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 (-0.540 kcal/mol/HA)
✓ Good fit quality (FQ -5.60)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (35.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.059
kcal/mol
LE
-0.540
kcal/mol/HA
Fit Quality
-5.60
FQ (Leeson)
HAC
39
heavy atoms
MW
532
Da
LogP
3.79
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 35.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 4
Clashes 15
Severe clashes 5
| Final rank | 15.389880677088504 | Score | -21.0594 |
|---|---|---|---|
| Inter norm | -0.853891 | Intra norm | 0.313907 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 18 clashes; 5 protein clashes; high strain Δ 46.9 | ||
| Residues | A:ALA212;A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:TYR98;A:VAL211 | ||
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2874 | 5.586767614242513 | -0.573085 | -17.849 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 5.733799445047356 | -0.725425 | -19.6013 | 4 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 1177 | 5.808693178673141 | -0.591318 | -17.8127 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 894 | 5.898756948559349 | -0.583064 | -17.4387 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 895 | 6.003961619708955 | -0.617247 | -17.326 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 897 | 6.395394256214189 | -0.609642 | -18.5379 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 985 | 6.8009366689193325 | -0.610397 | -17.2164 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 987 | 6.947237150976209 | -0.614374 | -9.73646 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2877 | 8.293467845307575 | -0.525818 | -14.1891 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1178 | 7.596498536608396 | -0.562075 | -16.5362 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 628 | 8.831605615092478 | -0.824026 | -22.9733 | 10 | 12 | 12 | 0.63 | 0.40 | - | yes | Open |
| 896 | 9.371808235389816 | -0.623182 | -16.3266 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2875 | 9.755045480945892 | -0.530005 | -12.986 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 986 | 10.115921425448608 | -0.514176 | -14.1297 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 627 | 11.125587770350409 | -0.816171 | -25.3445 | 8 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2876 | 12.299791920993336 | -0.507384 | -11.182 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 988 | 14.083596156520617 | -0.585552 | -12.263 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 629 | 15.389880677088504 | -0.853891 | -21.0594 | 8 | 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
-21.059kcal/mol
Ligand efficiency (LE)
-0.5400kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.604
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
531.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.79
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.82kcal/mol
Minimised FF energy
78.26kcal/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.