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 (-0.713 kcal/mol/HA)
✓ Good fit quality (FQ -7.30)
✗ Very high strain energy (33.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-26.387
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-7.30
FQ (Leeson)
HAC
37
heavy atoms
MW
497
Da
LogP
1.59
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 33.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 6
Clashes 8
Severe clashes 1
| Final rank | 7.780685289612809 | Score | -26.3868 |
|---|---|---|---|
| Inter norm | -0.639316 | Intra norm | -0.07384 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash; high strain Δ 31.3 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;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 | 0.79 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 | Open |
| 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 | Current |
| 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
-26.387kcal/mol
Ligand efficiency (LE)
-0.7132kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.301
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
496.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.59
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
133.47kcal/mol
Minimised FF energy
99.85kcal/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.