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 (-0.489 kcal/mol/HA)
✓ Good fit quality (FQ -4.89)
✗ Very high strain energy (35.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-16.617
kcal/mol
LE
-0.489
kcal/mol/HA
Fit Quality
-4.89
FQ (Leeson)
HAC
34
heavy atoms
MW
464
Da
LogP
0.99
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 35.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 55.57658181918738 | Score | -16.6171 |
|---|---|---|---|
| Inter norm | -0.600434 | Intra norm | 0.111695 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 18 clashes; 8 protein contact clashes | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:VAL156;A:VAL49 | ||
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 | 12 | Native recall | 0.60 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 877 | 3.857447919034857 | -0.570616 | -14.7968 | 0 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 880 | 4.5961667148282555 | -0.601952 | -20.6166 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 866 | 4.864209217622374 | -0.634879 | -21.0373 | 1 | 18 | 17 | 0.85 | 0.00 | - | no | Open |
| 872 | 5.003125212117427 | -0.632599 | -19.2353 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 867 | 5.30078440773163 | -0.606373 | -19.7543 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 876 | 6.755051744761572 | -0.57288 | -8.07071 | 0 | 15 | 12 | 0.60 | 0.00 | - | no | Open |
| 874 | 54.42369432530859 | -0.626596 | -18.2849 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 865 | 55.570417160589365 | -0.61984 | -18.9754 | 1 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 868 | 55.57658181918738 | -0.600434 | -16.6171 | 1 | 16 | 12 | 0.60 | 0.00 | - | no | Current |
| 879 | 56.550002808274606 | -0.738811 | -20.6638 | 1 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 871 | 55.77976207528753 | -0.663119 | -22.8765 | 2 | 19 | 18 | 0.90 | 0.20 | - | yes | Open |
| 873 | 57.51735746049259 | -0.605707 | -13.4565 | 1 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 875 | 57.533540786527304 | -0.718681 | -21.3839 | 1 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
| 869 | 57.703830182264944 | -0.617531 | -18.9599 | 2 | 18 | 17 | 0.85 | 0.00 | - | yes | Open |
| 878 | 57.7707648993221 | -0.753592 | -23.3915 | 0 | 21 | 18 | 0.90 | 0.00 | - | yes | Open |
| 870 | 57.78359505053971 | -0.780724 | -25.5784 | 0 | 20 | 17 | 0.85 | 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
-16.617kcal/mol
Ligand efficiency (LE)
-0.4887kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.890
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.99
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
218.38kcal/mol
Minimised FF energy
182.66kcal/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.