HY 24
PI 3
CLASH 5
| Final rank | 57.976 | Score | -19.426 |
|---|---|---|---|
| Inter norm | -0.637 | Intra norm | 0.112 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 21 clashes; 1 protein clash | ||
| Residues |
ALA32
ARG48
ASP52
ILE45
LEU94
MET53
NDP301
PHE56
PHE91
PRO88
SER44
SER86
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
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 | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 661 | 3.9534125250212915 | -0.539084 | -17.6713 | 0 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 670 | 5.302911838111157 | -0.623143 | -20.7284 | 0 | 13 | 12 | 0.60 | 0.00 | - | no | Open |
| 673 | 5.376951321364157 | -0.721597 | -20.3615 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 665 | 5.602785480619648 | -0.58204 | -17.5327 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 662 | 6.204550274643658 | -0.526159 | -19.6742 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 672 | 6.747198210916205 | -0.638524 | -24.3875 | 1 | 14 | 12 | 0.60 | 0.00 | - | no | Open |
| 671 | 56.705449159521564 | -0.617882 | -18.4392 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 667 | 56.267585914789 | -0.717017 | -25.7859 | 0 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 675 | 56.65139428764116 | -0.73125 | -24.359 | 0 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 668 | 56.97328320901291 | -0.676711 | -19.4543 | 1 | 19 | 14 | 0.70 | 0.00 | - | yes | Open |
| 674 | 57.786442039934336 | -0.636941 | -22.9389 | 0 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 666 | 57.97573970045298 | -0.636916 | -19.4259 | 1 | 19 | 15 | 0.75 | 0.00 | - | yes | Current |
| 676 | 58.10712127191333 | -0.631477 | -19.497 | 0 | 17 | 14 | 0.70 | 0.00 | - | yes | Open |
| 664 | 58.44254164882153 | -0.616315 | -18.2137 | 1 | 21 | 16 | 0.80 | 0.00 | - | yes | Open |
| 669 | 58.48977165206177 | -0.56872 | -13.6682 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 663 | 59.19434258309486 | -0.639883 | -18.0876 | 1 | 20 | 16 | 0.80 | 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
-19.426kcal/mol
Ligand efficiency (LE)
-0.5250kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.375
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
535.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.36
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
168.06kcal/mol
Minimised FF energy
142.41kcal/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.