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 (-0.581 kcal/mol/HA)
✓ Good fit quality (FQ -5.71)
✗ Very high strain energy (23.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-18.580
kcal/mol
LE
-0.581
kcal/mol/HA
Fit Quality
-5.71
FQ (Leeson)
HAC
32
heavy atoms
MW
428
Da
LogP
3.15
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 2
Clashes 10
Severe clashes 1
| Final rank | 7.250474306733145 | Score | -18.5804 |
|---|---|---|---|
| Inter norm | -0.74326 | Intra norm | 0.162621 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 14 clashes; 1 protein clash; high strain Δ 23.3 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR83;A:TRP47;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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1306 | 2.6632965477740185 | -0.563568 | -18.2056 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 865 | 3.318411598595411 | -1.02026 | -30.2859 | 4 | 21 | 1 | 0.05 | 0.00 | - | no | Open |
| 857 | 3.4141876953354355 | -0.944884 | -28.6511 | 4 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 1307 | 3.4558049493034186 | -0.468981 | -13.8299 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1917 | 3.472360734427278 | -0.914246 | -26.5124 | 2 | 21 | 17 | 0.85 | 0.20 | - | no | Open |
| 1308 | 3.530953649879152 | -0.521727 | -14.6248 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1303 | 3.531427224683225 | -0.548358 | -15.9612 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1304 | 3.542547119689803 | -0.474875 | -14.2227 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 868 | 3.700670787420635 | -0.851078 | -24.6771 | 3 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1302 | 3.706733888429295 | -0.479475 | -12.6142 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1914 | 3.708136139394973 | -0.694223 | -17.7463 | 4 | 20 | 15 | 0.75 | 0.20 | - | no | Open |
| 751 | 3.797355634740354 | -0.717416 | -23.6289 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1921 | 3.8906747884861845 | -0.789041 | -22.7883 | 2 | 19 | 17 | 0.85 | 0.20 | - | no | Open |
| 867 | 4.086401700063545 | -0.809938 | -21.6017 | 3 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 859 | 4.1191281260047825 | -0.714638 | -22.1201 | 3 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 761 | 4.219261320584193 | -0.813402 | -24.9049 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1926 | 4.490244944814448 | -0.797209 | -23.471 | 4 | 20 | 17 | 0.85 | 0.20 | - | no | Open |
| 1909 | 4.512833128923957 | -0.961676 | -27.9 | 4 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 1913 | 4.703551527537676 | -0.870334 | -24.8216 | 3 | 21 | 17 | 0.85 | 0.20 | - | no | Open |
| 862 | 4.7397235276077945 | -0.746366 | -21.4012 | 2 | 19 | 1 | 0.05 | 0.00 | - | no | Open |
| 1925 | 4.770660134744985 | -0.87892 | -25.8881 | 3 | 19 | 17 | 0.85 | 0.20 | - | no | Open |
| 1919 | 4.842088442221433 | -0.848842 | -22.1261 | 5 | 20 | 17 | 0.85 | 0.20 | - | no | Open |
| 1928 | 5.044534521614529 | -0.853628 | -24.7513 | 3 | 17 | 15 | 0.75 | 0.20 | - | no | Open |
| 748 | 5.046256935805195 | -0.646189 | -19.6839 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 754 | 5.262133461617888 | -0.80207 | -22.7988 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 875 | 5.335453404007643 | -0.633057 | -18.6633 | 2 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 752 | 5.499617372723758 | -0.790755 | -16.0214 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1912 | 5.925345385971219 | -0.843435 | -24.3415 | 1 | 15 | 12 | 0.60 | 0.00 | - | no | Open |
| 759 | 6.326251241176845 | -0.896749 | -26.2308 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 749 | 6.484450085173497 | -0.754931 | -23.0424 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 876 | 6.718522305323098 | -0.736086 | -23.7144 | 2 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 863 | 6.914571305200054 | -0.682929 | -19.9379 | 3 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 864 | 7.247996622684475 | -0.655414 | -20.1346 | 1 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 1312 | 53.29177574752717 | -0.522262 | -15.5287 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 866 | 53.6572873449359 | -0.902295 | -25.4976 | 3 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 1309 | 53.91300352396749 | -0.501237 | -16.2633 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1301 | 53.93812716135011 | -0.556978 | -15.172 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1310 | 54.672453994775495 | -0.634846 | -21.4711 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 750 | 54.70567446708426 | -0.720788 | -19.7682 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 757 | 54.71805789872367 | -0.678191 | -20.6216 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1918 | 54.770658281831274 | -0.869262 | -25.448 | 0 | 15 | 14 | 0.70 | 0.00 | - | no | Open |
| 1305 | 55.37829300698083 | -0.546185 | -12.6738 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 870 | 55.539125863529215 | -0.614128 | -19.5216 | 1 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1924 | 56.2631572390519 | -0.829598 | -21.215 | 2 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 1927 | 56.28530094470512 | -0.803503 | -24.4166 | 1 | 17 | 14 | 0.70 | 0.00 | - | no | Open |
| 873 | 4.618214434328604 | -0.933432 | -27.7739 | 4 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 860 | 5.9002881276516 | -0.774737 | -23.4524 | 4 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 760 | 5.951780054659353 | -0.891844 | -25.389 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1916 | 6.536988130513168 | -0.830945 | -24.6339 | 3 | 15 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1910 | 7.250474306733145 | -0.74326 | -18.5804 | 2 | 19 | 15 | 0.75 | 0.20 | - | yes | Current |
| 746 | 7.251296360113969 | -0.68152 | -14.5747 | 1 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 743 | 7.546998126957334 | -0.791787 | -24.0342 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 742 | 7.55690623989517 | -0.938418 | -24.6775 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 744 | 8.204121214457553 | -0.682782 | -21.7633 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1923 | 54.810759744413126 | -0.813344 | -24.7474 | 2 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 874 | 55.2202146267247 | -0.792781 | -23.6742 | 4 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 871 | 55.25059968752308 | -0.690779 | -21.5671 | 2 | 20 | 1 | 0.05 | 0.00 | - | yes | Open |
| 861 | 55.26702428130145 | -0.946084 | -28.3527 | 5 | 21 | 1 | 0.05 | 0.00 | - | yes | Open |
| 858 | 55.663722865074064 | -0.708094 | -13.6023 | 4 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1920 | 55.664785450454545 | -0.726884 | -22.4797 | 2 | 14 | 13 | 0.65 | 0.00 | - | yes | Open |
| 755 | 55.95337061996388 | -0.653742 | -19.4565 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1915 | 56.0954203340594 | -0.73966 | -22.1397 | 0 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 869 | 56.216448084037026 | -0.593515 | -17.3393 | 2 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 756 | 56.496274581993944 | -0.800784 | -23.5201 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1311 | 57.15071124634958 | -0.582042 | -16.8719 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1922 | 57.68133259722134 | -0.766868 | -23.5562 | 1 | 19 | 15 | 0.75 | 0.00 | - | yes | Open |
| 872 | 57.9307681129568 | -0.729569 | -22.3707 | 2 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 747 | 58.29187863341483 | -0.777352 | -21.0761 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 753 | 58.468808404978724 | -0.841038 | -22.3761 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1911 | 58.571697657776454 | -0.946724 | -30.1399 | 2 | 20 | 15 | 0.75 | 0.00 | - | yes | Open |
| 745 | 58.7644538144261 | -0.82481 | -25.4618 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 758 | 59.69163487499388 | -0.762997 | -17.7064 | 4 | 19 | 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
-18.580kcal/mol
Ligand efficiency (LE)
-0.5806kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.710
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
427.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.15
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
132.58kcal/mol
Minimised FF energy
109.14kcal/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.