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 (-0.765 kcal/mol/HA)
✓ Good fit quality (FQ -7.52)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (28.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.477
kcal/mol
LE
-0.765
kcal/mol/HA
Fit Quality
-7.52
FQ (Leeson)
HAC
32
heavy atoms
MW
433
Da
LogP
4.20
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 28.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 7
Severe clashes 0
| Final rank | 4.870768241917139 | Score | -24.4767 |
|---|---|---|---|
| Inter norm | -0.925958 | Intra norm | 0.161062 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 7 protein contact clashes; high strain Δ 29.0 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS13;A:MET163;A:MET213;A:NAP301;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 660 | 3.795738511824096 | -0.740854 | -23.4787 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 503 | 3.988941166107284 | -1.0814 | -35.9646 | 4 | 17 | 13 | 0.68 | 0.60 | - | no | Open |
| 494 | 3.9976456355938614 | -0.955068 | -26.488 | 6 | 15 | 12 | 0.63 | 0.40 | - | no | Open |
| 411 | 4.179224967531099 | -0.604346 | -12.6724 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 4.2079538946262245 | -0.542849 | -17.668 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 4.278584422778635 | -0.978743 | -32.4276 | 5 | 16 | 13 | 0.68 | 0.40 | - | no | Open |
| 502 | 4.390430401900558 | -0.817173 | -23.4263 | 5 | 15 | 12 | 0.63 | 0.40 | - | no | Open |
| 663 | 4.549679996003226 | -0.701548 | -15.3531 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 474 | 4.721705757086878 | -0.608148 | -20.3689 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 504 | 4.870768241917139 | -0.925958 | -24.4767 | 5 | 19 | 15 | 0.79 | 0.40 | - | no | Current |
| 498 | 5.0288508018692 | -0.833404 | -25.0908 | 5 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 501 | 5.083427611412111 | -0.845133 | -25.8109 | 8 | 18 | 14 | 0.74 | 0.40 | - | no | Open |
| 473 | 5.1913572471149765 | -0.631877 | -17.7249 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 455 | 5.192012366469978 | -0.775754 | -12.0747 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 482 | 5.230282650644279 | -0.633956 | -20.8965 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 412 | 5.26404058431113 | -0.625733 | -20.5562 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 449 | 5.29145744783457 | -0.730922 | -17.6053 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 478 | 5.405302461155027 | -0.526514 | -17.1768 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 499 | 5.5262845155147895 | -1.05537 | -29.5064 | 5 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 477 | 5.565773021984288 | -0.544493 | -16.8233 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 5.879973529956362 | -0.885559 | -27.3225 | 3 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 418 | 6.006345263291581 | -0.64667 | -16.0281 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 6.2264629756072445 | -0.727164 | -18.7076 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 495 | 6.699382192987704 | -1.01614 | -27.3564 | 9 | 16 | 13 | 0.68 | 0.40 | - | no | Open |
| 452 | 6.959601631747587 | -0.79477 | -20.0681 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 5.149244096415285 | -0.825168 | -25.986 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 457 | 5.315690621468081 | -0.840953 | -27.1211 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 451 | 5.494711029650935 | -0.72837 | -18.6427 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 480 | 6.004671401610363 | -0.524919 | -10.4028 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 446 | 6.211212866437372 | -0.779262 | -23.9659 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 448 | 6.266014492426665 | -0.75355 | -23.8291 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 491 | 6.306263210122003 | -1.16661 | -35.1801 | 5 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 413 | 6.793166012602316 | -0.555856 | -18.9206 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 454 | 7.104314659679892 | -0.848874 | -26.1661 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 447 | 7.138670824976789 | -0.711041 | -21.9002 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 476 | 7.235579660408884 | -0.572884 | -14.2935 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 492 | 7.366123557755595 | -0.900503 | -24.7239 | 4 | 17 | 12 | 0.63 | 0.40 | - | yes | Open |
| 662 | 7.7995268447585575 | -0.845584 | -20.7847 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 453 | 8.055687506671333 | -0.775982 | -22.1983 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 496 | 55.884180783345265 | -1.04868 | -28.066 | 5 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 661 | 56.14791273038879 | -0.684951 | -16.8307 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 481 | 56.414522399412526 | -0.592491 | -21.0329 | 0 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 417 | 56.477732338612455 | -0.767074 | -22.4594 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 410 | 56.53988120423411 | -0.692771 | -20.0878 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 450 | 57.345380226195864 | -0.799503 | -25.7211 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 500 | 58.01169473496874 | -0.954019 | -21.1319 | 3 | 17 | 13 | 0.68 | 0.20 | - | yes | Open |
| 456 | 58.3588014707584 | -0.792057 | -23.3039 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 475 | 59.350383609744604 | -0.658859 | -15.7459 | 6 | 15 | 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
-24.477kcal/mol
Ligand efficiency (LE)
-0.7649kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.522
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
432.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.20
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
85.77kcal/mol
Minimised FF energy
57.73kcal/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.