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.
✓ Acceptable LE (-0.209 kcal/mol/HA)
✓ Good fit quality (FQ -2.42)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (59.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-13.989
kcal/mol
LE
-0.209
kcal/mol/HA
Fit Quality
-2.42
FQ (Leeson)
HAC
67
heavy atoms
MW
939
Da
LogP
5.54
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: acceptable
Geometry reliability: low
Reason: geometry warning, clashes, strain 59.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 13
Severe clashes 1
| Final rank | 13.398149860971646 | Score | -13.9885 |
|---|---|---|---|
| Inter norm | -0.32272 | Intra norm | 0.11311 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 24 clashes; 1 protein clash; high strain Δ 75.0 | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:GLU51;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR180;A:THR54;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: 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 | 13 | Native recall | 0.65 |
| Jaccard | 0.50 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 966 | 7.924960003015377 | -0.230019 | -10.6205 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 971 | 8.622410915467011 | -0.262052 | -14.6976 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 963 | 8.668732509650429 | -0.262062 | -19.966 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 973 | 9.829918695358124 | -0.311862 | -14.6976 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2033 | 9.859658197352427 | -0.403028 | -4.90992 | 6 | 21 | 15 | 0.75 | 0.40 | - | no | Open |
| 2031 | 11.031232536328456 | -0.495192 | -21.8006 | 7 | 19 | 12 | 0.60 | 0.20 | - | no | Open |
| 2040 | 10.267799486580678 | -0.49344 | -21.1745 | 2 | 25 | 18 | 0.90 | 0.00 | - | yes | Open |
| 964 | 10.408910837040514 | -0.237622 | -10.2971 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2036 | 10.480489535050769 | -0.388256 | -23.9808 | 4 | 20 | 14 | 0.70 | 0.00 | - | yes | Open |
| 972 | 12.733866709987094 | -0.219659 | -8.63375 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2037 | 13.398149860971646 | -0.32272 | -13.9885 | 7 | 19 | 13 | 0.65 | 0.20 | - | yes | Current |
| 2039 | 15.008648071697358 | -0.387667 | -18.7564 | 9 | 23 | 16 | 0.80 | 0.20 | - | yes | Open |
| 2029 | 57.916787006582524 | -0.34104 | -18.6838 | 6 | 21 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2030 | 58.04003634870706 | -0.410412 | -21.6919 | 6 | 23 | 18 | 0.90 | 0.40 | - | yes | Open |
| 968 | 58.1921685393656 | -0.251457 | -6.81459 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2034 | 58.308985218766225 | -0.395443 | -12.0484 | 3 | 20 | 14 | 0.70 | 0.40 | - | yes | Open |
| 967 | 58.3695528382883 | -0.298086 | -10.1592 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 969 | 58.76365490072506 | -0.351447 | -19.3528 | 11 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2035 | 59.2106178894737 | -0.39712 | -19.9826 | 5 | 18 | 11 | 0.55 | 0.20 | - | yes | Open |
| 962 | 60.09819276727043 | -0.248705 | -24.6375 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2032 | 61.28527412652558 | -0.43473 | -20.7284 | 6 | 17 | 11 | 0.55 | 0.20 | - | yes | Open |
| 965 | 62.22827217570115 | -0.341314 | -18.1706 | 9 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 970 | 63.08438541607137 | -0.22874 | -12.9469 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2038 | 63.95618221165056 | -0.285993 | -13.0253 | 5 | 16 | 12 | 0.60 | 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
-13.989kcal/mol
Ligand efficiency (LE)
-0.2088kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-2.423
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
67HA
Physicochemical properties
Molecular weight
939.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.54
Lipinski: ≤ 5
Rotatable bonds
14
Conformational strain (MMFF94s)
Strain energy (ΔE)
59.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
216.97kcal/mol
Minimised FF energy
157.43kcal/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.