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 (-0.693 kcal/mol/HA)
✓ Good fit quality (FQ -6.99)
✗ Very high strain energy (24.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.252
kcal/mol
LE
-0.693
kcal/mol/HA
Fit Quality
-6.99
FQ (Leeson)
HAC
35
heavy atoms
MW
467
Da
LogP
4.06
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 24.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 3
Clashes 6
Severe clashes 0
| Final rank | 5.137296951984262 | Score | -24.2518 |
|---|---|---|---|
| Inter norm | -0.706686 | Intra norm | 0.013778 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | geometry warning; 17 clashes; 6 protein contact clashes; moderate strain Δ 19.6 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;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 | 15 | Native recall | 0.75 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 683 | 4.842418202521232 | -0.756988 | -24.4393 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 690 | 4.853805582179802 | -0.691825 | -23.2866 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 681 | 4.879981865273341 | -0.663369 | -20.4753 | 1 | 17 | 16 | 0.80 | 0.00 | - | no | Open |
| 688 | 5.137296951984262 | -0.706686 | -24.2518 | 1 | 19 | 15 | 0.75 | 0.00 | - | no | Current |
| 827 | 5.410312783800123 | -0.716005 | -22.2219 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 684 | 5.415057016014122 | -0.689366 | -22.5798 | 0 | 18 | 15 | 0.75 | 0.00 | - | no | Open |
| 692 | 5.467582340979076 | -0.697546 | -19.9074 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 826 | 5.511849774471397 | -0.709604 | -22.1325 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 836 | 5.935127283244742 | -0.667288 | -22.6668 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 833 | 5.948959576238479 | -0.545547 | -17.4763 | 0 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 687 | 54.97962212259708 | -0.654928 | -18.9748 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 689 | 54.99173757821467 | -0.711376 | -19.9625 | 1 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 691 | 55.1518658285479 | -0.670342 | -25.5927 | 0 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 682 | 55.567967777952724 | -0.666001 | -22.4804 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 828 | 6.891426663345081 | -0.746045 | -24.4144 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 835 | 7.587741269329144 | -0.671158 | -20.4591 | 0 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 686 | 56.87579612573545 | -0.592238 | -19.1957 | 0 | 18 | 17 | 0.85 | 0.00 | - | yes | Open |
| 685 | 57.086440873619665 | -0.645772 | -21.0833 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 829 | 57.10218441643644 | -0.511614 | -16.3254 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 832 | 57.5691230950428 | -0.644615 | -21.8265 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 831 | 57.98564369947482 | -0.648231 | -20.2593 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 834 | 59.45936203065946 | -0.58367 | -14.7814 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 825 | 60.08855744603995 | -0.5052 | -10.9512 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 830 | 60.222338429435666 | -0.544722 | -14.4467 | 0 | 18 | 0 | 0.00 | 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
-24.252kcal/mol
Ligand efficiency (LE)
-0.6929kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.989
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
466.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.06
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
161.97kcal/mol
Minimised FF energy
137.81kcal/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.