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 (-0.815 kcal/mol/HA)
✓ Good fit quality (FQ -7.94)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (21.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.273
kcal/mol
LE
-0.815
kcal/mol/HA
Fit Quality
-7.94
FQ (Leeson)
HAC
31
heavy atoms
MW
464
Da
LogP
3.89
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 21.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 22
π–π 2
Clashes 6
Severe clashes 1
| Final rank | 54.656889989975426 | Score | -25.2735 |
|---|---|---|---|
| Inter norm | -0.918206 | Intra norm | 0.102931 |
| Top1000 | no | Excluded | yes |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 11 clashes; 1 protein clash | ||
| Residues | A:ALA212;A:ALA96;A:ARG14;A:ASP161;A:LEU208;A:LEU209;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;A:VAL211 | ||
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: permissive.
| 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 | 9 | Native recall | 0.47 |
| Jaccard | 0.41 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 648 | 3.941548077387152 | -0.721316 | -21.3047 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 4.1054050122404675 | -0.515741 | -17.6869 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 631 | 4.120381881696829 | -0.804516 | -24.5148 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 504 | 4.181754976435263 | -0.558899 | -14.7767 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 465 | 4.38931646661363 | -0.95738 | -28.2255 | 7 | 13 | 8 | 0.42 | 0.40 | - | no | Open |
| 554 | 4.554953514019804 | -0.687016 | -19.5022 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 4.620411190303683 | -0.560689 | -15.6082 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 640 | 4.645773305579829 | -0.739198 | -22.865 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 4.79308127055452 | -0.742008 | -20.0937 | 3 | 11 | 8 | 0.42 | 0.40 | - | no | Open |
| 563 | 4.933279934249882 | -0.549182 | -14.0028 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 5.155951693518506 | -0.730999 | -22.3497 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 5.190302512181689 | -0.621423 | -15.7103 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 562 | 5.22019727362666 | -0.63284 | -18.9783 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 628 | 5.285071808501226 | -0.688371 | -20.8979 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 6.098052585187839 | -0.902159 | -19.6272 | 4 | 18 | 14 | 0.74 | 0.20 | - | no | Open |
| 510 | 53.827686269961504 | -0.524173 | -8.39182 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 54.365832617395604 | -0.787132 | -25.0003 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 645 | 54.374124448979096 | -0.770124 | -23.2397 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 54.643725247455215 | -0.746603 | -20.6037 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 54.86682664158249 | -1.02475 | -29.6978 | 2 | 17 | 16 | 0.84 | 0.20 | - | no | Open |
| 641 | 55.022928340118376 | -0.709887 | -23.3561 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 555 | 55.76673889427674 | -0.657573 | -16.369 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 56.23161782449392 | -0.775352 | -23.9857 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 548 | 56.59916437131442 | -0.636783 | -17.2794 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 508 | 54.39867782517955 | -0.711114 | -19.1124 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 462 | 54.656889989975426 | -0.918206 | -25.2735 | 5 | 12 | 9 | 0.47 | 0.40 | - | yes | Current |
| 507 | 54.65790864079545 | -0.608416 | -14.9395 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 632 | 54.72456069729792 | -0.722828 | -22.722 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 626 | 54.79147992961372 | -0.643384 | -19.5506 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 496 | 55.00002641993573 | -0.495624 | -18.6817 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 469 | 55.0803025712135 | -0.829352 | -23.9808 | 8 | 9 | 7 | 0.37 | 0.40 | - | yes | Open |
| 559 | 55.112517764827665 | -0.511779 | -15.8708 | 1 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 639 | 55.333063732378534 | -0.745248 | -20.7875 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 460 | 55.5877005644928 | -1.09736 | -33.1874 | 4 | 11 | 8 | 0.42 | 0.20 | - | yes | Open |
| 501 | 55.603657948349436 | -0.658212 | -19.4267 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 636 | 55.63614783630715 | -0.65491 | -20.3116 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 502 | 55.82517618938349 | -0.592933 | -19.2653 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 499 | 55.85111348633574 | -0.569343 | -16.5832 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 550 | 55.88137657588727 | -0.671286 | -19.8546 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 560 | 55.88695611858714 | -0.601677 | -19.0188 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 557 | 56.018229537269775 | -0.656464 | -19.6405 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 464 | 56.046595046842505 | -1.0229 | -32.1666 | 5 | 11 | 8 | 0.42 | 0.40 | - | yes | Open |
| 495 | 56.056617300729634 | -0.775571 | -20.2324 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 497 | 56.22887579194599 | -0.694132 | -20.3982 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 643 | 56.41839943808898 | -0.712358 | -19.7658 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 638 | 56.42521109225297 | -0.654625 | -18.8917 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 500 | 56.47852093055947 | -0.530287 | -17.9421 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 459 | 56.501185561831846 | -0.757955 | -18.0839 | 5 | 9 | 7 | 0.37 | 0.40 | - | yes | Open |
| 506 | 56.695995435625456 | -0.550942 | -16.5517 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 553 | 56.814705974189565 | -0.778024 | -21.4602 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 498 | 56.9288120615331 | -0.541575 | -15.8785 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 503 | 57.08265502740869 | -0.824845 | -20.3394 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 633 | 57.1432689688659 | -0.796828 | -24.5901 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 552 | 57.195507142431545 | -0.593584 | -15.4693 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 556 | 57.224766101610086 | -0.5916 | -14.4769 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 474 | 57.26926921478081 | -0.859004 | -20.8812 | 3 | 17 | 15 | 0.79 | 0.00 | - | yes | Open |
| 647 | 57.31692520455889 | -0.82046 | -22.7096 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 467 | 57.47647637089873 | -0.738387 | -19.9402 | 0 | 21 | 14 | 0.74 | 0.00 | - | yes | Open |
| 635 | 57.48515646581476 | -0.682386 | -20.1934 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 551 | 57.70203555404245 | -0.797165 | -23.7914 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 472 | 57.898766351701944 | -0.987738 | -27.1467 | 2 | 17 | 16 | 0.84 | 0.00 | - | yes | Open |
| 558 | 58.02673546525119 | -0.497824 | -16.9859 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 642 | 58.10829044155969 | -0.763495 | -21.5265 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 466 | 58.114916791751035 | -0.956884 | -27.4854 | 5 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 561 | 58.20833657270581 | -0.578841 | -16.6396 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 634 | 59.04813165833657 | -0.732772 | -20.5209 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 629 | 59.139662318923534 | -0.879127 | -22.3734 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 461 | 60.14690940768939 | -0.796728 | -22.8812 | 2 | 17 | 12 | 0.63 | 0.00 | - | yes | Open |
| 637 | 60.68145830260474 | -0.702031 | -21.64 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 463 | 61.26594431035178 | -0.803116 | -17.9416 | 3 | 16 | 13 | 0.68 | 0.00 | - | yes | Open |
| 470 | 61.72553314821356 | -0.803735 | -22.4394 | 2 | 18 | 15 | 0.79 | 0.00 | - | yes | Open |
| 627 | 63.15173964571097 | -0.696296 | -21.0861 | 2 | 19 | 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
-25.273kcal/mol
Ligand efficiency (LE)
-0.8153kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.943
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
464.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.02kcal/mol
Minimised FF energy
40.28kcal/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.