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 (-0.490 kcal/mol/HA)
✓ Good fit quality (FQ -5.02)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (30.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-18.126
kcal/mol
LE
-0.490
kcal/mol/HA
Fit Quality
-5.02
FQ (Leeson)
HAC
37
heavy atoms
MW
493
Da
LogP
3.67
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 30.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 4
Clashes 13
Severe clashes 2
| Final rank | 11.767212109053558 | Score | -18.1262 |
|---|---|---|---|
| Inter norm | -0.696667 | Intra norm | 0.20677 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 24 clashes; 2 protein clashes; high strain Δ 34.2 | ||
| Residues | A:ALA32;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2346 | 5.750994506133803 | -0.619475 | -21.5191 | 4 | 19 | 17 | 0.85 | 0.00 | - | no | Open |
| 1578 | 5.995456290753756 | -0.442541 | -14.5889 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2247 | 6.910292602120942 | -0.697186 | -17.441 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 809 | 6.952020850654601 | -0.592422 | -19.356 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3088 | 7.372279335342794 | -0.664986 | -14.2849 | 4 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 1715 | 7.836769346441749 | -0.548915 | -17.8873 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2248 | 8.16770987144596 | -0.739703 | -12.5182 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1575 | 8.549924016322672 | -0.496646 | -13.0568 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1043 | 9.922390153513915 | -0.98281 | -33.8871 | 13 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 1572 | 7.8412319767099365 | -0.538974 | -13.4085 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1046 | 8.177047521482747 | -0.794324 | -24.5477 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1048 | 8.815647992829662 | -0.913924 | -32.1424 | 15 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2249 | 8.831866877952159 | -0.722153 | -24.2491 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1711 | 8.98404899042751 | -0.516718 | -18.9626 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1574 | 9.037807119105102 | -0.597415 | -15.9514 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1710 | 9.111327385654574 | -0.496864 | -9.61254 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1714 | 9.187408275714851 | -0.456671 | -11.6162 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2245 | 9.566406431252368 | -0.861086 | -31.0607 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3093 | 9.599499808497804 | -0.552776 | -10.9743 | 3 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3090 | 9.773580091941783 | -0.602491 | -18.1141 | 4 | 13 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1577 | 10.050500404745685 | -0.604231 | -16.3694 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1573 | 10.053952751967463 | -0.644073 | -22.3155 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3094 | 10.866549469095583 | -0.723565 | -23.309 | 3 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 806 | 11.149148948441004 | -0.634366 | -20.754 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1716 | 11.22788309241015 | -0.524744 | -16.8547 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2250 | 11.301658619693852 | -0.75516 | -21.5357 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2244 | 11.42069179993254 | -0.88037 | -22.7445 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1576 | 11.537230793016901 | -0.498245 | -10.2586 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1713 | 11.640248050245418 | -0.528848 | -14.1154 | 9 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2342 | 11.767212109053558 | -0.696667 | -18.1262 | 6 | 16 | 15 | 0.75 | 0.20 | - | yes | Current |
| 3095 | 11.774760478918148 | -0.757789 | -22.5673 | 4 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 3089 | 11.812005320526302 | -0.666591 | -22.7221 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 810 | 11.85917958114339 | -0.600284 | -19.6369 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1045 | 11.896966802124325 | -0.959699 | -31.0987 | 9 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3092 | 11.908715917099858 | -0.65988 | -19.1518 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 805 | 11.999182935857963 | -0.644222 | -12.4849 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1042 | 12.109192204711709 | -0.763707 | -20.0666 | 9 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 807 | 12.158197151968073 | -0.466114 | -14.3065 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1049 | 12.587569482148275 | -0.678916 | -16.8902 | 11 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1712 | 12.691942838647865 | -0.508962 | -9.67492 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1047 | 12.844148791742079 | -0.819601 | -22.17 | 12 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3091 | 13.117025173975756 | -0.712391 | -23.6476 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 808 | 13.24157077386502 | -0.623533 | -12.3274 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2344 | 13.406668038058964 | -0.671444 | -17.1188 | 5 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2343 | 14.881133802685527 | -0.629867 | -17.6958 | 5 | 13 | 7 | 0.35 | 0.20 | - | yes | Open |
| 1044 | 16.033144931570998 | -0.705359 | 0.785648 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2347 | 16.40988118048191 | -0.657476 | -18.0494 | 6 | 13 | 8 | 0.40 | 0.20 | - | yes | Open |
| 2345 | 16.88490695813837 | -0.745122 | -17.8461 | 6 | 16 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2246 | 19.76079121037302 | -0.691614 | -20.5849 | 9 | 21 | 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
-18.126kcal/mol
Ligand efficiency (LE)
-0.4899kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.016
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
493.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.67
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.69kcal/mol
Minimised FF energy
73.72kcal/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.