Molecular metrics status: queued
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Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: weak
Geometry reliability: low
Reason: geometry warning, clashes
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 13
π–π 0
Clashes 10
Severe clashes 1
⚠ Hydrophobic exposure 36%
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 16
Exposed 9
LogP 2.76
H-bonds 7
Exposed fragments:
phenyl (4/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 7.976348063144693 | Score | -19.5289 |
|---|---|---|---|
| Inter norm | -0.696183 | Intra norm | 0.1044 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 28.4 | ||
| Residues | A:NDP301;B:ARG97;B:GLU43;B:ILE45;B:LEU94;B:LYS57;B:MET53;B:PHE56;B:PHE91;B:PRO88;B:SER44;B:SER86;B:THR54;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 | 11 | Native recall | 0.52 |
| Jaccard | 0.46 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.43 |
| H-bond same residue+role | 2 | Role recall | 0.33 |
| H-bond same residue | 2 | Residue recall | 0.33 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 602 | 3.4980537613957687 | -0.684213 | -23.5709 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 686 | 4.92437477206403 | -0.973172 | -27.5856 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2900 | 5.0201541838578745 | -0.573071 | -19.683 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1022 | 5.114437469287031 | -0.828931 | -26.0142 | 6 | 18 | 14 | 0.67 | 0.17 | - | no | Open |
| 685 | 5.216394513217241 | -0.882698 | -28.1892 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1044 | 6.003031949778492 | -0.709141 | -16.628 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1047 | 6.610661532767928 | -0.588855 | -16.7661 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1024 | 6.510680163617971 | -0.749251 | -21.643 | 6 | 18 | 15 | 0.71 | 0.33 | - | yes | Open |
| 2901 | 6.644118692637061 | -0.499245 | -16.8783 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 603 | 6.826511942276714 | -0.671396 | -21.3504 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1023 | 7.163305648661847 | -0.768911 | -16.4742 | 6 | 17 | 14 | 0.67 | 0.33 | - | yes | Open |
| 2898 | 7.77401337863153 | -0.68783 | -19.4084 | 9 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1025 | 7.976348063144693 | -0.696183 | -19.5289 | 7 | 14 | 11 | 0.52 | 0.33 | - | yes | Current |
| 1046 | 8.158597442904012 | -0.604681 | -15.966 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2899 | 9.02547777402997 | -0.737114 | -16.4763 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 687 | 9.121379438290813 | -0.833537 | -25.8139 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 684 | 10.101187914860692 | -1.02348 | -27.0051 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1045 | 10.625349900521783 | -0.605207 | -15.0878 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 601 | 11.716117144152117 | -0.801922 | -28.1702 | 10 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 600 | 13.680140018305867 | -0.732487 | -22.034 | 11 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.