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 (-0.909 kcal/mol/HA)
✓ Good fit quality (FQ -8.68)
✗ Very high strain energy (21.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.359
kcal/mol
LE
-0.909
kcal/mol/HA
Fit Quality
-8.68
FQ (Leeson)
HAC
29
heavy atoms
MW
410
Da
LogP
2.78
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 21.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 4
Clashes 11
Severe clashes 0
| Final rank | 5.467220745646232 | Score | -26.3587 |
|---|---|---|---|
| Inter norm | -1.00969 | Intra norm | 0.100765 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 11 protein contact clashes; high strain Δ 22.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 14 | Native recall | 0.74 |
| Jaccard | 0.64 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2316 | 3.960310142346869 | -0.773683 | -21.5569 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2471 | 5.022286124316827 | -0.810633 | -23.714 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2267 | 5.467220745646232 | -1.00969 | -26.3587 | 2 | 17 | 14 | 0.74 | 0.00 | - | no | Current |
| 2387 | 6.402022949492157 | -0.994423 | -27.702 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2472 | 6.644158458147587 | -0.871795 | -21.9547 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2268 | 5.871526055619512 | -1.10204 | -31.388 | 3 | 17 | 14 | 0.74 | 0.00 | - | yes | Open |
| 2388 | 5.889010366488222 | -1.03918 | -26.9312 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2317 | 6.742752502926955 | -0.820794 | -23.2766 | 6 | 13 | 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
-26.359kcal/mol
Ligand efficiency (LE)
-0.9089kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.676
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
410.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.42kcal/mol
Minimised FF energy
16.35kcal/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.