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 (-0.536 kcal/mol/HA)
✓ Good fit quality (FQ -5.49)
✗ Very high strain energy (32.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-19.836
kcal/mol
LE
-0.536
kcal/mol/HA
Fit Quality
-5.49
FQ (Leeson)
HAC
37
heavy atoms
MW
505
Da
LogP
2.13
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 32.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 13
Severe clashes 0
| Final rank | 56.99250837726805 | Score | -19.8358 |
|---|---|---|---|
| Inter norm | -0.66107 | Intra norm | 0.124967 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 1 |
| Artifact reason | geometry warning; 18 clashes; 13 protein contact clashes | ||
| Residues | A:ARG48;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:THR54;A:TRP47;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 | 10 | Native recall | 0.50 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1036 | 6.040167256888968 | -0.570276 | -13.6236 | 1 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1037 | 6.500205410908672 | -0.620362 | -7.52566 | 3 | 17 | 17 | 0.85 | 0.40 | - | no | Open |
| 1041 | 6.6335417783526545 | -0.61173 | -14.4941 | 2 | 11 | 10 | 0.50 | 0.20 | - | no | Open |
| 1030 | 55.840644265476705 | -0.687985 | -17.9249 | 3 | 20 | 16 | 0.80 | 0.60 | - | no | Open |
| 1039 | 55.95962592265152 | -0.646463 | -18.6632 | 2 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 1038 | 56.99250837726805 | -0.66107 | -19.8358 | 1 | 14 | 10 | 0.50 | 0.00 | - | no | Current |
| 1043 | 55.46851169828177 | -0.620437 | -15.503 | 1 | 18 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1042 | 55.73488370917697 | -0.736355 | -22.7584 | 3 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1044 | 55.862707120911196 | -0.591662 | -16.762 | 1 | 18 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1034 | 55.9253695510773 | -0.626949 | -15.7972 | 1 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1033 | 56.57634558011572 | -0.773302 | -26.0308 | 3 | 18 | 16 | 0.80 | 0.60 | - | yes | Open |
| 1031 | 57.364221994612116 | -0.648093 | -20.4471 | 1 | 17 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1029 | 57.677095888198714 | -0.742128 | -27.4152 | 2 | 15 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1032 | 60.33512018490798 | -0.659271 | -22.6612 | 1 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1035 | 61.670101345633064 | -0.574155 | -16.0253 | 2 | 15 | 10 | 0.50 | 0.20 | - | yes | Open |
| 1040 | 62.995162632540996 | -0.592893 | -13.4579 | 1 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.836kcal/mol
Ligand efficiency (LE)
-0.5361kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.489
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
504.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.13
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.85kcal/mol
Minimised FF energy
40.82kcal/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.