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 (-0.800 kcal/mol/HA)
✓ Good fit quality (FQ -7.94)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (27.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-26.403
kcal/mol
LE
-0.800
kcal/mol/HA
Fit Quality
-7.94
FQ (Leeson)
HAC
33
heavy atoms
MW
477
Da
LogP
1.81
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 27.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 1
Clashes 9
Severe clashes 1
| Final rank | 6.729709980923917 | Score | -26.4026 |
|---|---|---|---|
| Inter norm | -0.888053 | Intra norm | 0.0879746 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 32.5 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLN166;A:GLY205;A:LEU209;A:LYS13;A:MET163;A:NAP301;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:TRP221;A:TYR174;A:VAL206;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: 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 | 12 | Native recall | 0.63 |
| Jaccard | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 3.8840715490426887 | -0.722711 | -21.7454 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 446 | 4.35769441122194 | -0.911223 | -30.6016 | 3 | 16 | 14 | 0.74 | 0.20 | - | no | Open |
| 447 | 5.067846025116949 | -0.957055 | -28.4693 | 5 | 18 | 13 | 0.68 | 0.40 | - | no | Open |
| 452 | 5.1291715272872 | -0.775075 | -23.3235 | 5 | 16 | 13 | 0.68 | 0.40 | - | no | Open |
| 366 | 5.247009396814082 | -0.571614 | -17.3009 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 6.008765931258514 | -0.650242 | -20.613 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 6.082926958825837 | -0.857518 | -27.9425 | 3 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 490 | 6.346638730015562 | -0.717074 | -21.6745 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 367 | 6.384760529767993 | -0.649129 | -19.5902 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 7.290869591443741 | -0.603964 | -16.7595 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 5.522913112731401 | -0.72625 | -25.2614 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 483 | 6.396892644125071 | -0.7221 | -24.9222 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 361 | 6.575864139783592 | -0.59434 | -21.4473 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 451 | 6.688316365817855 | -0.952365 | -30.6657 | 7 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 448 | 6.729709980923917 | -0.888053 | -26.4026 | 4 | 18 | 12 | 0.63 | 0.40 | - | yes | Current |
| 487 | 6.806346688093569 | -0.731947 | -21.4574 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 362 | 6.839393997640773 | -0.615709 | -17.2499 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 434 | 6.873496918519347 | -0.522811 | -16.967 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 436 | 7.10053059660853 | -0.772552 | -22.9248 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 430 | 7.431076745847866 | -0.535033 | -16.9844 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 489 | 7.659385448545859 | -0.751505 | -23.7205 | 3 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 365 | 7.881357062750198 | -0.650064 | -21.2651 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 485 | 8.870862631968425 | -0.681485 | -18.7582 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 486 | 9.219719130430658 | -0.712182 | -19.3634 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 366 | 9.940726351765546 | -0.615714 | -20.8153 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 433 | 10.243289061210085 | -0.739347 | -22.6327 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 363 | 11.419125882890718 | -0.832714 | -26.2276 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 365 | 11.46264684441211 | -0.656114 | -20.0149 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 369 | 14.18280842945374 | -0.776682 | -22.8437 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 370 | 14.576079944322883 | -0.71461 | -21.5368 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 363 | 56.328610250795435 | -0.628498 | -20.8925 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 449 | 56.36327849321316 | -0.800246 | -25.344 | 11 | 14 | 11 | 0.58 | 0.40 | - | yes | Open |
| 445 | 56.75262840181659 | -0.841435 | -28.3143 | 8 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 431 | 56.8321064935309 | -0.711287 | -22.8056 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 488 | 57.71905130971411 | -0.649561 | -20.7203 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 484 | 59.44256791162809 | -0.633698 | -21.4301 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 435 | 59.9598923432017 | -0.838175 | -25.9773 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 368 | 60.39291892413463 | -0.592914 | -17.4802 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 367 | 63.8296401791971 | -0.659495 | -20.2432 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 364 | 64.20129428770224 | -0.655235 | -19.5358 | 8 | 17 | 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
-26.403kcal/mol
Ligand efficiency (LE)
-0.8001kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.938
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
476.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
26.23kcal/mol
Minimised FF energy
-1.32kcal/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.