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 (-1.060 kcal/mol/HA)
✓ Good fit quality (FQ -9.89)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (30.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.612
kcal/mol
LE
-1.060
kcal/mol/HA
Fit Quality
-9.89
FQ (Leeson)
HAC
27
heavy atoms
MW
370
Da
LogP
2.04
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 30.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 2
Clashes 11
Severe clashes 2
| Final rank | 6.787763548990358 | Score | -28.6118 |
|---|---|---|---|
| Inter norm | -1.19619 | Intra norm | 0.136491 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 5 clashes; 2 protein clashes; high strain Δ 26.3 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS178;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER95;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 3.145223226239307 | -1.1599 | -24.6899 | 6 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 342 | 3.5386477068925735 | -0.833103 | -14.8629 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 400 | 3.635770191804254 | -1.20273 | -27.473 | 7 | 18 | 15 | 0.79 | 0.40 | - | no | Open |
| 341 | 4.091343939500274 | -0.766748 | -15.8167 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 5.3496395493724185 | -1.17864 | -20.9516 | 7 | 20 | 16 | 0.84 | 0.40 | - | yes | Open |
| 399 | 6.787763548990358 | -1.19619 | -28.6118 | 7 | 20 | 15 | 0.79 | 0.40 | - | yes | Current |
| 398 | 9.271658571169846 | -1.27842 | -32.7479 | 11 | 20 | 15 | 0.79 | 0.40 | - | yes | Open |
| 397 | 11.21633425357164 | -1.30169 | -25.3475 | 13 | 17 | 13 | 0.68 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.612kcal/mol
Ligand efficiency (LE)
-1.0597kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.887
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
370.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.04
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-15.24kcal/mol
Minimised FF energy
-45.57kcal/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.