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 (-1.297 kcal/mol/HA)
✓ Good fit quality (FQ -11.62)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (25.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.128
kcal/mol
LE
-1.297
kcal/mol/HA
Fit Quality
-11.62
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
4.56
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 25.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 3
Clashes 8
Severe clashes 3
| Final rank | 8.390141378325266 | Score | -31.1285 |
|---|---|---|---|
| Inter norm | -1.26016 | Intra norm | -0.0368539 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 10 clashes; 3 protein clashes; high strain Δ 33.2 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98 | ||
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 | 0.68 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1207 | 2.430143154907441 | -1.19382 | -30.1867 | 6 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 1201 | 2.4590174680979047 | -1.26453 | -31.8913 | 6 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 1953 | 2.8400690927329624 | -0.734472 | -17.9639 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1908 | 3.305177520629858 | -0.730958 | -19.3589 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1958 | 3.6394876868458246 | -0.763068 | -17.911 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1955 | 3.6761661205884892 | -0.55105 | -11.9604 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1170 | 3.8348229988696003 | -0.930798 | -19.4897 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1563 | 4.5002173945509965 | -1.1615 | -23.9956 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1954 | 4.503117859188464 | -0.728145 | -16.7015 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1957 | 5.074169882563248 | -0.815124 | -17.3361 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1567 | 5.4202018677778625 | -0.888389 | -15.7861 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1565 | 5.4519267318111595 | -1.45598 | -31.2552 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1956 | 5.751487436525558 | -0.657139 | -16.3227 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1911 | 5.850036536798715 | -0.950209 | -26.6197 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1172 | 6.386292556677911 | -0.944628 | -20.0632 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1570 | 6.471207934876456 | -1.05511 | -25.0177 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1568 | 6.531054243391047 | -0.854058 | -19.9371 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1564 | 6.629182736230375 | -1.15211 | -25.1158 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1168 | 6.664891527018511 | -0.975766 | -17.9682 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1205 | 6.75309589925006 | -1.18499 | -32.4258 | 3 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1171 | 6.941663920851766 | -0.956894 | -24.0835 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1909 | 7.22878133022391 | -0.920036 | -23.2283 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1569 | 7.248502876011524 | -1.04523 | -23.6535 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1210 | 7.445536821069086 | -1.11972 | -27.0097 | 8 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1910 | 7.878953770499661 | -0.667251 | -16.9474 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1169 | 8.027539752005387 | -0.990568 | -25.18 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1566 | 8.297213516026027 | -1.06485 | -24.7992 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1204 | 8.390141378325266 | -1.26016 | -31.1285 | 9 | 13 | 13 | 0.68 | 0.60 | - | yes | Current |
| 1173 | 8.52512299003625 | -0.761459 | -19.3834 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1202 | 10.037222800942548 | -1.39302 | -32.2253 | 6 | 19 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1208 | 10.07271766611601 | -1.23696 | -30.1909 | 7 | 18 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1209 | 10.204050037001787 | -1.22425 | -29.639 | 4 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1206 | 10.367610776310922 | -1.33226 | -33.1999 | 7 | 18 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1571 | 10.768799511203035 | -1.08542 | -22.8271 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1572 | 11.085712337405427 | -0.940268 | -25.9868 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1203 | 11.367536281309768 | -1.31659 | -30.4671 | 3 | 19 | 14 | 0.74 | 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
-31.128kcal/mol
Ligand efficiency (LE)
-1.2970kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.624
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.56
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.12kcal/mol
Minimised FF energy
71.02kcal/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.