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 (-0.644 kcal/mol/HA)
✓ Good fit quality (FQ -6.21)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (31.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.313
kcal/mol
LE
-0.644
kcal/mol/HA
Fit Quality
-6.21
FQ (Leeson)
HAC
30
heavy atoms
MW
403
Da
LogP
3.03
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 19
π–π 3
Clashes 15
Severe clashes 3
| Final rank | 11.756233185818509 | Score | -19.3132 |
|---|---|---|---|
| Inter norm | -0.773779 | Intra norm | 0.130004 |
| Top1000 | no | Excluded | yes |
| Contacts | 11 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 14 clashes; 3 protein clashes; high strain Δ 36.3 | ||
| Residues | A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;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 | 10 | Native recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2349 | 4.415489065115561 | -0.786242 | -21.94 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1567 | 5.394431739714205 | -0.801813 | -16.7849 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1115 | 5.919676854696921 | -1.00438 | -24.0948 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1411 | 5.969510344493725 | -0.515336 | -9.51018 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1114 | 6.161219736074408 | -1.1298 | -31.8256 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1412 | 6.193171112562822 | -0.597341 | -17.1511 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 868 | 6.203211106058183 | -0.641769 | -15.5754 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1656 | 6.297735630010203 | -0.589848 | -8.19286 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1116 | 7.106218310122811 | -1.02359 | -26.6374 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2377 | 7.909107449075575 | -0.961525 | -24.1747 | 8 | 16 | 12 | 0.60 | 0.80 | - | no | Open |
| 2352 | 6.09809928940855 | -0.824829 | -19.4668 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1413 | 7.169864720885309 | -0.607592 | -10.7149 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1654 | 7.364433328345507 | -0.609846 | -18.503 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2353 | 7.377159263184851 | -0.772875 | -18.0143 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1112 | 7.425256354974543 | -0.987944 | -23.588 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1566 | 7.5712486459857 | -0.862909 | -22.2544 | 14 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2350 | 7.602411477890433 | -0.748442 | -19.7093 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1659 | 7.672192270595116 | -0.575351 | -17.5459 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1569 | 8.286004519863297 | -0.796455 | -20.5719 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2354 | 8.48231763823536 | -0.71959 | -22.2451 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1658 | 8.639852815700378 | -0.584284 | -13.4847 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2381 | 9.027690547390716 | -0.730775 | -16.7509 | 4 | 12 | 11 | 0.55 | 0.20 | - | yes | Open |
| 870 | 9.37430088420389 | -0.735159 | -20.6119 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1409 | 9.828971123335286 | -0.615232 | -11.5073 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1414 | 9.958060233475113 | -0.673679 | -20.1141 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 866 | 10.072348999583546 | -0.837563 | -15.4698 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2378 | 10.084080591961918 | -0.729942 | -13.5207 | 6 | 14 | 11 | 0.55 | 0.20 | - | yes | Open |
| 1657 | 10.177418010988141 | -0.687431 | -16.7999 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1570 | 10.200861604228875 | -0.769284 | -14.0605 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1410 | 10.474426262384297 | -0.659035 | -9.96236 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2376 | 10.487740224063499 | -0.891043 | -20.589 | 5 | 19 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1571 | 10.561094697540684 | -0.887025 | -22.2533 | 14 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1111 | 10.641120231433307 | -1.08015 | -25.8242 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2380 | 11.167140616946615 | -0.715146 | -13.3958 | 3 | 11 | 9 | 0.45 | 0.20 | - | yes | Open |
| 867 | 11.362234525880062 | -0.693667 | -11.0106 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1113 | 11.621520734952094 | -1.01458 | -21.3551 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 865 | 11.693210297672442 | -0.74994 | -19.7074 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2379 | 11.756233185818509 | -0.773779 | -19.3132 | 5 | 11 | 10 | 0.50 | 0.20 | - | yes | Current |
| 1655 | 11.76129635824057 | -0.630853 | -10.7336 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 869 | 11.979681131660378 | -0.710697 | -17.5276 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2351 | 12.4104422481305 | -0.84906 | -23.2838 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1568 | 13.31944456395102 | -0.757273 | -13.1279 | 9 | 16 | 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
-19.313kcal/mol
Ligand efficiency (LE)
-0.6438kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.210
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
403.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.03
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
95.11kcal/mol
Minimised FF energy
63.62kcal/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.