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 (-0.518 kcal/mol/HA)
✓ Good fit quality (FQ -5.23)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (48.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-18.142
kcal/mol
LE
-0.518
kcal/mol/HA
Fit Quality
-5.23
FQ (Leeson)
HAC
35
heavy atoms
MW
485
Da
LogP
-0.78
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 48.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 1
Clashes 7
Severe clashes 0
| Final rank | 7.348745816679402 | Score | -18.1415 |
|---|---|---|---|
| Inter norm | -0.609077 | Intra norm | 0.0907483 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 7 protein contact clashes; high strain Δ 70.8 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR180;A:THR54;A:TRP47;A:VAL30;A:VAL31;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 182 | 5.2707564009624495 | -0.324646 | -12.4187 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 177 | 6.451909408598954 | -0.446253 | -10.2753 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 179 | 6.656112325245584 | -0.520785 | -14.8647 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 187 | 7.041678521836246 | -0.451275 | -13.1152 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 201 | 7.348745816679402 | -0.609077 | -18.1415 | 4 | 19 | 15 | 0.75 | 0.20 | - | no | Current |
| 104 | 7.358826811953958 | -0.527939 | -12.1313 | 13 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 186 | 7.908864532082715 | -0.317433 | -9.9324 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 59 | 10.117953301805104 | -0.380618 | -5.69901 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 180 | 54.10526388388691 | -0.453867 | -7.88416 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 183 | 54.342984653764304 | -0.510746 | -17.2093 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 181 | 55.066546811378025 | -0.490176 | -16.5757 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 185 | 8.874373437582978 | -0.575628 | -18.5622 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 202 | 9.594486851986192 | -0.593854 | -15.6755 | 3 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 58 | 9.91712662433883 | -0.69978 | -22.9342 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 101 | 9.979144831598623 | -0.590807 | -16.7398 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 102 | 10.297529699155923 | -0.54246 | -16.6095 | 7 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 52 | 10.340766652532867 | -0.441329 | -11.6768 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 200 | 11.181600341673743 | -0.561017 | -14.6833 | 4 | 16 | 11 | 0.55 | 0.40 | - | yes | Open |
| 178 | 55.65682974047449 | -0.487037 | -12.1302 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 188 | 57.28199073165268 | -0.372193 | -7.40378 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 199 | 57.84152937881487 | -0.649111 | -19.074 | 7 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 105 | 57.8635795025279 | -0.603096 | -17.5576 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 206 | 58.35669327015495 | -0.809493 | -24.9885 | 5 | 20 | 14 | 0.70 | 0.20 | - | yes | Open |
| 57 | 58.49909809336844 | -0.548984 | -15.3474 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 54 | 58.642487085447605 | -0.773046 | -23.5965 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 53 | 59.10109507853129 | -0.519071 | -23.8585 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 56 | 59.34691343018508 | -0.629885 | -21.8707 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 184 | 59.57505470221908 | -0.448576 | -12.7425 | 7 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 203 | 60.54877080261583 | -0.705157 | -20.4331 | 7 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 100 | 60.83176455443292 | -0.901719 | -26.0699 | 10 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 205 | 60.930298555003034 | -0.733726 | -22.5665 | 8 | 13 | 11 | 0.55 | 0.40 | - | yes | Open |
| 55 | 60.981725656865365 | -0.474632 | -6.64606 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 204 | 62.6810818109805 | -0.598483 | -15.4948 | 7 | 12 | 9 | 0.45 | 0.00 | - | yes | Open |
| 103 | 63.84545481738672 | -0.7651 | -10.9832 | 10 | 25 | 0 | 0.00 | 0.00 | - | yes | Open |
| 106 | 67.30602145888746 | -0.772037 | -16.891 | 10 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 107 | 73.59926221380903 | -0.723188 | -14.1274 | 15 | 24 | 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
-18.142kcal/mol
Ligand efficiency (LE)
-0.5183kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.228
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
484.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.78
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
48.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
168.91kcal/mol
Minimised FF energy
120.00kcal/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.