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 (-0.675 kcal/mol/HA)
✓ Good fit quality (FQ -6.51)
✗ Very high strain energy (30.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.252
kcal/mol
LE
-0.675
kcal/mol/HA
Fit Quality
-6.51
FQ (Leeson)
HAC
30
heavy atoms
MW
448
Da
LogP
1.68
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 30.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 19
π–π 1
Clashes 6
Severe clashes 0
| Final rank | 4.494989461556778 | Score | -20.2523 |
|---|---|---|---|
| Inter norm | -0.624109 | Intra norm | -0.051642 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 6 protein contact clashes; high strain Δ 24.0 | ||
| Residues | A:ALA212;A:ARG14;A:LEU208;A:LEU209;A:LYS13;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TYR98 | ||
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 | 0.43 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1063 | 3.489241158179233 | -0.638702 | -20.7699 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1067 | 3.8005463888203055 | -0.587953 | -16.0312 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1071 | 4.0188503824868755 | -0.651094 | -18.7681 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 4.494989461556778 | -0.624109 | -20.2523 | 2 | 11 | 9 | 0.47 | 0.20 | - | no | Current |
| 1070 | 4.749325689675589 | -0.709915 | -23.1849 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 622 | 4.758755295527568 | -0.62725 | -18.368 | 3 | 12 | 8 | 0.42 | 0.20 | - | no | Open |
| 1077 | 5.02828670915213 | -0.828266 | -25.4786 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1079 | 5.371555070095162 | -0.564211 | -17.1814 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1075 | 5.488476788122449 | -0.648739 | -16.6338 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 5.817722494835567 | -0.648712 | -21.6326 | 1 | 11 | 8 | 0.42 | 0.00 | - | yes | Open |
| 1064 | 5.880783998935789 | -0.762479 | -22.5416 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1069 | 6.509860418563349 | -0.770273 | -21.5089 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1076 | 55.19478136276498 | -0.731334 | -21.8786 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1073 | 55.20360475197135 | -0.680544 | -20.1153 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1061 | 55.879984139178454 | -0.758598 | -22.8602 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1078 | 56.274494193507174 | -0.645771 | -19.5445 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 626 | 56.984110411647876 | -0.770516 | -22.8211 | 4 | 14 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1066 | 57.309725471311864 | -0.659284 | -20.9064 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1074 | 57.675419946738984 | -0.701628 | -21.5916 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1065 | 57.72368594493542 | -0.724259 | -20.9994 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 625 | 58.002570073487156 | -0.717005 | -21.3779 | 3 | 12 | 9 | 0.47 | 0.40 | - | yes | Open |
| 1072 | 58.38251674348037 | -0.620994 | -17.5946 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 621 | 58.47216295391583 | -0.897118 | -22.3645 | 2 | 18 | 16 | 0.84 | 0.20 | - | yes | Open |
| 1062 | 58.8858787467478 | -0.728565 | -20.852 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1068 | 59.13544645534879 | -0.878559 | -21.3921 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 627 | 59.38836693712599 | -1.00953 | -27.4714 | 2 | 17 | 15 | 0.79 | 0.00 | - | yes | Open |
| 628 | 59.821323151188004 | -0.713147 | -4.85127 | 1 | 21 | 15 | 0.79 | 0.20 | - | yes | Open |
| 1080 | 60.937583988346894 | -0.806893 | -20.225 | 5 | 15 | 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
-20.252kcal/mol
Ligand efficiency (LE)
-0.6751kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.512
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
448.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.68
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
162.23kcal/mol
Minimised FF energy
132.18kcal/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.