Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
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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 (-1.488 kcal/mol/HA)
✓ Good fit quality (FQ -13.33)
✓ Strong H-bond network (12 bonds)
✗ High strain energy (11.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-35.705
kcal/mol
LE
-1.488
kcal/mol/HA
Fit Quality
-13.33
FQ (Leeson)
HAC
24
heavy atoms
MW
324
Da
LogP
1.15
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 11.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 12
Hydrophobic 9
π–π 2
Clashes 8
Severe clashes 0
⚠ Hydrophobic exposure 47%
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 9
Exposed 8
LogP 1.15
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.547797422665081 | Score | -35.7054 |
|---|---|---|---|
| Inter norm | -1.49389 | Intra norm | 0.0061657 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 12 |
| Artifact reason | geometry warning; 12 clashes; 8 protein contact clashes; moderate strain Δ 13.2 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:LEU208;A:LYS13;A:LYS178;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;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 | 9 | Native recall | 0.47 |
| Jaccard | 0.41 | RMSD | - |
| H-bond strict | 6 | Strict recall | 1.00 |
| H-bond same residue+role | 5 | Role recall | 1.00 |
| H-bond same residue | 5 | Residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 330 | 3.05047488413324 | -1.15008 | -23.8022 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 260 | 3.547797422665081 | -1.49389 | -35.7054 | 12 | 12 | 9 | 0.47 | 1.00 | - | no | Current |
| 261 | 4.204023533941446 | -1.38335 | -31.9597 | 8 | 12 | 10 | 0.53 | 0.80 | - | yes | Open |
| 329 | 7.832212599085348 | -1.07272 | -25.4371 | 12 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 262 | 7.863525164133684 | -1.35658 | -31.3205 | 12 | 19 | 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
-35.705kcal/mol
Ligand efficiency (LE)
-1.4877kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.333
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
324.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.15
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
3.02kcal/mol
Minimised FF energy
-8.56kcal/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.