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 (-0.615 kcal/mol/HA)
✓ Good fit quality (FQ -6.16)
✗ Very high strain energy (29.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.920
kcal/mol
LE
-0.615
kcal/mol/HA
Fit Quality
-6.16
FQ (Leeson)
HAC
34
heavy atoms
MW
463
Da
LogP
1.53
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 29.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 6
Severe clashes 0
| Final rank | 54.08163966417761 | Score | -20.9196 |
|---|---|---|---|
| Inter norm | -0.728123 | Intra norm | 0.112839 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | geometry warning; 14 clashes; 6 protein contact clashes | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:SER86;A:THR83;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 | 0.65 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1605 | 3.1588074003271673 | -0.608688 | -18.5717 | 0 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1618 | 3.8369003827623267 | -0.64116 | -20.2576 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1601 | 3.93144186678271 | -0.715903 | -22.8001 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 1602 | 4.320292172863569 | -0.732107 | -20.8356 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1613 | 4.678370170206609 | -0.691038 | -22.6808 | 2 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 1615 | 4.8022510309289475 | -0.591258 | -13.641 | 1 | 17 | 16 | 0.80 | 0.20 | - | no | Open |
| 1616 | 5.216230902400127 | -0.694483 | -22.2258 | 2 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 1620 | 5.344845183894786 | -0.636657 | -17.143 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1617 | 5.683183286281492 | -0.798681 | -23.9269 | 1 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 1606 | 53.31267611278559 | -0.667379 | -21.6326 | 1 | 16 | 12 | 0.60 | 0.00 | - | no | Open |
| 1608 | 53.316965812699 | -0.649911 | -21.2635 | 2 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 1604 | 53.538090361062245 | -0.786872 | -27.1379 | 1 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 1609 | 54.08163966417761 | -0.728123 | -20.9196 | 1 | 18 | 15 | 0.75 | 0.00 | - | no | Current |
| 1610 | 55.086836897863975 | -0.797384 | -25.6545 | 1 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 1614 | 55.35975567749378 | -0.675678 | -22.5696 | 2 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1612 | 55.668143165071875 | -0.812916 | -22.9737 | 1 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1611 | 56.28313283384909 | -0.697023 | -24.4572 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1619 | 56.502378095906494 | -0.721697 | -19.705 | 0 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1603 | 56.784558556448395 | -0.629064 | -18.1878 | 2 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1607 | 56.87477982360974 | -0.66658 | -18.8594 | 0 | 18 | 15 | 0.75 | 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
-20.920kcal/mol
Ligand efficiency (LE)
-0.6153kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.156
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
462.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.53
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
204.73kcal/mol
Minimised FF energy
175.46kcal/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.