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 (-0.797 kcal/mol/HA)
✓ Good fit quality (FQ -7.84)
✗ High strain energy (17.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.510
kcal/mol
LE
-0.797
kcal/mol/HA
Fit Quality
-7.84
FQ (Leeson)
HAC
32
heavy atoms
MW
433
Da
LogP
3.21
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 17.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 4
Clashes 4
Severe clashes 0
| Final rank | 3.4946831611465887 | Score | -25.5097 |
|---|---|---|---|
| Inter norm | -0.905103 | Intra norm | 0.107926 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 13 clashes; 4 protein contact clashes; moderate strain Δ 15.6 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174;A:VAL206;D:HIS267 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| 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 | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 425 | 2.628212829965432 | -0.920232 | -27.0346 | 1 | 18 | 14 | 0.74 | 0.00 | - | no | Open |
| 428 | 2.8453304328667435 | -0.924444 | -27.5066 | 2 | 18 | 14 | 0.74 | 0.20 | - | no | Open |
| 549 | 3.457529237564331 | -0.698753 | -21.5775 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 427 | 3.4946831611465887 | -0.905103 | -25.5097 | 1 | 16 | 14 | 0.74 | 0.00 | - | no | Current |
| 426 | 3.7259228117587933 | -0.934481 | -26.0996 | 1 | 18 | 14 | 0.74 | 0.00 | - | no | Open |
| 646 | 4.6705171783826085 | -0.593808 | -14.4305 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 5.270573537667395 | -0.622043 | -17.9812 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 645 | 6.486326724507455 | -0.649781 | -18.6579 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 429 | 4.557907944990918 | -0.982697 | -28.5447 | 2 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 551 | 4.99666084728087 | -0.602868 | -17.9818 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 552 | 5.51605662283569 | -0.602072 | -18.0385 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 647 | 6.433536231007473 | -0.64547 | -18.824 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 550 | 6.678794562632069 | -0.629804 | -16.8528 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 648 | 7.984759721304229 | -0.602121 | -14.9534 | 4 | 13 | 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
-25.510kcal/mol
Ligand efficiency (LE)
-0.7972kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.839
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
432.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.21
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.40kcal/mol
Minimised FF energy
18.42kcal/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.