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.
✓ Good LE (-0.368 kcal/mol/HA)
✓ Good fit quality (FQ -3.77)
✓ Strong H-bond network (14 bonds)
✗ Very high strain energy (50.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-13.636
kcal/mol
LE
-0.368
kcal/mol/HA
Fit Quality
-3.77
FQ (Leeson)
HAC
37
heavy atoms
MW
496
Da
LogP
3.70
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 50.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 14
Hydrophobic 24
π–π 6
Clashes 21
Severe clashes 6
| Final rank | 20.320912728979277 | Score | -13.6362 |
|---|---|---|---|
| Inter norm | -0.814908 | Intra norm | 0.446363 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 14 |
| Artifact reason | excluded; hard geometry fail; 1 severe clash; 6 protein clashes; high strain Δ 57.9 | ||
| Residues | A:ALA170;A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| 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 | 4 | Strict recall | 0.67 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1719 | 6.084068177825755 | -0.421284 | -6.84932 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1722 | 6.65164325408822 | -0.4765 | -9.49122 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 882 | 6.912713919592961 | -0.740107 | -27.4761 | 6 | 17 | 14 | 0.74 | 0.00 | - | no | Open |
| 1343 | 7.204353751986924 | -0.584924 | -18.677 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1589 | 7.259424866501643 | -0.552672 | -15.475 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 883 | 8.686771090942566 | -0.812209 | -24.408 | 1 | 13 | 12 | 0.63 | 0.00 | - | no | Open |
| 1021 | 9.303179687303201 | -0.972816 | -28.3594 | 5 | 20 | 13 | 0.68 | 0.20 | - | no | Open |
| 1502 | 9.615822284949518 | -0.661759 | -13.8749 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1023 | 8.099915983445435 | -0.879472 | -25.5164 | 12 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1720 | 8.455564645515508 | -0.502656 | -14.3474 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1587 | 8.869724618198232 | -0.579875 | -15.0799 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 886 | 9.12206988212019 | -0.789118 | -20.604 | 2 | 14 | 12 | 0.63 | 0.00 | - | yes | Open |
| 1504 | 9.168129420825656 | -0.699418 | -25.9129 | 14 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1501 | 9.216845321851638 | -0.633606 | -14.7184 | 14 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1723 | 9.669634217517853 | -0.507718 | -19.888 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1027 | 9.808868162021739 | -0.846862 | -21.828 | 7 | 19 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1347 | 10.266710687378986 | -0.838101 | -15.2066 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1345 | 10.439579529028013 | -0.575341 | -16.8508 | 10 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1503 | 10.477854621563965 | -0.708693 | -23.1949 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1718 | 10.495833736179684 | -0.45232 | -14.077 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1025 | 10.606971985869516 | -0.876459 | -20.7425 | 4 | 15 | 14 | 0.74 | 0.20 | - | yes | Open |
| 1590 | 10.607757338123596 | -0.511299 | -12.967 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1586 | 10.75323084285494 | -0.563551 | -16.5246 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 881 | 11.219509543937395 | -0.914971 | -21.5319 | 11 | 16 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1588 | 11.622827943012481 | -0.627719 | -10.5556 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1341 | 11.752108828258004 | -0.706557 | -18.9469 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1721 | 11.982406067674617 | -0.417517 | -12.2611 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1505 | 12.310215646849736 | -0.769384 | -12.8873 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1499 | 12.340137445366647 | -0.663208 | -19.9784 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 885 | 12.370130717376192 | -0.601572 | -18.6806 | 12 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1022 | 12.374519695640814 | -1.06595 | -28.6719 | 8 | 22 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1026 | 12.480706340136177 | -1.09559 | -37.7297 | 9 | 21 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1344 | 13.242032605890923 | -0.568745 | -9.77295 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1592 | 13.257372436495242 | -0.593547 | -15.923 | 14 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1500 | 13.509959817860892 | -0.757349 | -20.2841 | 16 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1346 | 13.611375616634033 | -0.619969 | -18.6847 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1342 | 13.812888144834428 | -0.503081 | -14.0762 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1724 | 14.350032865432613 | -0.567462 | -12.883 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1591 | 14.357573065801171 | -0.51038 | -19.1396 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1024 | 16.573220491404435 | -0.857286 | -20.0653 | 10 | 19 | 13 | 0.68 | 0.40 | - | yes | Open |
| 884 | 20.320912728979277 | -0.814908 | -13.6362 | 14 | 16 | 14 | 0.74 | 0.60 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-13.636kcal/mol
Ligand efficiency (LE)
-0.3685kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.773
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
496.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.70
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
50.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
139.41kcal/mol
Minimised FF energy
89.37kcal/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.