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 (-0.965 kcal/mol/HA)
✓ Good fit quality (FQ -9.21)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (31.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.979
kcal/mol
LE
-0.965
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.46
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 14
Severe clashes 2
| Final rank | 9.741665444279889 | Score | -27.9794 |
|---|---|---|---|
| Inter norm | -0.951366 | Intra norm | -0.0134404 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 11 clashes; 2 protein clashes; high strain Δ 38.2 | ||
| Residues | A:ALA32;A:ARG97;A:ASP52;A:GLY96;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:THR61;A:VAL30;A:VAL31 | ||
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: permissive.
| 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 | 12 | Native recall | 0.60 |
| Jaccard | 0.52 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 971 | 3.2904871119912085 | -1.24923 | -34.7407 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1241 | 3.8272864692771584 | -0.823726 | -23.5143 | 3 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 1530 | 4.11420261987769 | -0.656597 | -17.8131 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 742 | 4.543265357791389 | -0.914274 | -25.4358 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2319 | 4.681918810373528 | -0.836623 | -26.9127 | 6 | 16 | 12 | 0.60 | 0.40 | - | no | Open |
| 2226 | 4.708903584105318 | -0.964292 | -26.8272 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1189 | 4.739888270377758 | -0.814106 | -24.5946 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1532 | 4.89091818909871 | -0.747857 | -21.5504 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 741 | 5.686492941687903 | -1.06553 | -28.5535 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1698 | 5.892587765031347 | -0.537254 | -16.5086 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1302 | 6.136537006370849 | -0.744578 | -19.8732 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 973 | 6.430891436174653 | -0.991753 | -24.0941 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2230 | 6.463704293162274 | -0.909887 | -23.1216 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 972 | 6.57275521314203 | -1.18973 | -32.2935 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1192 | 7.370500931723624 | -0.736047 | -16.9897 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1005 | 7.4082249670019555 | -0.78572 | -18.1656 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 988 | 8.512956722771559 | -0.72742 | -20.1748 | 3 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 1531 | 5.198003181857905 | -0.722556 | -20.2264 | 4 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2317 | 5.486425176596659 | -0.952989 | -29.0709 | 4 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1535 | 5.624267618928126 | -0.764019 | -22.0844 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1533 | 5.8723665373146945 | -0.720048 | -22.2985 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2227 | 5.906480797020729 | -0.905718 | -24.8096 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1006 | 5.99617685457487 | -0.894501 | -26.4446 | 8 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1240 | 6.055857409810714 | -0.925547 | -26.4723 | 6 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2322 | 6.449327437757825 | -0.801386 | -18.6085 | 3 | 15 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2228 | 6.613639056348155 | -0.981011 | -28.2007 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1697 | 6.642152072467665 | -0.619713 | -17.7203 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1242 | 6.77553453803957 | -0.790688 | -21.5525 | 5 | 18 | 1 | 0.05 | 0.00 | - | yes | Open |
| 970 | 6.939851771520181 | -1.19952 | -35.4419 | 14 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2320 | 7.447920053877624 | -0.972043 | -25.7882 | 3 | 17 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2229 | 7.555142526632983 | -0.971307 | -27.4903 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 974 | 8.181567849445038 | -1.03518 | -27.653 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1004 | 8.434738391545302 | -0.891023 | -25.3744 | 9 | 24 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1007 | 9.001389053910739 | -0.801719 | -20.078 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1191 | 9.017777740043474 | -0.967475 | -29.398 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2321 | 9.116054338428498 | -1.05698 | -28.7357 | 8 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1536 | 9.440630359197588 | -0.645559 | -16.7178 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2316 | 9.741665444279889 | -0.951366 | -27.9794 | 6 | 15 | 12 | 0.60 | 0.20 | - | yes | Current |
| 1303 | 9.872562906110575 | -0.777837 | -18.265 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2318 | 9.941370223132225 | -0.865819 | -22.9235 | 3 | 12 | 8 | 0.40 | 0.20 | - | yes | Open |
| 969 | 10.282551384972876 | -1.15184 | -32.517 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1190 | 10.461955303965746 | -0.841228 | -23.5805 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 975 | 10.71185986021271 | -1.09701 | -28.8048 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1534 | 11.101726943755594 | -0.745573 | -15.9926 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1243 | 11.500466512839035 | -1.0763 | -32.068 | 10 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 984 | 12.557928276031902 | -0.823147 | -22.5926 | 6 | 23 | 1 | 0.05 | 0.00 | - | yes | Open |
| 989 | 12.667437109932376 | -0.875222 | -17.7108 | 6 | 21 | 1 | 0.05 | 0.00 | - | yes | Open |
| 985 | 12.703119658383176 | -0.821467 | -20.2484 | 6 | 19 | 1 | 0.05 | 0.00 | - | yes | Open |
| 987 | 12.804268347704422 | -0.868059 | -21.0772 | 5 | 22 | 1 | 0.05 | 0.00 | - | yes | Open |
| 986 | 13.24090764633014 | -0.769706 | -21.4487 | 5 | 21 | 1 | 0.05 | 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
-27.979kcal/mol
Ligand efficiency (LE)
-0.9648kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.210
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.46
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
3.73kcal/mol
Minimised FF energy
-27.94kcal/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.