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 (-1.074 kcal/mol/HA)
✓ Good fit quality (FQ -10.02)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (27.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-29.009
kcal/mol
LE
-1.074
kcal/mol/HA
Fit Quality
-10.02
FQ (Leeson)
HAC
27
heavy atoms
MW
368
Da
LogP
3.37
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 27.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 13
Severe clashes 1
| Final rank | 7.427970208443857 | Score | -29.0088 |
|---|---|---|---|
| Inter norm | -1.06187 | Intra norm | -0.0125332 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 32.0 | ||
| Residues | A:ALA96;A:ARG14;A:ASN127;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS178;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;D:HIS267 | ||
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.56 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1261 | 2.352614741984156 | -0.878877 | -21.1933 | 4 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 242 | 2.447476914358483 | -0.908357 | -21.8806 | 4 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 1630 | 4.715524846739253 | -0.640004 | -10.8948 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1625 | 6.074173377966746 | -0.80556 | -21.7333 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1266 | 6.824087810079796 | -1.00085 | -26.9301 | 6 | 18 | 16 | 0.84 | 0.60 | - | no | Open |
| 1267 | 5.514664466722928 | -1.05141 | -26.1335 | 6 | 15 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1264 | 6.048290580478811 | -0.858725 | -20.6534 | 4 | 17 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1627 | 6.4706031071443855 | -0.772871 | -23.0795 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1263 | 7.427970208443857 | -1.06187 | -29.0088 | 5 | 20 | 14 | 0.74 | 0.60 | - | yes | Current |
| 1633 | 8.471081879326855 | -0.939358 | -18.9139 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1623 | 8.8787829524571 | -0.557583 | -12.8201 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1632 | 9.29755773218558 | -0.659444 | -17.2243 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1622 | 11.622027407212617 | -0.807135 | -21.8272 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1619 | 12.158462089191984 | -0.59039 | -11.4685 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1620 | 12.483486148698473 | -0.809041 | -11.3455 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1628 | 57.20569199706915 | -0.766764 | -11.9344 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1626 | 57.29859762330209 | -0.682621 | -10.3988 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1262 | 58.043689460527446 | -0.991328 | -20.1182 | 5 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1629 | 59.530653812090854 | -0.715619 | -16.0066 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1631 | 59.74134408162453 | -0.617577 | -14.5273 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1621 | 60.97370136158834 | -0.801387 | -20.8088 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1624 | 61.275380495880434 | -0.764099 | -18.1143 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1265 | 62.718700127462505 | -1.0153 | -21.1272 | 7 | 20 | 15 | 0.79 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.009kcal/mol
Ligand efficiency (LE)
-1.0744kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.024
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
368.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.37
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.96kcal/mol
Minimised FF energy
51.83kcal/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.