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 (-1.024 kcal/mol/HA)
✓ Good fit quality (FQ -9.88)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (21.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.720
kcal/mol
LE
-1.024
kcal/mol/HA
Fit Quality
-9.88
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
2.87
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 21.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 19
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 5.574880790406462 | Score | -30.7204 |
|---|---|---|---|
| Inter norm | -1.09519 | Intra norm | 0.0711788 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 7 |
| Artifact reason | geometry warning; 16 clashes; 7 protein contact clashes; high strain Δ 30.5 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:TYR174 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1775 | 5.206213798195639 | -0.569137 | -10.4171 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1740 | 5.307691197251932 | -0.64664 | -16.6125 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1183 | 5.574880790406462 | -1.09519 | -30.7204 | 7 | 13 | 11 | 0.58 | 0.60 | - | no | Current |
| 1737 | 5.588900462013154 | -0.572351 | -8.57734 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3149 | 5.804592544161588 | -0.687521 | -18.766 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3277 | 5.807198653040353 | -0.647031 | -17.4637 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1739 | 5.881416049253384 | -0.626567 | -18.556 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1181 | 5.916327844696929 | -0.95404 | -24.8911 | 6 | 16 | 12 | 0.63 | 0.40 | - | no | Open |
| 1292 | 6.0726185637222345 | -0.656904 | -14.857 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1736 | 6.646519658280501 | -0.797361 | -21.3187 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3150 | 6.996921885811275 | -0.763961 | -21.4635 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1416 | 7.520192294663652 | -0.861256 | -16.5889 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3151 | 7.549306682482059 | -0.723516 | -17.0489 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 3280 | 6.150003806450116 | -0.682968 | -13.4828 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1291 | 6.484008254702521 | -0.55963 | -14.5914 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1184 | 6.808006712247863 | -1.01531 | -28.2169 | 10 | 15 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1779 | 7.406178432920676 | -0.481026 | -9.43225 | 7 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1179 | 7.485100798169473 | -0.980776 | -22.8635 | 7 | 13 | 10 | 0.53 | 0.60 | - | yes | Open |
| 1417 | 7.928655178839425 | -0.903246 | -24.1784 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1776 | 8.034781710109126 | -0.618503 | -14.56 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1781 | 8.089170249104003 | -0.52066 | -13.085 | 10 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1778 | 8.111078555347587 | -0.66171 | -19.1835 | 9 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1293 | 8.122434962369168 | -0.869268 | -22.1003 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3146 | 8.200968647410825 | -0.736156 | -18.0428 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1290 | 8.370334834290299 | -0.77004 | -20.1313 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1780 | 8.461875034603791 | -0.584384 | -18.7487 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3145 | 8.631945720409053 | -0.827279 | -24.2484 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1738 | 8.641402149924378 | -0.65553 | -14.4326 | 11 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1420 | 8.852325542135791 | -0.826838 | -25.6359 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1735 | 9.033914668218241 | -0.650261 | -12.9351 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3144 | 9.231547534341564 | -0.721393 | -16.2247 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3147 | 9.363333081730113 | -0.97949 | -22.319 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1777 | 9.490833239807811 | -0.592106 | -11.0389 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3275 | 9.54528406750826 | -0.684576 | -16.4352 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3282 | 9.7007558666861 | -0.830068 | -17.489 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3279 | 9.890141497228438 | -0.767361 | -17.6993 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1418 | 9.985570704963996 | -0.914722 | -19.2993 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1180 | 10.242794171317406 | -1.0286 | -29.0579 | 8 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
| 3278 | 10.519607722464785 | -0.770804 | -18.2331 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3148 | 10.660765633411732 | -0.870793 | -17.8719 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1419 | 11.24062392665763 | -0.769734 | -16.3028 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1182 | 12.014601952732153 | -0.979457 | -24.3168 | 13 | 20 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1294 | 12.443428560683 | -0.70343 | -18.3909 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3276 | 12.509352123122184 | -0.784352 | -22.853 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1421 | 12.552229956178776 | -0.857929 | -22.7313 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3281 | 14.013056430005784 | -0.707382 | -19.0655 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1289 | 14.24898242290118 | -0.703563 | -17.9713 | 7 | 21 | 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
-30.720kcal/mol
Ligand efficiency (LE)
-1.0240kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.878
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
407.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.87
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.68kcal/mol
Minimised FF energy
66.24kcal/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.