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 (-0.889 kcal/mol/HA)
✓ Good fit quality (FQ -8.48)
✓ Strong H-bond network (11 bonds)
✗ Very high strain energy (31.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.773
kcal/mol
LE
-0.889
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
29
heavy atoms
MW
418
Da
LogP
1.14
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 31.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 24
π–π 4
Clashes 9
Severe clashes 0
| Final rank | 5.608996817893494 | Score | -25.7728 |
|---|---|---|---|
| Inter norm | -0.999909 | Intra norm | 0.11119 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 11 |
| Artifact reason | geometry warning; 10 clashes; 9 protein contact clashes; high strain Δ 37.5 | ||
| Residues | A:ARG14;A:ASP161;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.63 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2216 | 5.608996817893494 | -0.999909 | -25.7728 | 11 | 12 | 12 | 0.63 | 0.60 | - | no | Current |
| 2038 | 5.925648572679045 | -0.774686 | -20.6764 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2040 | 6.261918051144163 | -0.877408 | -23.3577 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2213 | 6.733353378878111 | -0.748892 | -17.1013 | 3 | 15 | 12 | 0.63 | 0.20 | - | no | Open |
| 2214 | 6.245155679169779 | -0.978225 | -25.5438 | 3 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2218 | 6.704826876013939 | -1.00668 | -28.0605 | 6 | 15 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2041 | 7.676231572011049 | -1.07649 | -31.9899 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2042 | 7.795629816735927 | -0.85266 | -28.3542 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2215 | 8.333716775367618 | -0.751101 | -22.4148 | 4 | 15 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2217 | 8.355461292151967 | -0.729575 | -25.5553 | 3 | 16 | 15 | 0.79 | 0.20 | - | yes | Open |
| 2046 | 8.639476441582932 | -0.743484 | -23.0852 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2039 | 9.162871821127412 | -1.17956 | -30.0286 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2221 | 9.22332140547826 | -0.735198 | -23.9957 | 3 | 13 | 11 | 0.58 | 0.20 | - | yes | Open |
| 2045 | 9.33159749149705 | -1.03622 | -30.4265 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2222 | 10.042156677776184 | -1.0426 | -34.1478 | 7 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
| 2037 | 10.339874597865357 | -1.00417 | -26.2492 | 10 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2043 | 10.385321030019924 | -1.07269 | -31.0979 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2044 | 10.53473013675572 | -0.859783 | -22.1977 | 13 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2220 | 11.276127810295833 | -1.05759 | -31.0616 | 5 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
| 2219 | 16.490180599913682 | -0.882953 | -24.759 | 6 | 18 | 13 | 0.68 | 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
-25.773kcal/mol
Ligand efficiency (LE)
-0.8887kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.483
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.14
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.67kcal/mol
Minimised FF energy
-8.34kcal/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.