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 (-0.913 kcal/mol/HA)
✓ Good fit quality (FQ -9.06)
✓ Good H-bonds (3 bonds)
✗ High strain energy (11.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.146
kcal/mol
LE
-0.913
kcal/mol/HA
Fit Quality
-9.06
FQ (Leeson)
HAC
33
heavy atoms
MW
469
Da
LogP
2.43
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 11.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 2
Clashes 9
Severe clashes 0
| Final rank | 5.142267070290366 | Score | -30.1462 |
|---|---|---|---|
| Inter norm | -0.96498 | Intra norm | 0.0514592 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 13 clashes; 9 protein contact clashes; high strain Δ 21.5 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:GLY214;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 343 | 3.812752552123337 | -0.994563 | -31.4469 | 6 | 18 | 14 | 0.74 | 0.20 | - | no | Open |
| 344 | 3.8705243401228744 | -0.870754 | -28.115 | 3 | 16 | 14 | 0.74 | 0.00 | - | no | Open |
| 347 | 4.356298300693849 | -0.965998 | -30.8745 | 4 | 17 | 15 | 0.79 | 0.20 | - | no | Open |
| 351 | 4.379586910799428 | -0.969195 | -33.0114 | 5 | 18 | 14 | 0.74 | 0.20 | - | no | Open |
| 477 | 4.389746743148744 | -0.489235 | -15.7609 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 478 | 5.101064648093625 | -0.509403 | -14.2208 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 350 | 5.142267070290366 | -0.96498 | -30.1462 | 3 | 19 | 15 | 0.79 | 0.00 | - | no | Current |
| 355 | 5.247370235052955 | -0.612381 | -15.2624 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 359 | 5.360352943942462 | -0.72041 | -23.1843 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 475 | 5.774198577861414 | -0.456512 | -12.9251 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 7.694967007527174 | -0.538491 | -14.0072 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 348 | 4.878707951509122 | -0.934625 | -31.8094 | 5 | 17 | 13 | 0.68 | 0.20 | - | yes | Open |
| 342 | 5.833367815917855 | -0.896866 | -28.1377 | 5 | 17 | 14 | 0.74 | 0.20 | - | yes | Open |
| 354 | 5.847562371311991 | -0.65567 | -18.9976 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 349 | 5.970706771991042 | -0.817193 | -27.7005 | 4 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 358 | 6.943685250944132 | -0.64618 | -20.4915 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 476 | 6.961132261695528 | -0.607793 | -18.0138 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 474 | 7.064209232112513 | -0.595766 | -18.7824 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 357 | 7.121210526073309 | -0.510579 | -13.6016 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 481 | 7.430854451805857 | -0.476256 | -13.496 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 345 | 9.797896602715781 | -0.983616 | -28.2511 | 8 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 480 | 56.557544805031874 | -0.456017 | -12.0125 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 356 | 56.71320713716938 | -0.565556 | -15.5944 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 346 | 58.20044515834379 | -0.968374 | -24.9045 | 5 | 18 | 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
-30.146kcal/mol
Ligand efficiency (LE)
-0.9135kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.064
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
468.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
174.24kcal/mol
Minimised FF energy
162.50kcal/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.