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 (-0.706 kcal/mol/HA)
✓ Good fit quality (FQ -7.01)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (21.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.302
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-7.01
FQ (Leeson)
HAC
33
heavy atoms
MW
468
Da
LogP
4.60
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 21.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 4
Clashes 9
Severe clashes 0
| Final rank | 55.14117812174992 | Score | -23.3022 |
|---|---|---|---|
| Inter norm | -0.743185 | Intra norm | 0.0367828 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 9 protein contact clashes | ||
| Residues | A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 386 | 4.219453268762867 | -0.611273 | -19.9677 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 4.389401009806216 | -0.980044 | -33.6803 | 5 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 407 | 4.406274469583082 | -0.604981 | -16.6399 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 4.529607992939293 | -0.600132 | -19.3831 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 4.542080962318288 | -0.598029 | -18.8865 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 373 | 4.5645821919286504 | -0.902655 | -28.8302 | 3 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 388 | 4.706434256628442 | -0.57482 | -20.8116 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 391 | 4.82580175741979 | -0.606318 | -20.2026 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 404 | 4.881017553160937 | -0.590505 | -19.7848 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 5.201736758719649 | -0.734487 | -24.828 | 2 | 16 | 14 | 0.74 | 0.20 | - | no | Open |
| 389 | 5.320547070726503 | -0.864279 | -29.2099 | 3 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 399 | 5.328680989452245 | -0.540254 | -12.677 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 481 | 5.329188138536998 | -0.665397 | -22.1937 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 5.425294092579525 | -0.872094 | -24.1789 | 3 | 15 | 14 | 0.74 | 0.20 | - | no | Open |
| 388 | 5.527752669172703 | -0.908724 | -27.2409 | 3 | 16 | 14 | 0.74 | 0.20 | - | no | Open |
| 382 | 5.571640980315277 | -0.857947 | -26.9769 | 7 | 10 | 9 | 0.47 | 0.40 | - | no | Open |
| 392 | 5.6153663193672365 | -0.556622 | -13.7225 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 380 | 6.237859910008191 | -0.882384 | -22.8212 | 3 | 16 | 13 | 0.68 | 0.20 | - | no | Open |
| 489 | 6.241968736410809 | -0.577392 | -18.4943 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 6.49709158467979 | -0.603771 | -20.4074 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 369 | 7.635425118948389 | -0.844544 | -23.7505 | 4 | 18 | 14 | 0.74 | 0.20 | - | no | Open |
| 400 | 54.327234270536 | -0.610839 | -21.8376 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 389 | 54.400392175797606 | -0.613254 | -21.5742 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 54.44075908747284 | -0.574063 | -18.0438 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 384 | 54.651180586534 | -0.631221 | -22.4295 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 387 | 54.948204801272766 | -0.598223 | -21.163 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 55.025446663444754 | -0.619907 | -20.6134 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 55.11928453134976 | -1.04789 | -34.0856 | 4 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 377 | 55.14117812174992 | -0.743185 | -23.3022 | 4 | 16 | 14 | 0.74 | 0.00 | - | no | Current |
| 402 | 55.749346400661736 | -0.629804 | -14.3808 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 398 | 56.2719942640934 | -0.529824 | -16.1143 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 56.44202781760647 | -0.898848 | -26.1429 | 3 | 16 | 13 | 0.68 | 0.20 | - | no | Open |
| 374 | 57.34821281207432 | -0.836006 | -20.9551 | 7 | 15 | 11 | 0.58 | 0.40 | - | no | Open |
| 494 | 5.422286817064304 | -0.608421 | -17.9439 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 487 | 6.966412454823932 | -0.622513 | -17.9757 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 483 | 7.355057825911928 | -0.667723 | -22.7651 | 3 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 499 | 8.226982319595765 | -0.685084 | -22.9784 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 501 | 8.733270621144547 | -0.72695 | -24.828 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 500 | 9.026714328376661 | -0.633729 | -22.4851 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 385 | 54.7240870755039 | -0.58198 | -21.1437 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 381 | 55.227112309153824 | -0.88525 | -23.6682 | 3 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 406 | 55.512786213289324 | -0.657716 | -19.8302 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 391 | 55.63555487280513 | -0.986538 | -32.1535 | 4 | 19 | 15 | 0.79 | 0.40 | - | yes | Open |
| 375 | 55.98499602217265 | -0.892176 | -29.718 | 9 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 371 | 56.338439339978244 | -0.997667 | -34.0764 | 5 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 384 | 56.34785890215691 | -0.985179 | -30.6997 | 5 | 18 | 15 | 0.79 | 0.40 | - | yes | Open |
| 379 | 56.37235878808654 | -0.831821 | -25.39 | 5 | 11 | 10 | 0.53 | 0.40 | - | yes | Open |
| 395 | 56.49759166516982 | -0.52761 | -17.3423 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 386 | 56.70846136066069 | -0.910331 | -26.807 | 4 | 17 | 15 | 0.79 | 0.40 | - | yes | Open |
| 368 | 56.98750925007884 | -0.944987 | -32.5657 | 9 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 491 | 57.08885652247868 | -0.6557 | -19.1749 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 397 | 57.09541079498806 | -0.5372 | -17.6504 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 372 | 57.38346094025793 | -0.928016 | -31.4319 | 4 | 17 | 14 | 0.74 | 0.40 | - | yes | Open |
| 394 | 57.45347060514955 | -0.527668 | -16.3343 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 493 | 57.74467394123017 | -0.635597 | -19.9102 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 492 | 57.77487501569145 | -0.596494 | -13.231 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 396 | 57.77784329335643 | -0.555793 | -14.3217 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 390 | 57.896356112050626 | -0.826728 | -27.586 | 6 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 488 | 57.958937521007584 | -0.657809 | -20.374 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 490 | 57.98464120921412 | -0.634947 | -20.5764 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 485 | 58.381005127531246 | -0.71633 | -23.119 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 486 | 58.44179897381428 | -0.603043 | -20.0779 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 502 | 58.6404976972828 | -0.63921 | -20.5106 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 495 | 58.67773894109469 | -0.695172 | -20.7211 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 480 | 59.43994879066766 | -0.619232 | -21.3311 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 497 | 59.521191371674185 | -0.615662 | -18.6562 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 496 | 60.063505436266716 | -0.640984 | -23.0239 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 498 | 60.10158844527602 | -0.659193 | -22.5021 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 390 | 60.12243609734436 | -0.57843 | -19.5354 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 387 | 60.175820388443306 | -0.890667 | -25.9414 | 4 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 484 | 60.83762336983778 | -0.668728 | -23.0687 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 482 | 61.06203370068978 | -0.701193 | -19.7974 | 8 | 12 | 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
-23.302kcal/mol
Ligand efficiency (LE)
-0.7061kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.006
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
467.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.60
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.08kcal/mol
Minimised FF energy
29.89kcal/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.