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 (-0.609 kcal/mol/HA)
✓ Good fit quality (FQ -6.23)
✗ Very high strain energy (59.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.527
kcal/mol
LE
-0.609
kcal/mol/HA
Fit Quality
-6.23
FQ (Leeson)
HAC
37
heavy atoms
MW
503
Da
LogP
1.49
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 59.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 7.641119035703079 | Score | -22.5272 |
|---|---|---|---|
| Inter norm | -0.580197 | Intra norm | -0.028652 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | geometry warning; 14 clashes; 7 protein contact clashes; high strain Δ 60.3 | ||
| Residues | A:ARG48;A:ASP52;A:ILE45;A:LEU94;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;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 | 13 | Native recall | 0.65 |
| Jaccard | 0.54 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 648 | 3.654048777040276 | -0.460593 | -18.7111 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 650 | 4.276327406338073 | -0.473844 | -18.113 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 757 | 4.470783622620282 | -0.564526 | -18.871 | 2 | 18 | 13 | 0.65 | 0.00 | - | no | Open |
| 652 | 4.988962342108749 | -0.456595 | -16.3848 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 749 | 5.007481566539756 | -0.568231 | -18.2276 | 0 | 18 | 13 | 0.65 | 0.00 | - | no | Open |
| 759 | 5.1902556663508 | -0.617813 | -21.2356 | 1 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 640 | 5.204641784337701 | -0.412403 | -11.0914 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 751 | 5.232239438700562 | -0.606627 | -19.6771 | 0 | 18 | 13 | 0.65 | 0.00 | - | no | Open |
| 771 | 5.28324080082365 | -0.573935 | -18.3575 | 0 | 14 | 10 | 0.50 | 0.00 | - | no | Open |
| 642 | 5.913373748990659 | -0.396204 | -14.8692 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 758 | 6.310439773447799 | -0.56831 | -19.2357 | 1 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 644 | 6.607181796605833 | -0.404749 | -12.5783 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 768 | 7.0583281576802 | -0.634418 | -22.0687 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 772 | 7.154793813516009 | -0.551023 | -15.4795 | 0 | 13 | 9 | 0.45 | 0.00 | - | no | Open |
| 753 | 7.641119035703079 | -0.580197 | -22.5272 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Current |
| 654 | 53.67795360127522 | -0.45806 | -13.4492 | 2 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 647 | 54.42781281342558 | -0.407712 | -12.8784 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 655 | 54.557847021330616 | -0.380001 | -12.5835 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 752 | 56.11766390368315 | -0.689924 | -24.4634 | 1 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 763 | 56.14896048770573 | -0.670928 | -24.0801 | 1 | 15 | 11 | 0.55 | 0.00 | - | no | Open |
| 750 | 56.261934033309416 | -0.608479 | -18.4468 | 0 | 21 | 16 | 0.80 | 0.00 | - | no | Open |
| 760 | 56.33449369464164 | -0.660562 | -22.1644 | 1 | 17 | 15 | 0.75 | 0.00 | - | no | Open |
| 646 | 55.35347237282498 | -0.382487 | -14.0081 | 1 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 645 | 55.40229001611615 | -0.534679 | -18.8382 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 761 | 55.51051473398724 | -0.650436 | -19.1027 | 0 | 17 | 15 | 0.75 | 0.00 | - | yes | Open |
| 643 | 55.699087167352815 | -0.463505 | -17.4386 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 765 | 55.75691810755007 | -0.61185 | -21.5002 | 1 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 653 | 55.83419170326622 | -0.376397 | -13.1292 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 764 | 56.331713135523 | -0.578755 | -17.3039 | 0 | 14 | 11 | 0.55 | 0.00 | - | yes | Open |
| 769 | 56.39287016389826 | -0.580772 | -22.3616 | 1 | 15 | 11 | 0.55 | 0.00 | - | yes | Open |
| 641 | 56.42794222808606 | -0.471519 | -14.9788 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 770 | 56.6372303362315 | -0.686759 | -20.6889 | 0 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 649 | 56.67979554622855 | -0.467635 | -17.6656 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 767 | 56.74191448450843 | -0.700959 | -18.0036 | 2 | 20 | 17 | 0.85 | 0.40 | - | yes | Open |
| 762 | 56.809215515860934 | -0.697034 | -22.7082 | 1 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 755 | 57.40935423509804 | -0.697033 | -22.5037 | 2 | 19 | 16 | 0.80 | 0.20 | - | yes | Open |
| 766 | 57.48102088371495 | -0.620407 | -21.2466 | 1 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 756 | 57.52316110628624 | -0.635409 | -19.8797 | 2 | 17 | 17 | 0.85 | 0.20 | - | yes | Open |
| 754 | 58.23659201973931 | -0.672207 | -19.8644 | 0 | 20 | 17 | 0.85 | 0.00 | - | yes | Open |
| 651 | 59.161335702096714 | -0.563468 | -19.4954 | 2 | 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
-22.527kcal/mol
Ligand efficiency (LE)
-0.6088kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.233
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
502.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.49
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
59.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
194.05kcal/mol
Minimised FF energy
134.83kcal/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.