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 (-0.491 kcal/mol/HA)
✓ Good fit quality (FQ -5.35)
✗ Very high strain energy (63.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.565
kcal/mol
LE
-0.491
kcal/mol/HA
Fit Quality
-5.35
FQ (Leeson)
HAC
48
heavy atoms
MW
665
Da
LogP
3.91
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 63.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 2
Clashes 13
Severe clashes 4
| Final rank | 62.04718782650286 | Score | -23.565 |
|---|---|---|---|
| Inter norm | -0.46491 | Intra norm | -0.0260285 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 19 clashes; 4 protein clashes | ||
| Residues | A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR54;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 | 11 | Native recall | 0.55 |
| 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: 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 175 | 6.275542488399826 | -0.230337 | -10.0884 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 177 | 6.590816676586569 | -0.297682 | -14.7996 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 122 | 6.623908820373664 | -0.392232 | -22.8137 | 2 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 121 | 7.38657313809238 | -0.321982 | -16.1743 | 3 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 126 | 7.493058812238245 | -0.325898 | -13.1866 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 174 | 7.52647633159325 | -0.296025 | -10.172 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 233 | 7.6319290184965975 | -0.406985 | -16.0343 | 1 | 20 | 19 | 0.95 | 0.00 | - | no | Open |
| 232 | 8.98296648088481 | -0.479979 | -19.3352 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 130 | 9.613309366169023 | -0.367896 | -20.2919 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 124 | 54.90678412804392 | -0.446751 | -21.3675 | 4 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 176 | 55.08095717655768 | -0.422474 | -17.7921 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 179 | 55.441059436710546 | -0.307973 | -16.8502 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 181 | 55.4644396591611 | -0.309166 | -16.1363 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 123 | 56.03713740231415 | -0.361384 | -18.2614 | 3 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 129 | 9.063943532926253 | -0.353734 | -19.554 | 3 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 132 | 9.21411647823986 | -0.319689 | -17.7198 | 2 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 235 | 9.632875282411014 | -0.40778 | -18.0707 | 0 | 20 | 18 | 0.90 | 0.00 | - | yes | Open |
| 178 | 55.54832617343075 | -0.355277 | -17.897 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 128 | 55.85736192058398 | -0.377757 | -22.9116 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 180 | 56.73329863084768 | -0.328082 | -16.7695 | 2 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 136 | 57.05145470516479 | -0.357664 | -15.5151 | 5 | 10 | 1 | 0.05 | 0.00 | - | yes | Open |
| 127 | 57.38136765086828 | -0.397318 | -18.2109 | 3 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 135 | 57.95106297431023 | -0.442919 | -19.3927 | 3 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 238 | 58.70619646020666 | -0.542864 | -22.7362 | 0 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 234 | 58.81723665573986 | -0.554031 | -24.3529 | 2 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 237 | 59.02381195613867 | -0.478612 | -20.8327 | 0 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 133 | 59.169384455664925 | -0.38743 | -14.5111 | 2 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 239 | 59.638485396091426 | -0.469957 | -20.6378 | 3 | 12 | 10 | 0.50 | 0.20 | - | yes | Open |
| 131 | 59.78931090831168 | -0.294202 | -15.3285 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 125 | 61.46460320297299 | -0.459124 | -21.609 | 3 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 236 | 62.04718782650286 | -0.46491 | -23.565 | 2 | 13 | 11 | 0.55 | 0.20 | - | yes | Current |
| 134 | 63.28921586966261 | -0.401364 | -20.4469 | 2 | 14 | 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
-23.565kcal/mol
Ligand efficiency (LE)
-0.4909kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.348
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
48HA
Physicochemical properties
Molecular weight
664.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
63.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
145.99kcal/mol
Minimised FF energy
82.42kcal/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.