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 (-0.718 kcal/mol/HA)
✓ Good fit quality (FQ -7.07)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (21.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.990
kcal/mol
LE
-0.718
kcal/mol/HA
Fit Quality
-7.07
FQ (Leeson)
HAC
32
heavy atoms
MW
434
Da
LogP
3.50
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 21.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 4
Clashes 4
Severe clashes 0
| Final rank | 4.597080988345055 | Score | -22.99 |
|---|---|---|---|
| Inter norm | -0.985915 | Intra norm | 0.267478 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 14 clashes; 4 protein contact clashes; high strain Δ 34.6 | ||
| Residues | A:ALA170;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO99;A:TRP221;A:TYR174 | ||
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 | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1406 | 4.597080988345055 | -0.985915 | -22.99 | 7 | 15 | 11 | 0.58 | 0.60 | - | no | Current |
| 1404 | 4.661917681470836 | -0.82314 | -23.9565 | 4 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 3499 | 4.710478616573362 | -0.670633 | -22.313 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2131 | 5.97113929719616 | -0.575467 | -14.5233 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2132 | 6.5542935964349205 | -0.68026 | -22.1842 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2123 | 6.672741907279237 | -0.590838 | -21.5145 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2127 | 7.717351609018184 | -0.652045 | -19.1483 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2125 | 7.750248059263065 | -0.640842 | -22.5904 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3504 | 8.229408185792026 | -0.859572 | -33.8612 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3503 | 8.706219372901863 | -0.665477 | -26.3443 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1405 | 5.7479251539054985 | -0.785898 | -30.7464 | 4 | 16 | 16 | 0.84 | 0.40 | - | yes | Open |
| 3497 | 7.0204175697363596 | -0.649422 | -18.5732 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3506 | 7.184725648542509 | -0.720953 | -21.8427 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1413 | 7.1859422124202785 | -0.966079 | -21.9788 | 7 | 18 | 13 | 0.68 | 0.60 | - | yes | Open |
| 3505 | 7.738642189576931 | -0.619665 | -19.6418 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1408 | 7.810830650880446 | -0.936013 | -33.7764 | 5 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 3507 | 8.321725388643328 | -0.61981 | -20.6343 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1412 | 8.422852477168364 | -0.886485 | -23.4202 | 7 | 18 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2124 | 8.515970032523061 | -0.748819 | -21.3543 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2129 | 8.632322088371021 | -0.684813 | -15.2213 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1411 | 8.785940220908063 | -0.735865 | -24.2711 | 5 | 12 | 11 | 0.58 | 0.60 | - | yes | Open |
| 3498 | 9.258651404018638 | -0.702783 | -19.1563 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1409 | 9.669341810718509 | -1.02054 | -36.6574 | 8 | 15 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1414 | 9.757141253879212 | -0.94632 | -24.0378 | 9 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2126 | 9.90165099956009 | -0.628696 | -26.6578 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3502 | 10.196185795286425 | -0.713848 | -25.5859 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2121 | 10.331879163539698 | -0.650216 | -11.4523 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1407 | 56.35447134801713 | -0.855775 | -21.4011 | 8 | 15 | 12 | 0.63 | 0.60 | - | yes | Open |
| 3508 | 59.44618331896669 | -0.658809 | -18.4045 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3501 | 59.72221200964438 | -0.661087 | -21.9454 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2122 | 60.0408513723887 | -0.640144 | -23.4261 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2128 | 60.084965041717744 | -0.657502 | -24.2603 | 10 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3500 | 60.142599288718245 | -0.685896 | -21.2838 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2130 | 60.62519173416365 | -0.658992 | -22.3718 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1410 | 61.20997923312359 | -0.953088 | -24.7181 | 9 | 17 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1415 | 61.25658247783677 | -0.918798 | -21.2035 | 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
-22.990kcal/mol
Ligand efficiency (LE)
-0.7184kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.065
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
434.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.50
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
120.12kcal/mol
Minimised FF energy
98.31kcal/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.