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 (-1.133 kcal/mol/HA)
✓ Good fit quality (FQ -10.93)
✓ Good H-bonds (5 bonds)
✗ High strain energy (11.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-33.999
kcal/mol
LE
-1.133
kcal/mol/HA
Fit Quality
-10.93
FQ (Leeson)
HAC
30
heavy atoms
MW
426
Da
LogP
3.31
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 11.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 9
Severe clashes 0
| Final rank | 4.227549295338338 | Score | -33.999 |
|---|---|---|---|
| Inter norm | -1.09127 | Intra norm | -0.0420274 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 9 protein contact clashes; moderate strain Δ 14.2 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206;A:VAL211 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | 0.67 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 431 | 3.631181098855875 | -0.645244 | -18.9969 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 434 | 4.227549295338338 | -1.09127 | -33.999 | 5 | 16 | 14 | 0.74 | 0.40 | - | no | Current |
| 432 | 4.559003259065976 | -0.724067 | -19.6786 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 436 | 5.200352637604098 | -0.931978 | -27.9593 | 4 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 537 | 5.245437618088034 | -0.803348 | -24.1308 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 435 | 5.303378366681805 | -1.09425 | -32.209 | 4 | 15 | 13 | 0.68 | 0.40 | - | no | Open |
| 566 | 6.489512529977004 | -0.624723 | -20.1926 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 565 | 5.861781522553681 | -0.59299 | -15.413 | 6 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 564 | 7.322858874402824 | -0.6671 | -19.022 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 538 | 7.7257945914587225 | -0.796452 | -16.0337 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 539 | 10.35353164877357 | -0.829773 | -24.6469 | 5 | 15 | 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
-33.999kcal/mol
Ligand efficiency (LE)
-1.1333kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.932
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
425.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.31
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.28kcal/mol
Minimised FF energy
4.98kcal/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.