py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.747 kcal/mol/HA)
✓ Good fit quality (FQ -7.34)
✗ Very high strain energy (24.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.888
kcal/mol
LE
-0.747
kcal/mol/HA
Fit Quality
-7.34
FQ (Leeson)
HAC
32
heavy atoms
MW
435
Da
LogP
0.65
cLogP
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 2
Severe clashes 0
| Final rank | 3.610981735712587 | Score | -23.8878 |
|---|---|---|---|
| Inter norm | -0.758568 | Intra norm | 0.0120745 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 13 clashes; 2 protein contact clashes; high strain Δ 26.9 | ||
| Residues | A:NDP301;B:ARG48;B:ASP52;B:ILE45;B:LEU94;B:MET53;B:PHE56;B:PHE91;B:PRO88;B:SER44;B:SER86;B:THR83;B:TRP47;B:VAL156;B:VAL49;B:VAL87 | ||
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:NDP301; B:ALA32; B:ARG97; B:ASP52; B:GLY157; B:ILE45; B:LEU94; B:LYS57; B:MET53; B:PHE55; B:PHE56; B:PHE91; B:PRO88; B:SER86; B:THR180; B:THR83; B:TYR162; B:VAL156; B:VAL30; B:VAL31; B:VAL87 | ||
| Current overlap | 12 | Native recall | 0.57 |
| Jaccard | 0.48 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 696 | 3.610981735712587 | -0.758568 | -23.8878 | 1 | 16 | 12 | 0.57 | 0.00 | - | no | Current |
| 693 | 4.085602005855498 | -0.704945 | -23.1113 | 1 | 20 | 17 | 0.81 | 0.00 | - | no | Open |
| 697 | 4.163423230648344 | -0.854036 | -24.2387 | 1 | 20 | 18 | 0.86 | 0.00 | - | no | Open |
| 685 | 4.23461607874702 | -0.832023 | -24.9795 | 1 | 21 | 18 | 0.86 | 0.00 | - | no | Open |
| 686 | 4.347906685773361 | -0.554062 | -15.8077 | 1 | 11 | 8 | 0.38 | 0.00 | - | no | Open |
| 688 | 4.602213466082693 | -0.646611 | -14.8482 | 1 | 18 | 14 | 0.67 | 0.00 | - | no | Open |
| 694 | 5.267078630146593 | -0.793475 | -24.3561 | 1 | 19 | 18 | 0.86 | 0.00 | - | no | Open |
| 687 | 53.77478225739354 | -0.736545 | -23.5602 | 1 | 17 | 16 | 0.76 | 0.00 | - | no | Open |
| 689 | 54.11364938603942 | -0.708001 | -20.9342 | 1 | 15 | 13 | 0.62 | 0.00 | - | no | Open |
| 690 | 54.125530115725724 | -0.921161 | -28.0447 | 1 | 20 | 18 | 0.86 | 0.00 | - | no | Open |
| 691 | 54.143308804176705 | -0.520913 | -15.2246 | 1 | 10 | 7 | 0.33 | 0.17 | - | no | Open |
| 692 | 54.712771389708934 | -0.537902 | -17.0126 | 1 | 13 | 9 | 0.43 | 0.00 | - | no | Open |
| 699 | 5.002453438480102 | -0.774088 | -20.9243 | 2 | 17 | 17 | 0.81 | 0.00 | - | yes | Open |
| 700 | 5.572610449209327 | -0.622267 | -19.1936 | 1 | 18 | 14 | 0.67 | 0.00 | - | yes | Open |
| 698 | 55.32201350023294 | -0.564031 | -16.8084 | 0 | 12 | 6 | 0.29 | 0.00 | - | yes | Open |
| 695 | 56.64804480159266 | -0.599192 | -19.9787 | 1 | 11 | 8 | 0.38 | 0.17 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.888kcal/mol
Ligand efficiency (LE)
-0.7465kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.341
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
434.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.65
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
235.18kcal/mol
Minimised FF energy
210.73kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. It will be calculated automatically
the next time this pose is loaded if a receptor PDB path is stored.