Molecular metrics status: done
Cached molecular metrics are available for this pose.
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.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.685 kcal/mol/HA)
✓ Good fit quality (FQ -6.96)
✗ Very high strain energy (21.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.655
kcal/mol
LE
-0.685
kcal/mol/HA
Fit Quality
-6.96
FQ (Leeson)
HAC
36
heavy atoms
MW
481
Da
LogP
5.01
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 21.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 0
| Final rank | 4.350338939990905 | Score | -24.6555 |
|---|---|---|---|
| Inter norm | -0.726066 | Intra norm | 0.0411924 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | geometry warning; 14 clashes; 5 protein contact clashes; high strain Δ 22.0 | ||
| Residues | A:ALA32;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR54;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.73 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1901 | 3.813320685633798 | -0.629863 | -21.0671 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1908 | 4.350338939990905 | -0.726066 | -24.6555 | 1 | 18 | 16 | 0.80 | 0.00 | - | no | Current |
| 1894 | 4.99036972511015 | -0.776466 | -25.0259 | 0 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 1902 | 5.032221009120559 | -0.67067 | -21.5234 | 0 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 1897 | 5.486617619338673 | -0.610747 | -21.7595 | 1 | 14 | 11 | 0.55 | 0.00 | - | no | Open |
| 1907 | 5.816070842568658 | -0.712561 | -24.2302 | 0 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1904 | 5.9725124119045025 | -0.754954 | -26.3144 | 0 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1898 | 6.021140291254321 | -0.698834 | -24.4955 | 0 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1892 | 6.478805577430673 | -0.722671 | -24.9882 | 1 | 18 | 16 | 0.80 | 0.00 | - | no | Open |
| 1899 | 55.502533057472846 | -0.742122 | -24.3996 | 0 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 1893 | 55.74307291875543 | -0.718163 | -20.582 | 0 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1900 | 55.95282949846298 | -0.76456 | -24.1689 | 2 | 19 | 17 | 0.85 | 0.00 | - | no | Open |
| 1896 | 56.97309091989475 | -0.851756 | -26.8666 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 1889 | 7.208446177498278 | -0.615759 | -19.749 | 1 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1906 | 7.291606048711517 | -0.706765 | -24.0744 | 0 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1891 | 7.478741697608388 | -0.670419 | -22.3692 | 1 | 15 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1895 | 56.72343372882995 | -0.731619 | -24.8279 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1905 | 56.81526304275887 | -0.630639 | -20.9122 | 0 | 22 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1903 | 57.51413870768998 | -0.608112 | -10.259 | 1 | 13 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1890 | 57.904152707300746 | -0.701883 | -25.5158 | 0 | 19 | 15 | 0.75 | 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
-24.655kcal/mol
Ligand efficiency (LE)
-0.6849kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.961
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
480.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.01
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
91.55kcal/mol
Minimised FF energy
70.55kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.