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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.076 kcal/mol/HA)
✓ Good fit quality (FQ -9.91)
✓ Good H-bonds (4 bonds)
✗ High strain energy (18.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.980
kcal/mol
LE
-1.076
kcal/mol/HA
Fit Quality
-9.91
FQ (Leeson)
HAC
26
heavy atoms
MW
344
Da
LogP
3.80
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 18.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 15
Severe clashes 5
| Final rank | 62.56409004457617 | Score | -27.9805 |
|---|---|---|---|
| Inter norm | -0.939617 | Intra norm | -0.136558 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 14 clashes; 5 protein clashes | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:TRP47;A:VAL30;A:VAL31;A:VAL49 | ||
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2895 | 3.5680366603155624 | -0.875622 | -17.9281 | 2 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 2899 | 4.248941167689489 | -0.859109 | -17.5979 | 2 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 2965 | 5.308998017938502 | -0.823275 | -13.2672 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2897 | 5.4955598640357195 | -0.961178 | -32.5747 | 4 | 16 | 12 | 0.60 | 0.60 | - | no | Open |
| 1977 | 6.128192467707609 | -0.669275 | -12.3648 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2972 | 6.194229119201112 | -0.759884 | -24.8264 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2969 | 5.4826108951854104 | -0.799545 | -15.008 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1983 | 5.48304453668463 | -0.748913 | -23.2812 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2975 | 5.793326680599963 | -0.867062 | -27.5297 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2966 | 6.279142669862784 | -0.920731 | -17.9824 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2893 | 6.4666777375179905 | -1.05125 | -32.6316 | 5 | 18 | 14 | 0.70 | 0.60 | - | yes | Open |
| 2901 | 6.8441236080302135 | -0.946837 | -29.7856 | 4 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2891 | 6.899870697519042 | -0.969732 | -18.8968 | 3 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1975 | 7.352614391475464 | -0.783317 | -24.7821 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2973 | 7.556308040680262 | -0.807806 | -13.1415 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1979 | 7.585627526526178 | -0.875149 | -29.1481 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1981 | 7.701763351511589 | -0.795936 | -15.9514 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2964 | 7.886850331576594 | -0.854572 | -16.2031 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2970 | 8.536235146237935 | -0.896245 | -18.7475 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1978 | 8.644023613410653 | -0.790913 | -22.6078 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2900 | 8.725908158089055 | -0.844865 | -19.9325 | 4 | 7 | 6 | 0.30 | 0.20 | - | yes | Open |
| 2971 | 8.82514382914119 | -0.914161 | -29.0172 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1982 | 9.556985410314299 | -0.708518 | -26.3645 | 2 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1973 | 9.746988212221206 | -1.00647 | -17.7989 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1972 | 10.613239270658962 | -0.873823 | -24.9601 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2892 | 10.842537185624233 | -1.02671 | -24.4977 | 5 | 10 | 7 | 0.35 | 0.20 | - | yes | Open |
| 2894 | 11.600767925025217 | -0.855338 | -26.0604 | 3 | 15 | 12 | 0.60 | 0.20 | - | yes | Open |
| 2967 | 58.26173349716666 | -0.983468 | -27.7945 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2898 | 58.58646118643031 | -0.848977 | -17.4653 | 3 | 11 | 9 | 0.45 | 0.20 | - | yes | Open |
| 1976 | 59.49070500352732 | -0.653322 | -21.0698 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2968 | 60.1173914487811 | -0.739205 | -22.7182 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2974 | 60.53293236544626 | -0.803751 | -23.9808 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1974 | 61.18086007502781 | -0.864941 | -27.6485 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2896 | 61.4266105010899 | -1.03491 | -31.8934 | 8 | 11 | 7 | 0.35 | 0.20 | - | yes | Open |
| 1980 | 61.8958568934499 | -0.746372 | -20.1676 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2890 | 62.56409004457617 | -0.939617 | -27.9805 | 4 | 14 | 11 | 0.55 | 0.20 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.980kcal/mol
Ligand efficiency (LE)
-1.0762kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.915
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
344.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.57kcal/mol
Minimised FF energy
86.13kcal/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.