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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.773 kcal/mol/HA)
✓ Good fit quality (FQ -7.45)
✗ High strain energy (14.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.183
kcal/mol
LE
-0.773
kcal/mol/HA
Fit Quality
-7.45
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
4.83
cLogP
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 4.941176211073369 | Score | -23.1829 |
|---|---|---|---|
| Inter norm | -0.814242 | Intra norm | 0.04148 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | geometry warning; 15 clashes; 8 protein contact clashes; moderate strain Δ 14.3 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;A: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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1774 | 3.573288050063608 | -0.772999 | -21.9004 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2504 | 3.660721520100676 | -0.729517 | -21.5858 | 1 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 1862 | 3.87219139404224 | -0.815061 | -23.24 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 1859 | 4.044797902455198 | -0.841637 | -24.6125 | 2 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 1775 | 4.083144695775258 | -0.728624 | -21.6912 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1853 | 4.10184010020892 | -0.880758 | -27.1162 | 2 | 20 | 17 | 0.85 | 0.20 | - | no | Open |
| 1867 | 4.119210628346155 | -0.827872 | -25.7791 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 2510 | 4.1921996790157605 | -0.70955 | -21.5318 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 4.2026533814878615 | -1.07778 | -24.1679 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1769 | 4.306591512368701 | -0.764589 | -21.6771 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1856 | 4.44984162506596 | -0.826813 | -25.0381 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 1865 | 4.489069700446324 | -0.853108 | -26.2028 | 2 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 1857 | 4.60207313262103 | -0.870965 | -25.5233 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 1860 | 4.941176211073369 | -0.814242 | -23.1829 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Current |
| 2512 | 4.9499879180043935 | -0.533637 | -15.8118 | 1 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 1772 | 5.084244868679373 | -0.720538 | -19.5788 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2515 | 5.08998407023543 | -0.723521 | -21.8715 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1770 | 5.539903271014922 | -0.661452 | -20.0834 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 5.609142162413652 | -0.97887 | -28.4095 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1777 | 5.827949941320511 | -0.826804 | -24.4048 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2507 | 6.028855781518878 | -0.674504 | -18.8887 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 6.069152296260166 | -0.848161 | -20.0064 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1861 | 54.23584161740301 | -0.866582 | -27.591 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 671 | 55.84034710540824 | -1.0461 | -31.3666 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2513 | 56.752684427219364 | -0.511399 | -15.524 | 1 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 669 | 57.88244178748334 | -0.876207 | -24.1328 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1855 | 7.426943019173197 | -0.821617 | -22.7875 | 1 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 2505 | 7.663017115939302 | -0.746292 | -21.2169 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1868 | 53.97468230510326 | -0.855091 | -27.5803 | 1 | 14 | 10 | 0.50 | 0.00 | - | yes | Open |
| 1866 | 55.06104951731334 | -0.84078 | -25.006 | 1 | 16 | 12 | 0.60 | 0.00 | - | yes | Open |
| 2509 | 55.63878368400333 | -0.708493 | -20.9189 | 1 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2508 | 55.73331777063794 | -0.650146 | -18.1186 | 4 | 13 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1780 | 55.80983335278023 | -0.740289 | -22.3618 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1779 | 55.99983980577713 | -0.680155 | -19.0918 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2514 | 56.14429881458122 | -0.634465 | -17.5186 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 665 | 56.26304349817779 | -0.970114 | -28.504 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 668 | 56.38329802096 | -0.64718 | -18.107 | 1 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1778 | 56.779784950041396 | -0.739517 | -20.636 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2511 | 56.836178833386235 | -0.837185 | -23.5688 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1776 | 56.85110481560109 | -0.694955 | -18.2006 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1771 | 57.31615126997281 | -0.932011 | -24.247 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2506 | 57.52170037018265 | -0.793715 | -22.691 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1863 | 57.59809028730185 | -0.89876 | -26.375 | 3 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1854 | 57.75508683658262 | -0.974356 | -27.3918 | 2 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1864 | 58.08813499175179 | -0.767908 | -21.731 | 1 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1773 | 58.49758287988025 | -0.763956 | -24.47 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1858 | 58.8597175338021 | -0.981518 | -26.8425 | 3 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
| 667 | 60.42742215940044 | -0.63983 | -9.58648 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.183kcal/mol
Ligand efficiency (LE)
-0.7728kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.454
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
397.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.83
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
85.72kcal/mol
Minimised FF energy
71.58kcal/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.