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 (-0.919 kcal/mol/HA)
✓ Good fit quality (FQ -8.96)
✓ Good H-bonds (3 bonds)
✗ High strain energy (14.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.498
kcal/mol
LE
-0.919
kcal/mol/HA
Fit Quality
-8.96
FQ (Leeson)
HAC
31
heavy atoms
MW
412
Da
LogP
5.02
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 14.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 4
Clashes 12
Severe clashes 2
| Final rank | 8.447835441660777 | Score | -28.4981 |
|---|---|---|---|
| Inter norm | -0.983282 | Intra norm | 0.0639872 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 14 clashes; 2 protein clashes; moderate strain Δ 14.4 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLN166;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TRP221;A:TYR174;A:VAL164;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 | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 642 | 3.8897859429743247 | -0.70206 | -22.8143 | 2 | 12 | 10 | 0.53 | 0.20 | - | no | Open |
| 2497 | 4.21532470949885 | -0.716404 | -20.096 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2493 | 4.9206212246164025 | -0.640665 | -19.7998 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2496 | 5.208211107859108 | -0.677599 | -21.175 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2501 | 5.2739426036361285 | -0.611922 | -17.7832 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2491 | 5.8190029691846235 | -0.725795 | -21.5256 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2502 | 6.506554598295468 | -0.647729 | -20.6667 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2492 | 55.05608069016595 | -0.612794 | -19.2409 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2495 | 55.79102811686668 | -0.617054 | -15.0529 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2500 | 5.012169448831498 | -0.704328 | -21.5334 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2490 | 6.765135918693883 | -0.755268 | -22.5184 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 647 | 7.1874759485559085 | -0.719183 | -21.2854 | 3 | 15 | 13 | 0.68 | 0.20 | - | yes | Open |
| 638 | 7.582175414264516 | -0.95989 | -29.1057 | 1 | 17 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2489 | 7.747508119732405 | -0.836428 | -24.5932 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 643 | 7.841446822318458 | -1.04159 | -29.086 | 1 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 645 | 7.977851500616752 | -0.971913 | -29.9416 | 0 | 18 | 13 | 0.68 | 0.00 | - | yes | Open |
| 648 | 8.447835441660777 | -0.983282 | -28.4981 | 3 | 20 | 14 | 0.74 | 0.00 | - | yes | Current |
| 2499 | 55.88477099285925 | -0.667512 | -20.8023 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2503 | 56.05938764386232 | -0.786858 | -23.8628 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2494 | 56.69382338075711 | -0.657024 | -19.9068 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2488 | 57.346879209847806 | -0.791156 | -23.401 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 637 | 57.746312913748255 | -0.960609 | -24.5017 | 1 | 20 | 15 | 0.79 | 0.20 | - | yes | Open |
| 2498 | 58.151540371003534 | -0.672947 | -16.4679 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 639 | 58.23778282054868 | -0.939654 | -27.3753 | 1 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 641 | 58.970783515155986 | -0.635712 | -19.5418 | 4 | 15 | 11 | 0.58 | 0.20 | - | yes | Open |
| 640 | 61.527006946014 | -0.996376 | -22.3609 | 3 | 19 | 15 | 0.79 | 0.40 | - | yes | Open |
| 644 | 61.867830440497535 | -0.8794 | -26.5779 | 3 | 19 | 13 | 0.68 | 0.00 | - | yes | Open |
| 646 | 63.110376741157374 | -0.949705 | -21.7273 | 3 | 19 | 15 | 0.79 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.498kcal/mol
Ligand efficiency (LE)
-0.9193kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.956
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
411.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.02
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
92.37kcal/mol
Minimised FF energy
78.17kcal/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.