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 (-0.635 kcal/mol/HA)
✓ Good fit quality (FQ -6.35)
✗ Very high strain energy (31.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-21.586
kcal/mol
LE
-0.635
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
34
heavy atoms
MW
463
Da
LogP
1.43
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 31.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 1
Clashes 5
Severe clashes 0
| Final rank | 4.576968853356978 | Score | -21.5859 |
|---|---|---|---|
| Inter norm | -0.701699 | Intra norm | 0.0668197 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 11 clashes; 5 protein contact clashes; high strain Δ 32.1 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;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: permissive.
| 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 | 0.50 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1800 | 3.192995042814929 | -0.666482 | -19.5956 | 1 | 16 | 12 | 0.60 | 0.00 | - | no | Open |
| 1712 | 3.852309507173588 | -0.740658 | -23.1814 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1720 | 4.041475288126007 | -0.711065 | -24.1449 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1716 | 4.39232578635824 | -0.682733 | -21.5601 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1797 | 4.573080037112168 | -0.732454 | -23.9797 | 1 | 20 | 15 | 0.75 | 0.20 | - | no | Open |
| 1799 | 4.576968853356978 | -0.701699 | -21.5859 | 1 | 16 | 12 | 0.60 | 0.20 | - | no | Current |
| 1723 | 4.645652209172564 | -0.740475 | -26.1491 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1724 | 5.324635239472977 | -0.715558 | -21.0734 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1715 | 5.329875143919994 | -0.657376 | -22.1009 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1809 | 5.7094446096767095 | -0.700127 | -19.268 | 1 | 20 | 17 | 0.85 | 0.20 | - | no | Open |
| 1811 | 5.7401879531940585 | -0.762086 | -24.3652 | 2 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 1721 | 53.883265066727375 | -0.64254 | -20.7416 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1722 | 54.18895745625761 | -0.674571 | -20.5181 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1714 | 54.49632132726808 | -0.640732 | -18.8551 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1719 | 54.57943991446807 | -0.658254 | -23.9656 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1802 | 55.009085085725 | -0.789943 | -23.4261 | 1 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 1804 | 55.3547913067628 | -0.716942 | -22.6573 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 1798 | 55.57448442123359 | -0.716794 | -16.8477 | 1 | 17 | 15 | 0.75 | 0.20 | - | no | Open |
| 1808 | 5.258365990403331 | -0.691236 | -19.0268 | 2 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1807 | 54.22172094920189 | -0.652744 | -22.6324 | 1 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1801 | 54.766080237386284 | -0.714425 | -23.1078 | 1 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1806 | 55.01311487972341 | -0.676746 | -21.1357 | 2 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1713 | 55.21619935175384 | -0.708345 | -22.1161 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1711 | 55.278694716865154 | -0.622768 | -18.9073 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1805 | 55.33280609114375 | -0.725146 | -22.8862 | 1 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1812 | 55.67171030508722 | -0.662607 | -19.9533 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1803 | 55.89989271176973 | -0.743185 | -25.5761 | 3 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1718 | 56.34810804689525 | -0.579787 | -17.7791 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1710 | 56.63998815049071 | -0.672228 | -17.5114 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1717 | 56.79149628766385 | -0.785071 | -23.3202 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1709 | 56.973941864856805 | -0.662562 | -21.0627 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1810 | 58.535454443647325 | -0.839785 | -26.5027 | 1 | 20 | 16 | 0.80 | 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
-21.586kcal/mol
Ligand efficiency (LE)
-0.6349kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.353
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
462.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.43
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
203.58kcal/mol
Minimised FF energy
172.07kcal/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.