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 (-0.549 kcal/mol/HA)
✓ Good fit quality (FQ -5.62)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (47.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.304
kcal/mol
LE
-0.549
kcal/mol/HA
Fit Quality
-5.62
FQ (Leeson)
HAC
37
heavy atoms
MW
504
Da
LogP
1.92
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 47.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 1
Clashes 8
Severe clashes 0
| Final rank | 7.091993269240239 | Score | -20.3042 |
|---|---|---|---|
| Inter norm | -0.702864 | Intra norm | 0.154101 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 17 clashes; 8 protein contact clashes; high strain Δ 42.7 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR83;A:TRP47;A:TYR162;A:VAL156;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 | 16 | Native recall | 0.80 |
| Jaccard | 0.70 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1080 | 6.027524583017487 | -0.660082 | -17.2443 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1087 | 6.360494847730022 | -0.57741 | -22.0862 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1092 | 6.4905874208131005 | -0.609537 | -19.65 | 1 | 14 | 13 | 0.65 | 0.00 | - | no | Open |
| 1088 | 6.984560407961615 | -0.585764 | -21.8785 | 0 | 15 | 14 | 0.70 | 0.00 | - | no | Open |
| 1078 | 7.091993269240239 | -0.702864 | -20.3042 | 3 | 19 | 16 | 0.80 | 0.20 | - | no | Current |
| 1077 | 7.938468671682138 | -0.565693 | -9.79573 | 1 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 1083 | 56.19091231223968 | -0.612971 | -21.2732 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1085 | 56.54915323883521 | -0.579997 | -20.4106 | 0 | 17 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1091 | 56.99212523659179 | -0.612002 | -19.1634 | 0 | 21 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1086 | 57.51701498989513 | -0.540654 | -21.6423 | 0 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1081 | 57.85662053506577 | -0.609143 | -15.3193 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1084 | 58.14332189353265 | -0.576597 | -19.2486 | 1 | 15 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1090 | 59.000176439747776 | -0.582033 | -18.6202 | 1 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1079 | 59.30885489974342 | -0.551789 | -21.9656 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1089 | 59.91077149199354 | -0.716421 | -14.1142 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1082 | 60.79498036997836 | -0.713469 | -14.7726 | 0 | 19 | 16 | 0.80 | 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
-20.304kcal/mol
Ligand efficiency (LE)
-0.5488kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.618
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
503.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.92
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
47.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
242.72kcal/mol
Minimised FF energy
195.62kcal/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.