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 (-1.208 kcal/mol/HA)
✓ Good fit quality (FQ -10.49)
✓ Strong H-bond network (11 bonds)
✗ High strain energy (10.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.582
kcal/mol
LE
-1.208
kcal/mol/HA
Fit Quality
-10.49
FQ (Leeson)
HAC
22
heavy atoms
MW
296
Da
LogP
1.83
cLogP
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 21
π–π 1
Clashes 4
Severe clashes 0
| Final rank | 2.4004023492030724 | Score | -26.5823 |
|---|---|---|---|
| Inter norm | -1.23742 | Intra norm | 0.0291334 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 11 |
| Artifact reason | geometry warning; 11 clashes; 4 protein contact clashes | ||
| Residues | A:NDP301;B:ALA32;B:ASP52;B:GLY157;B:ILE45;B:MET53;B:PHE55;B:PHE56;B:PRO88;B:SER44;B:SER86;B:THR180;B:THR83;B:TYR162;B:VAL156;B:VAL30;B:VAL31;B:VAL87 | ||
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:NDP301; B:ALA32; B:ARG97; B:ASP52; B:GLY157; B:ILE45; B:LEU94; B:LYS57; B:MET53; B:PHE55; B:PHE56; B:PHE91; B:PRO88; B:SER86; B:THR180; B:THR83; B:TYR162; B:VAL156; B:VAL30; B:VAL31; B:VAL87 | ||
| Current overlap | 17 | Native recall | 0.81 |
| Jaccard | 0.77 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.57 |
| H-bond same residue+role | 4 | Role recall | 0.67 |
| H-bond same residue | 4 | Residue recall | 0.67 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 230 | 1.7972984638498872 | -1.67254 | -37.1541 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 2.4004023492030724 | -1.23742 | -26.5823 | 11 | 18 | 17 | 0.81 | 0.67 | - | no | Current |
| 254 | 2.535986888857927 | -1.63666 | -35.606 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 2.634788302715577 | -1.20522 | -25.9334 | 6 | 18 | 17 | 0.81 | 0.67 | - | no | Open |
| 256 | 2.755501728414221 | -1.60761 | -36.108 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 2.766972898471771 | -1.65565 | -37.1036 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 229 | 2.853947949080875 | -1.5954 | -35.5409 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 215 | 2.880668670991616 | -1.19731 | -25.8291 | 9 | 18 | 17 | 0.81 | 0.67 | - | no | Open |
| 184 | 3.2395149883614733 | -1.03998 | -23.2386 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 255 | 3.5097639402484626 | -1.50656 | -33.4296 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 256 | 3.5559040375004214 | -1.18914 | -27.1667 | 4 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 257 | 3.626163778508446 | -1.16212 | -24.8998 | 4 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 258 | 4.478692184007521 | -1.32294 | -29.7007 | 5 | 18 | 1 | 0.05 | 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
-26.582kcal/mol
Ligand efficiency (LE)
-1.2083kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.490
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
296.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.83
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
20.89kcal/mol
Minimised FF energy
10.26kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. It will be calculated automatically
the next time this pose is loaded if a receptor PDB path is stored.