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 (-1.312 kcal/mol/HA)
✓ Good fit quality (FQ -10.76)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (23.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.936
kcal/mol
LE
-1.312
kcal/mol/HA
Fit Quality
-10.76
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
-0.53
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 23.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 20
π–π 3
Clashes 4
Severe clashes 0
| Final rank | 1.9834483987050242 | Score | -24.9362 |
|---|---|---|---|
| Inter norm | -1.4796 | Intra norm | 0.167164 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 4 clashes; 4 protein contact clashes; high strain Δ 28.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;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 | 0.70 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1728 | 1.8768500769955772 | -1.46993 | -26.9835 | 9 | 11 | 10 | 0.53 | 0.40 | - | no | Open |
| 1745 | 1.9834483987050242 | -1.4796 | -24.9362 | 6 | 15 | 14 | 0.74 | 0.40 | - | no | Current |
| 1733 | 2.228029426087275 | -1.56417 | -24.0185 | 8 | 14 | 14 | 0.74 | 0.60 | - | no | Open |
| 1749 | 2.6686075151339974 | -1.40889 | -22.7764 | 7 | 13 | 13 | 0.68 | 0.60 | - | no | Open |
| 2384 | 2.7665709012998856 | -0.800212 | -10.3619 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2386 | 3.063855139650708 | -0.705845 | -15.1068 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2383 | 3.3691070679647694 | -0.959669 | -18.6897 | 6 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2380 | 3.7728355845938437 | -0.868045 | -13.6551 | 4 | 6 | 0 | 0.00 | 0.00 | - | no | Open |
| 2381 | 4.192362665201653 | -0.926177 | -14.9424 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2387 | 4.027534994665723 | -0.774964 | -17.7489 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1730 | 4.184816189649055 | -1.57481 | -31.1023 | 9 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2376 | 4.195270266235503 | -0.772547 | -11.2454 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1736 | 4.235644058595453 | -1.72474 | -30.9389 | 12 | 13 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1740 | 4.362540520889233 | -1.5377 | -28.1586 | 13 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2379 | 4.395695783244731 | -0.691419 | -14.7706 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1737 | 4.471584691160689 | -1.48494 | -23.8955 | 13 | 12 | 11 | 0.58 | 0.60 | - | yes | Open |
| 2375 | 4.590753002006133 | -0.827752 | -15.665 | 6 | 6 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2374 | 4.648031556519652 | -0.738606 | -14.4039 | 3 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1731 | 4.687035226113764 | -1.49332 | -29.8656 | 7 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1724 | 4.733114329638083 | -1.81285 | -31.3278 | 13 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1725 | 5.070475388954626 | -1.563 | -22.8651 | 9 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1748 | 5.191030239372292 | -1.61044 | -26.3482 | 12 | 13 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1750 | 5.350947100194247 | -1.72325 | -31.1372 | 10 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1746 | 5.422463829297065 | -1.53361 | -30.1418 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1732 | 5.789168079486881 | -1.49176 | -26.5702 | 12 | 12 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1720 | 5.844183254661189 | -1.60197 | -27.377 | 13 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2377 | 5.91533057492604 | -0.814325 | -14.8362 | 7 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2373 | 5.964246747470154 | -0.932802 | -14.2765 | 5 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1743 | 6.017278855873055 | -1.5126 | -30.6945 | 10 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1727 | 6.0228273266289385 | -1.77901 | -33.9013 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1735 | 6.047166506282892 | -1.60349 | -31.8335 | 10 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1747 | 6.090022499357254 | -1.46347 | -31.2729 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1723 | 6.2173732351415385 | -1.76481 | -33.8778 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1739 | 6.432889719420583 | -1.49872 | -28.1324 | 10 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1721 | 6.6873148479210744 | -1.68278 | -27.1559 | 11 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1742 | 6.870627313515039 | -1.65378 | -31.4661 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1729 | 53.68157246368138 | -1.55262 | -25.3144 | 10 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2385 | 54.4463891797473 | -0.779176 | -13.8316 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2382 | 54.64345394835052 | -0.607939 | -8.72254 | 5 | 5 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1751 | 54.67885502729105 | -1.62829 | -31.6119 | 10 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2372 | 55.102080780144014 | -0.881783 | -13.7554 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1738 | 55.28656080891448 | -1.76052 | -31.9977 | 12 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2378 | 55.46882946601546 | -0.722593 | -14.837 | 5 | 6 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1744 | 55.81541597793679 | -1.40235 | -26.5901 | 5 | 14 | 9 | 0.47 | 0.20 | - | yes | Open |
| 1741 | 56.14817845781458 | -1.33485 | -19.8743 | 9 | 16 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1726 | 56.26815783120112 | -1.94463 | -34.8227 | 13 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1734 | 56.43104277264373 | -1.67285 | -30.1159 | 11 | 12 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1722 | 56.46358177993412 | -1.77833 | -31.4787 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.936kcal/mol
Ligand efficiency (LE)
-1.3124kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.758
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.53
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.83kcal/mol
Minimised FF energy
61.39kcal/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.