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 (-0.950 kcal/mol/HA)
✓ Good fit quality (FQ -9.16)
✗ High strain energy (16.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.504
kcal/mol
LE
-0.950
kcal/mol/HA
Fit Quality
-9.16
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
3.42
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 6
Clashes 11
Severe clashes 1
| Final rank | 56.26304349817779 | Score | -28.504 |
|---|---|---|---|
| Inter norm | -0.970114 | Intra norm | 0.0199817 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 13 | Native recall | 0.68 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1774 | 3.573288050063608 | -0.772999 | -21.9004 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2504 | 3.660721520100676 | -0.729517 | -21.5858 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1862 | 3.87219139404224 | -0.815061 | -23.24 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1859 | 4.044797902455198 | -0.841637 | -24.6125 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1775 | 4.083144695775258 | -0.728624 | -21.6912 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1853 | 4.10184010020892 | -0.880758 | -27.1162 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1867 | 4.119210628346155 | -0.827872 | -25.7791 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2510 | 4.1921996790157605 | -0.70955 | -21.5318 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 4.2026533814878615 | -1.07778 | -24.1679 | 3 | 17 | 14 | 0.74 | 0.20 | - | no | Open |
| 1769 | 4.306591512368701 | -0.764589 | -21.6771 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1856 | 4.44984162506596 | -0.826813 | -25.0381 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1865 | 4.489069700446324 | -0.853108 | -26.2028 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1857 | 4.60207313262103 | -0.870965 | -25.5233 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1860 | 4.941176211073369 | -0.814242 | -23.1829 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2512 | 4.9499879180043935 | -0.533637 | -15.8118 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1772 | 5.084244868679373 | -0.720538 | -19.5788 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2515 | 5.08998407023543 | -0.723521 | -21.8715 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1770 | 5.539903271014922 | -0.661452 | -20.0834 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 5.609142162413652 | -0.97887 | -28.4095 | 0 | 18 | 14 | 0.74 | 0.00 | - | no | Open |
| 1777 | 5.827949941320511 | -0.826804 | -24.4048 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2507 | 6.028855781518878 | -0.674504 | -18.8887 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 6.069152296260166 | -0.848161 | -20.0064 | 2 | 20 | 15 | 0.79 | 0.20 | - | no | Open |
| 1861 | 54.23584161740301 | -0.866582 | -27.591 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 55.84034710540824 | -1.0461 | -31.3666 | 3 | 16 | 13 | 0.68 | 0.00 | - | no | Open |
| 2513 | 56.752684427219364 | -0.511399 | -15.524 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 57.88244178748334 | -0.876207 | -24.1328 | 3 | 16 | 15 | 0.79 | 0.20 | - | no | Open |
| 1855 | 7.426943019173197 | -0.821617 | -22.7875 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2505 | 7.663017115939302 | -0.746292 | -21.2169 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1868 | 53.97468230510326 | -0.855091 | -27.5803 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1866 | 55.06104951731334 | -0.84078 | -25.006 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2509 | 55.63878368400333 | -0.708493 | -20.9189 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2508 | 55.73331777063794 | -0.650146 | -18.1186 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1780 | 55.80983335278023 | -0.740289 | -22.3618 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1779 | 55.99983980577713 | -0.680155 | -19.0918 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2514 | 56.14429881458122 | -0.634465 | -17.5186 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 665 | 56.26304349817779 | -0.970114 | -28.504 | 1 | 18 | 13 | 0.68 | 0.00 | - | yes | Current |
| 668 | 56.38329802096 | -0.64718 | -18.107 | 1 | 11 | 9 | 0.47 | 0.20 | - | yes | Open |
| 1778 | 56.779784950041396 | -0.739517 | -20.636 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2511 | 56.836178833386235 | -0.837185 | -23.5688 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1776 | 56.85110481560109 | -0.694955 | -18.2006 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1771 | 57.31615126997281 | -0.932011 | -24.247 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2506 | 57.52170037018265 | -0.793715 | -22.691 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1863 | 57.59809028730185 | -0.89876 | -26.375 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1854 | 57.75508683658262 | -0.974356 | -27.3918 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1864 | 58.08813499175179 | -0.767908 | -21.731 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1773 | 58.49758287988025 | -0.763956 | -24.47 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1858 | 58.8597175338021 | -0.981518 | -26.8425 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 667 | 60.42742215940044 | -0.63983 | -9.58648 | 2 | 20 | 14 | 0.74 | 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
-28.504kcal/mol
Ligand efficiency (LE)
-0.9501kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.165
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.10kcal/mol
Minimised FF energy
59.01kcal/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.