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 (-0.750 kcal/mol/HA)
✓ Good fit quality (FQ -7.50)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (55.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.483
kcal/mol
LE
-0.750
kcal/mol/HA
Fit Quality
-7.50
FQ (Leeson)
HAC
34
heavy atoms
MW
491
Da
LogP
0.68
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 55.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 24
π–π 2
Clashes 15
Severe clashes 1
| Final rank | 10.017601772255048 | Score | -25.4826 |
|---|---|---|---|
| Inter norm | -0.907876 | Intra norm | 0.158389 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 52.9 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.59 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 423 | 6.235444614885987 | -0.921178 | -28.5461 | 4 | 13 | 11 | 0.58 | 0.20 | - | no | Open |
| 424 | 6.5752281328867355 | -1.00078 | -28.5431 | 7 | 14 | 12 | 0.63 | 0.40 | - | no | Open |
| 468 | 6.827904118123914 | -0.746868 | -24.6373 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 7.401065038593859 | -0.779113 | -26.4587 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 6.751124317430976 | -0.70137 | -19.2185 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 602 | 7.494104916731109 | -0.827691 | -22.9203 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 467 | 8.007040405112697 | -0.677413 | -17.4227 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 420 | 8.66704616002394 | -0.810841 | -22.9533 | 4 | 16 | 15 | 0.79 | 0.20 | - | yes | Open |
| 421 | 9.458859204989842 | -0.907133 | -29.9858 | 3 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 422 | 10.017601772255048 | -0.907876 | -25.4826 | 10 | 16 | 13 | 0.68 | 0.40 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.483kcal/mol
Ligand efficiency (LE)
-0.7495kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.499
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
490.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.68
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
55.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
178.93kcal/mol
Minimised FF energy
123.20kcal/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.