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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.597 kcal/mol/HA)
✓ Good fit quality (FQ -6.07)
✗ Very high strain energy (20.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.496
kcal/mol
LE
-0.597
kcal/mol/HA
Fit Quality
-6.07
FQ (Leeson)
HAC
36
heavy atoms
MW
521
Da
LogP
6.39
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 20.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 3
Clashes 10
Severe clashes 1
| Final rank | 56.88502145992925 | Score | -21.4958 |
|---|---|---|---|
| Inter norm | -0.700519 | Intra norm | 0.103414 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE182;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;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 | 0.64 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 707 | 4.018919766779002 | -0.58477 | -18.8696 | 0 | 11 | 10 | 0.50 | 0.00 | - | no | Open |
| 710 | 4.411062729751931 | -0.74906 | -21.9445 | 0 | 22 | 18 | 0.90 | 0.00 | - | no | Open |
| 716 | 6.562349564278564 | -0.677987 | -19.0214 | 1 | 19 | 14 | 0.70 | 0.00 | - | yes | Open |
| 712 | 6.718072229773145 | -0.747968 | -24.9322 | 0 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 706 | 6.766630857830311 | -0.711649 | -18.7494 | 0 | 22 | 18 | 0.90 | 0.00 | - | yes | Open |
| 717 | 7.025217096901895 | -0.624554 | -18.034 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 722 | 7.137149831332038 | -0.665309 | -22.9043 | 0 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 720 | 7.2240206912878735 | -0.723239 | -21.5342 | 1 | 12 | 10 | 0.50 | 0.00 | - | yes | Open |
| 705 | 7.580291643995115 | -0.61206 | -20.3839 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 715 | 56.75751004151227 | -0.743949 | -23.4426 | 0 | 16 | 14 | 0.70 | 0.00 | - | yes | Open |
| 708 | 56.88502145992925 | -0.700519 | -21.4958 | 1 | 21 | 16 | 0.80 | 0.00 | - | yes | Current |
| 718 | 56.94821200157307 | -0.592943 | -17.7717 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 723 | 57.10697016806896 | -0.751453 | -23.4626 | 1 | 16 | 14 | 0.70 | 0.00 | - | yes | Open |
| 721 | 57.264277097037585 | -0.582551 | -15.9036 | 0 | 16 | 15 | 0.75 | 0.00 | - | yes | Open |
| 713 | 57.30040430681296 | -0.654921 | -19.2781 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 709 | 57.77094401733217 | -0.587935 | -18.6776 | 0 | 13 | 11 | 0.55 | 0.00 | - | yes | Open |
| 724 | 58.221916145914825 | -0.590507 | -16.6296 | 1 | 12 | 10 | 0.50 | 0.00 | - | yes | Open |
| 719 | 58.253308629916944 | -0.608572 | -13.0448 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 714 | 58.95969925382864 | -0.649858 | -16.4597 | 1 | 20 | 15 | 0.75 | 0.00 | - | yes | Open |
| 711 | 59.41710694625181 | -0.686926 | -19.4394 | 1 | 20 | 16 | 0.80 | 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
-21.496kcal/mol
Ligand efficiency (LE)
-0.5971kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.069
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
520.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.39
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
110.09kcal/mol
Minimised FF energy
89.42kcal/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.