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 (-0.696 kcal/mol/HA)
✓ Good fit quality (FQ -7.17)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (31.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-26.435
kcal/mol
LE
-0.696
kcal/mol/HA
Fit Quality
-7.17
FQ (Leeson)
HAC
38
heavy atoms
MW
519
Da
LogP
2.52
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 19
Severe clashes 1
| Final rank | 59.888711794691346 | Score | -26.4351 |
|---|---|---|---|
| Inter norm | -0.728931 | Intra norm | 0.0332704 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:PRO93;A:THR54;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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 | 17 | Native recall | 0.85 |
| Jaccard | 0.74 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.29 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1027 | 6.822704372144355 | -0.624761 | -17.7279 | 1 | 17 | 12 | 0.60 | 0.20 | - | no | Open |
| 1010 | 6.951751574540021 | -0.646538 | -25.7143 | 6 | 17 | 16 | 0.80 | 0.80 | - | no | Open |
| 1026 | 7.094287334300263 | -0.639275 | -23.7617 | 1 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1007 | 8.05176775701517 | -0.647097 | -23.4754 | 2 | 21 | 17 | 0.85 | 0.20 | - | no | Open |
| 1015 | 8.398258772771907 | -0.521279 | -14.9385 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1005 | 57.657619813151406 | -0.630418 | -20.2269 | 2 | 16 | 11 | 0.55 | 0.00 | - | no | Open |
| 1022 | 7.299943420607154 | -0.653108 | -26.2625 | 1 | 13 | 10 | 0.50 | 0.00 | - | yes | Open |
| 1009 | 55.805742056293134 | -0.630072 | -16.803 | 1 | 21 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1014 | 56.2875781932553 | -0.651308 | -23.8815 | 1 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1013 | 56.78374927155866 | -0.598157 | -16.2061 | 2 | 18 | 17 | 0.85 | 0.40 | - | yes | Open |
| 1028 | 56.90150959242682 | -0.684463 | -22.8726 | 1 | 22 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1019 | 57.02520469114295 | -0.686472 | -24.0861 | 1 | 21 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1012 | 57.15269072922803 | -0.621102 | -23.7081 | 2 | 16 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1011 | 57.30563772090751 | -0.605626 | -21.6388 | 1 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 1025 | 57.758925345189866 | -0.670238 | -17.3409 | 4 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1023 | 57.868460667105666 | -0.651571 | -23.6812 | 1 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1020 | 58.34787606194498 | -0.612191 | -20.4774 | 0 | 22 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1017 | 58.86457689985148 | -0.614434 | -20.1777 | 0 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1008 | 59.888711794691346 | -0.728931 | -26.4351 | 4 | 20 | 17 | 0.85 | 0.40 | - | yes | Current |
| 1006 | 60.00789818717066 | -0.629589 | -22.342 | 1 | 14 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1021 | 60.196004145692974 | -0.63783 | -27.1067 | 1 | 15 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1016 | 61.003200045112486 | -0.670707 | -22.0919 | 0 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 1024 | 61.47334636016435 | -0.774733 | -28.3258 | 3 | 19 | 16 | 0.80 | 0.60 | - | yes | Open |
| 1018 | 63.28505917139624 | -0.653678 | -19.3117 | 1 | 20 | 16 | 0.80 | 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
-26.435kcal/mol
Ligand efficiency (LE)
-0.6957kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.172
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
518.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.52
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.92kcal/mol
Minimised FF energy
43.47kcal/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.