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 (-0.930 kcal/mol/HA)
✓ Good fit quality (FQ -8.97)
✓ Strong H-bond network (11 bonds)
✗ High strain energy (17.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.912
kcal/mol
LE
-0.930
kcal/mol/HA
Fit Quality
-8.97
FQ (Leeson)
HAC
30
heavy atoms
MW
424
Da
LogP
3.38
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 17.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 19
π–π 4
Clashes 7
Severe clashes 0
| Final rank | 5.441456136641121 | Score | -27.9124 |
|---|---|---|---|
| Inter norm | -1.0419 | Intra norm | 0.111218 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 11 |
| Artifact reason | geometry warning; 14 clashes; 7 protein contact clashes; high strain Δ 35.4 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;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 | 0.64 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1649 | 5.333648864793163 | -0.613779 | -16.5337 | 9 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1102 | 5.441456136641121 | -1.0419 | -27.9124 | 11 | 17 | 14 | 0.74 | 0.40 | - | no | Current |
| 1757 | 5.681947767273271 | -0.629212 | -18.1899 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1107 | 5.730183091843363 | -1.07855 | -25.3471 | 9 | 14 | 10 | 0.53 | 0.40 | - | no | Open |
| 1648 | 5.833224717354181 | -0.683893 | -17.4247 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 836 | 6.374634700028764 | -1.03672 | -24.0005 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1106 | 6.646748781882616 | -1.1538 | -30.0904 | 8 | 14 | 11 | 0.58 | 0.40 | - | no | Open |
| 1753 | 6.784704677492144 | -0.572911 | -16.4561 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 834 | 6.888828999689371 | -1.01363 | -24.5368 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1258 | 6.8893744549802385 | -0.734084 | -21.0655 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1651 | 6.223863805568116 | -0.620258 | -16.0695 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1259 | 6.619362283199684 | -0.707941 | -16.4544 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1756 | 7.041127745997336 | -0.543463 | -17.1369 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1754 | 7.075319933906573 | -0.560272 | -7.38926 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1652 | 7.789353211604111 | -0.671589 | -19.0356 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1752 | 7.8742435556442 | -0.535969 | -9.61538 | 8 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1257 | 8.150019283074524 | -0.746177 | -19.0405 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1261 | 8.386212133273318 | -0.66331 | -15.8744 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1101 | 8.602880548359057 | -0.997282 | -22.4805 | 12 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1262 | 8.91890239050011 | -0.859874 | -15.7312 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1105 | 9.123247883539273 | -0.951534 | -22.2594 | 6 | 16 | 10 | 0.53 | 0.20 | - | yes | Open |
| 1103 | 9.196694270333829 | -0.958248 | -24.1973 | 11 | 10 | 7 | 0.37 | 0.60 | - | yes | Open |
| 1755 | 9.642112054979481 | -0.653079 | -12.6885 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1647 | 9.691635428885467 | -0.69092 | -10.8165 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1260 | 10.1522055635924 | -0.715289 | -13.3683 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1653 | 11.004721009462527 | -0.742765 | -20.0858 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1104 | 11.291023384292068 | -1.0696 | -26.6766 | 12 | 18 | 11 | 0.58 | 0.60 | - | yes | Open |
| 837 | 12.342979661086977 | -1.07508 | -26.8228 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1650 | 12.37335647916204 | -0.808289 | -20.7608 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 838 | 13.263100767643111 | -0.92026 | -26.5657 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 833 | 13.392958787118673 | -1.01314 | -23.8046 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 835 | 20.888161135049366 | -0.996371 | -18.6358 | 14 | 19 | 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
-27.912kcal/mol
Ligand efficiency (LE)
-0.9304kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.975
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
423.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.38
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.65kcal/mol
Minimised FF energy
59.56kcal/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.