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
Weak
No SASA yet
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA missing
Strain ΔE
30.9 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.80, Jaccard 0.73, H-bond role recall 0.60
Reason: 12 internal clashes
12 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.775 kcal/mol/HA)
✓ Good fit quality (FQ -7.55)
✓ Strong H-bond network (13 bonds)
✗ Very high strain energy (30.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-24.020
kcal/mol
LE
-0.775
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
31
heavy atoms
MW
449
Da
LogP
0.91
cLogP
Interaction summary
HB 13
HY 24
PI 3
CLASH 0
Interaction summary
HB 13
HY 24
PI 3
CLASH 0
| Final rank | 10.081 | Score | -24.020 |
|---|---|---|---|
| Inter norm | -0.843 | Intra norm | 0.068 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 12 clashes; 2 protein clashes; high strain Δ 37.4 | ||
| Residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
PRO88
PRO93
THR180
TYR162
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: 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 | 16 | Native recall | 0.80 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 5 | Strict recall | 0.71 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2260 | 3.14724019652826 | -1.0551 | -30.9043 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3196 | 5.136048579167499 | -0.838335 | -25.9744 | 9 | 17 | 11 | 0.55 | 0.20 | - | no | Open |
| 3197 | 5.20097195670882 | -0.790917 | -23.0209 | 7 | 19 | 17 | 0.85 | 0.40 | - | no | Open |
| 2350 | 5.289250349822516 | -0.729055 | -21.2511 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3195 | 5.65514558211459 | -0.756831 | -22.2178 | 7 | 18 | 17 | 0.85 | 0.40 | - | no | Open |
| 3848 | 6.0038341976356175 | -0.708854 | -20.9839 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 3192 | 6.441102399968017 | -0.781816 | -18.9861 | 4 | 18 | 16 | 0.80 | 0.00 | - | no | Open |
| 2262 | 6.573297377882593 | -1.00816 | -28.0678 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2347 | 5.799412740118183 | -0.654159 | -21.6442 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3847 | 5.973366932852875 | -0.58464 | -20.0479 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3845 | 6.25126610515658 | -0.631851 | -18.3829 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2257 | 6.25577237216327 | -0.822481 | -27.7997 | 9 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2351 | 6.36804630650511 | -0.78397 | -20.7853 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3189 | 6.685156210348343 | -0.907207 | -23.191 | 10 | 19 | 17 | 0.85 | 0.60 | - | yes | Open |
| 3846 | 6.874571387630934 | -0.781668 | -24.4719 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2344 | 7.1076617645969264 | -0.804197 | -21.4019 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2348 | 7.259781782254329 | -0.861067 | -23.541 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2261 | 7.31427310274013 | -0.799045 | -22.9378 | 11 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3849 | 7.557501610212481 | -0.693437 | -19.4445 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2258 | 7.610238480029024 | -0.939095 | -26.5492 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3193 | 8.306322092320112 | -0.855063 | -25.5864 | 10 | 17 | 16 | 0.80 | 0.80 | - | yes | Open |
| 2256 | 8.3135838803556 | -1.03687 | -31.3613 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2346 | 8.314327223036223 | -0.771748 | -22.8533 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2345 | 8.496407969022366 | -0.622338 | -13.2632 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2343 | 8.572586830463608 | -0.684448 | -15.7137 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2352 | 8.812489062965827 | -0.741111 | -22.8108 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2259 | 9.30343687597112 | -0.951859 | -26.8278 | 13 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3194 | 9.453107082248735 | -0.843129 | -21.3432 | 9 | 14 | 10 | 0.50 | 0.20 | - | yes | Open |
| 3191 | 10.080694715660417 | -0.843022 | -24.0197 | 9 | 18 | 16 | 0.80 | 0.60 | - | yes | Current |
| 2349 | 10.669423560542398 | -0.741851 | -18.6963 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3198 | 11.066798145749036 | -0.915104 | -26.3369 | 6 | 18 | 15 | 0.75 | 0.80 | - | yes | Open |
| 2255 | 11.533976230474154 | -1.0013 | -22.1458 | 10 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3190 | 11.88710757828361 | -1.06286 | -27.943 | 11 | 15 | 10 | 0.50 | 0.20 | - | yes | Open |
| 3843 | 12.32323272879669 | -0.687477 | -19.949 | 7 | 12 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3850 | 13.342214058473285 | -0.584575 | -15.4364 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3844 | 13.847472298375893 | -0.765176 | -21.43 | 4 | 13 | 0 | 0.00 | 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
-24.020kcal/mol
Ligand efficiency (LE)
-0.7748kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.549
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.91
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.85kcal/mol
Minimised FF energy
36.98kcal/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.