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 (-0.530 kcal/mol/HA)
✓ Good fit quality (FQ -5.31)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-18.029
kcal/mol
LE
-0.530
kcal/mol/HA
Fit Quality
-5.31
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 24.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 10
Severe clashes 0
| Final rank | 7.751089032724352 | Score | -18.0286 |
|---|---|---|---|
| Inter norm | -0.716399 | Intra norm | 0.186145 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | geometry warning; 22 clashes; 10 protein contact clashes; high strain Δ 27.6 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET163;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TRP221;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 | 12 | Native recall | 0.63 |
| Jaccard | 0.48 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2483 | 4.920496913081546 | -0.731579 | -22.3435 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1842 | 6.0955894180862344 | -0.591573 | -16.9942 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1481 | 7.59891030942053 | -0.69342 | -24.5369 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1038 | 7.751089032724352 | -0.716399 | -18.0286 | 5 | 18 | 12 | 0.63 | 0.00 | - | no | Current |
| 1479 | 7.767140855736665 | -0.761578 | -26.2765 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1844 | 7.553234903670745 | -0.568537 | -20.077 | 3 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1480 | 8.504776749278534 | -0.787007 | -19.7508 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1843 | 9.21876261512332 | -0.588979 | -14.9647 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1040 | 10.741657747848091 | -1.01763 | -32.8747 | 10 | 17 | 15 | 0.79 | 0.80 | - | yes | Open |
| 2484 | 11.59956448897017 | -0.760382 | -22.134 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2482 | 11.870258638769174 | -0.6957 | -19.8761 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1039 | 12.767590907091888 | -1.01208 | -28.9648 | 8 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.029kcal/mol
Ligand efficiency (LE)
-0.5303kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.306
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.20
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
77.63kcal/mol
Minimised FF energy
53.08kcal/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.