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 (-0.587 kcal/mol/HA)
✓ Good fit quality (FQ -5.87)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (42.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.951
kcal/mol
LE
-0.587
kcal/mol/HA
Fit Quality
-5.87
FQ (Leeson)
HAC
34
heavy atoms
MW
463
Da
LogP
2.49
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 42.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 1
Clashes 7
Severe clashes 2
| Final rank | 9.686656942221035 | Score | -19.9514 |
|---|---|---|---|
| Inter norm | -1.0213 | Intra norm | 0.434491 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 16 clashes; 2 protein clashes; high strain Δ 53.7 | ||
| Residues | A:ALA96;A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER95;A:TYR174;A:TYR98;A:VAL164 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.50 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1613 | 7.736120229076166 | -0.529864 | -7.16598 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1239 | 8.72386178262099 | -0.611125 | -16.7317 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 891 | 8.85603299772989 | -0.714865 | -16.8707 | 10 | 14 | 14 | 0.74 | 0.80 | - | no | Open |
| 1061 | 9.415712583318854 | -1.01269 | -31.9259 | 13 | 17 | 9 | 0.47 | 0.40 | - | no | Open |
| 1518 | 9.535822871672837 | -0.76868 | -17.8174 | 16 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1062 | 6.062467174552658 | -0.959352 | -31.5935 | 8 | 19 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1615 | 7.742716966023687 | -0.525276 | -14.2302 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1238 | 8.066987813513524 | -0.57582 | -9.7643 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 890 | 8.425618828698564 | -0.683505 | -15.6271 | 6 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1236 | 8.77300839956277 | -0.673216 | -18.0724 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1610 | 8.890863192937562 | -0.666164 | -13.3471 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1060 | 9.108644424076884 | -0.905896 | -14.3311 | 7 | 17 | 11 | 0.58 | 0.20 | - | yes | Open |
| 894 | 9.433241839988234 | -0.671629 | -10.5641 | 5 | 14 | 11 | 0.58 | 0.20 | - | yes | Open |
| 1058 | 9.650731162150382 | -0.964031 | -30.1953 | 9 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1057 | 9.686656942221035 | -1.0213 | -19.9514 | 8 | 17 | 12 | 0.63 | 0.20 | - | yes | Current |
| 892 | 9.773728883570453 | -0.824883 | -23.7829 | 12 | 13 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1520 | 9.961329486854654 | -0.774519 | -19.7781 | 16 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1609 | 10.020188971823131 | -0.533627 | -10.2337 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1235 | 10.024709993849607 | -0.508219 | -7.54657 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1237 | 10.54445396989478 | -0.656583 | -13.2688 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1240 | 10.60401728509031 | -0.615609 | -18.3867 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1516 | 10.838757240609185 | -0.698184 | -21.3371 | 16 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 893 | 11.183246598455668 | -0.945078 | -27.2269 | 14 | 17 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1519 | 11.872199872766934 | -0.778227 | -21.2656 | 14 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1614 | 11.906313247273264 | -0.518466 | -15.9367 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1611 | 12.0068361853094 | -0.630467 | -16.0659 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1515 | 12.086615932253306 | -0.710791 | -16.3167 | 13 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1612 | 12.325965503370396 | -0.673945 | -10.7309 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1517 | 12.711251775759505 | -0.641906 | -13.7776 | 14 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 889 | 13.397286891444425 | -0.830728 | -21.6731 | 12 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1059 | 14.219219184773088 | -0.877259 | -15.1271 | 11 | 15 | 10 | 0.53 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.951kcal/mol
Ligand efficiency (LE)
-0.5868kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.872
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
42.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.81kcal/mol
Minimised FF energy
64.08kcal/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.