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 (-0.647 kcal/mol/HA)
✓ Good fit quality (FQ -6.42)
✗ Very high strain energy (35.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.366
kcal/mol
LE
-0.647
kcal/mol/HA
Fit Quality
-6.42
FQ (Leeson)
HAC
33
heavy atoms
MW
471
Da
LogP
1.54
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 20
π–π 0
Clashes 9
Severe clashes 3
| Final rank | 10.486696002617517 | Score | -21.3655 |
|---|---|---|---|
| Inter norm | -0.701442 | Intra norm | 0.0540027 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 12 clashes; 3 protein clashes; high strain Δ 44.9 | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;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 | 12 | Native recall | 0.60 |
| Jaccard | 0.48 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 532 | 4.770442877693168 | -0.567283 | -17.4665 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 5.109574213778034 | -0.618959 | -19.228 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 6.774172544704101 | -0.613463 | -19.2165 | 1 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 482 | 9.293891184868055 | -0.808959 | -21.7723 | 4 | 20 | 17 | 0.85 | 0.40 | - | no | Open |
| 535 | 7.098763569295453 | -0.505231 | -15.1036 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 480 | 7.804777200493802 | -0.639075 | -16.6446 | 2 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 477 | 8.210129509625046 | -0.710033 | -22.6436 | 4 | 19 | 19 | 0.95 | 0.20 | - | yes | Open |
| 528 | 8.218984989629886 | -0.530987 | -14.4845 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 530 | 8.862260841449228 | -0.553174 | -18.3619 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 478 | 9.038859020288022 | -0.71094 | -18.7518 | 1 | 17 | 14 | 0.70 | 0.00 | - | yes | Open |
| 529 | 9.889262723398122 | -0.619151 | -18.0174 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 476 | 10.486696002617517 | -0.701442 | -21.3655 | 2 | 17 | 12 | 0.60 | 0.20 | - | yes | Current |
| 481 | 55.91961421316209 | -0.691662 | -20.0346 | 4 | 18 | 18 | 0.90 | 0.20 | - | yes | Open |
| 534 | 55.98206295116119 | -0.522248 | -15.3159 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 475 | 59.612027452374484 | -0.556207 | -12.5399 | 4 | 19 | 17 | 0.85 | 0.40 | - | yes | Open |
| 531 | 60.377650581625716 | -0.575121 | -16.0515 | 8 | 16 | 0 | 0.00 | 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
-21.366kcal/mol
Ligand efficiency (LE)
-0.6474kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.424
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.54
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.23kcal/mol
Minimised FF energy
17.88kcal/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.