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 (-0.541 kcal/mol/HA)
✓ Good fit quality (FQ -5.78)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (41.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.820
kcal/mol
LE
-0.541
kcal/mol/HA
Fit Quality
-5.78
FQ (Leeson)
HAC
44
heavy atoms
MW
607
Da
LogP
3.95
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 41.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 4
Clashes 15
Severe clashes 2
| Final rank | 11.559469917061858 | Score | -23.8198 |
|---|---|---|---|
| Inter norm | -0.579467 | Intra norm | 0.0381073 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 16 clashes; 2 protein clashes; high strain Δ 42.4 | ||
| Residues | A:ARG97;A:ASP52;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:THR54;A:THR83;A:VAL156;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.55 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 219 | 4.6302099942158925 | -0.503435 | -20.6429 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 139 | 5.794697303459581 | -0.392755 | -18.0678 | 3 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 217 | 6.116056632700398 | -0.50366 | -23.1694 | 0 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 7.619680315638954 | -0.494608 | -15.7059 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 213 | 8.172789639007322 | -0.580209 | -26.3337 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 215 | 9.068038958891496 | -0.603154 | -21.3249 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 140 | 9.672599851697436 | -0.400196 | -15.5328 | 5 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 241 | 10.053624366210254 | -0.560046 | -30.1296 | 1 | 13 | 10 | 0.50 | 0.00 | - | no | Open |
| 240 | 7.341478671968607 | -0.584644 | -25.7145 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 222 | 8.07721139061682 | -0.516534 | -17.9777 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 137 | 8.575914499429317 | -0.396661 | -16.5688 | 2 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 245 | 8.881429646481902 | -0.573363 | -19.1523 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 220 | 9.438224068420311 | -0.602712 | -19.2251 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 214 | 9.96079017008822 | -0.520144 | -26.0539 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 246 | 10.489749462601512 | -0.608072 | -18.308 | 2 | 20 | 18 | 0.90 | 0.00 | - | yes | Open |
| 216 | 11.234574649205847 | -0.49917 | -18.3088 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 244 | 11.559469917061858 | -0.579467 | -23.8198 | 3 | 14 | 12 | 0.60 | 0.20 | - | yes | Current |
| 242 | 12.209807756178435 | -0.581409 | -25.4869 | 1 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 221 | 12.806466053653423 | -0.59562 | -21.5257 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 218 | 58.63076534262176 | -0.579693 | -21.4408 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 138 | 58.913850953012265 | -0.516596 | -20.5496 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 243 | 63.24444273701941 | -0.606511 | -27.6238 | 3 | 15 | 12 | 0.60 | 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
-23.820kcal/mol
Ligand efficiency (LE)
-0.5414kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.784
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
606.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.95
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
154.54kcal/mol
Minimised FF energy
112.60kcal/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.