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 (-0.627 kcal/mol/HA)
✓ Good fit quality (FQ -6.47)
✗ Very high strain energy (22.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.842
kcal/mol
LE
-0.627
kcal/mol/HA
Fit Quality
-6.47
FQ (Leeson)
HAC
38
heavy atoms
MW
516
Da
LogP
3.30
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 22.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 0
| Final rank | 5.458281007882524 | Score | -23.8423 |
|---|---|---|---|
| Inter norm | -0.650408 | Intra norm | 0.0229787 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | geometry warning; 18 clashes; 5 protein contact clashes; high strain Δ 25.9 | ||
| Residues | A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:THR83;A:TRP47;A:VAL156;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 | 14 | Native recall | 0.70 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 894 | 5.053446271664161 | -0.673818 | -26.7582 | 2 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 902 | 5.458281007882524 | -0.650408 | -23.8423 | 2 | 19 | 14 | 0.70 | 0.20 | - | no | Current |
| 897 | 5.752082320004691 | -0.588823 | -21.9323 | 0 | 15 | 10 | 0.50 | 0.00 | - | no | Open |
| 895 | 6.336742723931842 | -0.57057 | -14.2154 | 0 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 887 | 6.872940493201637 | -0.589342 | -17.5361 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 884 | 6.944322479794866 | -0.676952 | -25.3021 | 2 | 18 | 16 | 0.80 | 0.00 | - | no | Open |
| 900 | 7.060987758012511 | -0.638718 | -25.2848 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 896 | 7.270605376800479 | -0.631851 | -21.9753 | 2 | 17 | 15 | 0.75 | 0.20 | - | no | Open |
| 883 | 7.693361695242808 | -0.75976 | -28.7833 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 890 | 55.94896781715288 | -0.554122 | -18.1134 | 0 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 899 | 56.059602830386304 | -0.648104 | -20.6686 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 901 | 56.1220568546551 | -0.608532 | -25.878 | 0 | 15 | 10 | 0.50 | 0.00 | - | no | Open |
| 885 | 55.657136685214276 | -0.596798 | -28.9021 | 1 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 898 | 56.23878020225021 | -0.538462 | -16.8296 | 0 | 15 | 11 | 0.55 | 0.00 | - | yes | Open |
| 888 | 56.485184667392744 | -0.666509 | -23.2566 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 892 | 56.81592180928288 | -0.64637 | -24.6137 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 886 | 56.91036317493371 | -0.645877 | -22.2951 | 0 | 23 | 19 | 0.95 | 0.00 | - | yes | Open |
| 891 | 57.14515212356115 | -0.58451 | -20.9111 | 1 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 893 | 58.22544698978943 | -0.653429 | -18.6239 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 904 | 58.34910934902213 | -0.668007 | -20.8311 | 0 | 22 | 17 | 0.85 | 0.00 | - | yes | Open |
| 889 | 58.506138200792904 | -0.633837 | -23.2469 | 1 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 882 | 58.72184623540606 | -0.614228 | -21.8294 | 2 | 17 | 17 | 0.85 | 0.20 | - | yes | Open |
| 903 | 59.11401023335494 | -0.651467 | -21.8618 | 2 | 14 | 11 | 0.55 | 0.20 | - | yes | Open |
| 881 | 59.637410801924204 | -0.660179 | -26.6016 | 1 | 15 | 14 | 0.70 | 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
-23.842kcal/mol
Ligand efficiency (LE)
-0.6274kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.468
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
515.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
127.16kcal/mol
Minimised FF energy
104.22kcal/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.