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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.887 kcal/mol/HA)
✓ Good fit quality (FQ -7.95)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (16.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.292
kcal/mol
LE
-0.887
kcal/mol/HA
Fit Quality
-7.95
FQ (Leeson)
HAC
24
heavy atoms
MW
340
Da
LogP
3.34
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 3
Clashes 20
Severe clashes 4
| Final rank | 11.95034435488239 | Score | -21.2916 |
|---|---|---|---|
| Inter norm | -1.05659 | Intra norm | 0.16944 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 7 clashes; 4 protein clashes; moderate strain Δ 17.9 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:ASP165;A:CYS168;A:GLN166;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER95;A:TYR174;A:VAL164 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.44 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1370 | 2.6465910966268873 | -1.04763 | -22.0878 | 1 | 14 | 12 | 0.63 | 0.00 | - | no | Open |
| 1368 | 3.2876693550988687 | -1.06477 | -26.2729 | 1 | 15 | 13 | 0.68 | 0.00 | - | no | Open |
| 1364 | 3.602721244583072 | -1.09085 | -24.1927 | 6 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 1371 | 4.058395351931927 | -1.14105 | -26.7059 | 3 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 1369 | 4.2751692054653905 | -1.10227 | -21.3225 | 2 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 1792 | 4.9439622016269515 | -0.919368 | -16.1457 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1788 | 5.901168191680162 | -0.986641 | -14.2814 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1367 | 6.5877190178282214 | -1.22097 | -28.9189 | 4 | 15 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1786 | 7.77459149530689 | -0.979084 | -23.9116 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1791 | 7.881146697715474 | -0.783118 | -17.0869 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1789 | 8.020008379892406 | -1.06385 | -22.0827 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1793 | 8.69230348762009 | -0.924301 | -20.8136 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1790 | 9.024632868844039 | -0.881161 | -21.1491 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1787 | 10.11152815061737 | -1.03554 | -25.0142 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1365 | 10.784961452483486 | -1.10824 | -20.9629 | 6 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1366 | 11.95034435488239 | -1.05659 | -21.2916 | 6 | 17 | 11 | 0.58 | 0.20 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.292kcal/mol
Ligand efficiency (LE)
-0.8871kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.951
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.34
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.33kcal/mol
Minimised FF energy
46.95kcal/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.