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 (-0.676 kcal/mol/HA)
✓ Good fit quality (FQ -6.92)
✗ High strain energy (19.2 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
ℹ SASA not computed
Score
-25.001
kcal/mol
LE
-0.676
kcal/mol/HA
Fit Quality
-6.92
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
4.43
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 19.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 0
Hydrophobic 24
π–π 6
Clashes 6
Severe clashes 1
| Final rank | 6.732147949674597 | Score | -25.0006 |
|---|---|---|---|
| Inter norm | -0.704644 | Intra norm | 0.0289522 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 0 |
| Artifact reason | excluded; geometry warning; 18 clashes; 1 protein clash; high strain Δ 22.1 | ||
| Residues | A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:LYS114;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:TRP221;A:TYR174;A:TYR98;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
Hydrogen bonds
No hydrogen bonds detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 394 | 4.824031120225275 | -0.559793 | -17.9593 | 0 | 16 | 15 | 0.79 | 0.00 | - | no | Open |
| 393 | 4.8342966363052895 | -0.874586 | -28.7263 | 2 | 16 | 15 | 0.79 | 0.00 | - | no | Open |
| 401 | 5.544913036571565 | -0.837917 | -25.4211 | 2 | 14 | 12 | 0.63 | 0.00 | - | no | Open |
| 524 | 5.71545161130506 | -0.531814 | -22.122 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 523 | 5.853583757572163 | -0.475833 | -14.4118 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 400 | 5.991578804880139 | -0.6343 | -23.2541 | 0 | 16 | 15 | 0.79 | 0.00 | - | no | Open |
| 533 | 6.016219807250548 | -0.503386 | -16.6918 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 6.271765321214856 | -0.532132 | -26.5306 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 717 | 6.359048231967443 | -0.366984 | -12.9882 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 720 | 6.454657660615654 | -0.439902 | -16.8067 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 538 | 6.461885054046319 | -0.485127 | -22.026 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 588 | 6.469183471884971 | -0.642205 | -21.2297 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 6.557615301449495 | -0.660037 | -17.1485 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 712 | 6.820650888681524 | -0.391361 | -14.3591 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 527 | 7.163080623390221 | -0.625227 | -23.7366 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 7.391532983625233 | -0.715721 | -21.8731 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 537 | 7.6183813565571885 | -0.587778 | -19.2357 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 713 | 7.769950286759409 | -0.481214 | -15.2582 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 8.260915333543338 | -0.552057 | -24.578 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 718 | 8.686843616583896 | -0.450704 | -19.2841 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 6.732147949674597 | -0.704644 | -25.0006 | 0 | 16 | 15 | 0.79 | 0.00 | - | yes | Current |
| 531 | 7.074134258414574 | -0.475045 | -19.5657 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 529 | 7.461715263826837 | -0.463645 | -17.571 | 0 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 528 | 7.486579424380058 | -0.511433 | -21.3373 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 587 | 7.531982670403918 | -0.586933 | -20.6302 | 0 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 397 | 7.780685289612809 | -0.639316 | -26.3868 | 1 | 15 | 15 | 0.79 | 0.00 | - | yes | Open |
| 534 | 7.870906154971624 | -0.549002 | -23.6055 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 398 | 7.953263128225099 | -0.8172 | -28.1181 | 2 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 719 | 8.062327028852009 | -0.470867 | -13.935 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 396 | 8.068583176739661 | -0.769401 | -19.7046 | 0 | 15 | 14 | 0.74 | 0.00 | - | yes | Open |
| 711 | 8.236743801116575 | -0.579801 | -22.5862 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 579 | 8.261263508834592 | -0.708317 | -21.9743 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 585 | 8.383207669517338 | -0.707315 | -24.7732 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 716 | 8.552341082283359 | -0.374775 | -12.8459 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 581 | 8.603768764228624 | -0.683635 | -27.2741 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 526 | 8.830135839323713 | -0.478375 | -19.3293 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 540 | 9.305664535969818 | -0.553463 | -23.5298 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 402 | 9.672259340185855 | -0.599865 | -14.2895 | 1 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 580 | 10.447446779426922 | -0.645172 | -24.8712 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 584 | 10.720186707206247 | -0.783426 | -21.1736 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 399 | 56.65304746631722 | -0.56375 | -17.945 | 0 | 15 | 12 | 0.63 | 0.00 | - | yes | Open |
| 532 | 57.0975813531502 | -0.584451 | -23.4639 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 539 | 57.32768770998607 | -0.461476 | -15.804 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 715 | 57.421555140899216 | -0.539862 | -20.0272 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 714 | 57.73022582961767 | -0.443412 | -16.8325 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 525 | 58.73819404495769 | -0.410954 | -18.5926 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 586 | 59.099750611742564 | -0.791936 | -27.0296 | 1 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 535 | 59.36500216101931 | -0.535377 | -21.3038 | 3 | 14 | 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
-25.001kcal/mol
Ligand efficiency (LE)
-0.6757kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.918
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.43
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
130.94kcal/mol
Minimised FF energy
111.76kcal/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.