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 (-0.516 kcal/mol/HA)
✓ Good fit quality (FQ -5.32)
✗ Very high strain energy (33.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.599
kcal/mol
LE
-0.516
kcal/mol/HA
Fit Quality
-5.32
FQ (Leeson)
HAC
38
heavy atoms
MW
517
Da
LogP
1.88
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 33.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 12
Severe clashes 1
| Final rank | 58.29120286658544 | Score | -19.5994 |
|---|---|---|---|
| Inter norm | -0.589616 | Intra norm | 0.073844 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 19 clashes; 1 protein clash | ||
| Residues | A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:SER44;A:SER86;A:THR54;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 | 11 | Native recall | 0.55 |
| Jaccard | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1087 | 4.3225639031029095 | -0.469067 | -15.5351 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1682 | 4.822428782793232 | -0.574973 | -20.0078 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1086 | 5.101010899152662 | -0.371815 | -12.4097 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1295 | 5.39625897207715 | -0.573677 | -19.4394 | 1 | 19 | 14 | 0.70 | 0.00 | - | no | Open |
| 1081 | 5.58153289922701 | -0.390228 | -16.9009 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1683 | 6.25042891583922 | -0.632302 | -24.5332 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1681 | 6.668996345435847 | -0.58732 | -20.2461 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1293 | 7.0457761337255125 | -0.617927 | -20.7888 | 0 | 22 | 18 | 0.90 | 0.00 | - | no | Open |
| 1290 | 8.325171038175231 | -0.602483 | -21.9589 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1088 | 54.635239060174506 | -0.327996 | -12.1045 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1083 | 54.65827673669226 | -0.398049 | -12.2755 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1084 | 55.00743541524278 | -0.432147 | -14.5629 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1082 | 55.03045979470512 | -0.479943 | -17.464 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1679 | 55.231811450195046 | -0.491455 | -18.9609 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1680 | 55.946621095636715 | -0.494738 | -15.8783 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1677 | 56.948725080742264 | -0.609203 | -20.8517 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1292 | 55.72704045128034 | -0.582274 | -22.0607 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1085 | 55.89650249869848 | -0.36287 | -11.9186 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1678 | 56.04238587597847 | -0.732998 | -25.1507 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1289 | 57.50156813780052 | -0.664958 | -26.7266 | 1 | 17 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1676 | 57.83556884909578 | -0.588264 | -25.1347 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1296 | 57.85165481072552 | -0.569824 | -17.2283 | 1 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1291 | 58.29120286658544 | -0.589616 | -19.5994 | 1 | 14 | 11 | 0.55 | 0.00 | - | yes | Current |
| 1294 | 60.273316324365645 | -0.58113 | -21.5496 | 1 | 12 | 10 | 0.50 | 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
-19.599kcal/mol
Ligand efficiency (LE)
-0.5158kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.317
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
516.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.88
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
161.73kcal/mol
Minimised FF energy
128.32kcal/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.