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 (-1.009 kcal/mol/HA)
✓ Good fit quality (FQ -9.53)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (25.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.253
kcal/mol
LE
-1.009
kcal/mol/HA
Fit Quality
-9.53
FQ (Leeson)
HAC
28
heavy atoms
MW
415
Da
LogP
3.30
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 25.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 6
Clashes 13
Severe clashes 0
| Final rank | 6.709009201969063 | Score | -28.253 |
|---|---|---|---|
| Inter norm | -0.995902 | Intra norm | -0.0131324 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 13 protein contact clashes; high strain Δ 24.9 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1532 | 3.932067929382038 | -0.878124 | -29.2423 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1530 | 4.193008042131931 | -0.849596 | -24.1773 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1129 | 4.929328034077283 | -0.968529 | -26.3477 | 2 | 14 | 12 | 0.63 | 0.00 | - | no | Open |
| 1123 | 5.003230670778581 | -1.03317 | -28.8028 | 3 | 17 | 13 | 0.68 | 0.20 | - | no | Open |
| 1533 | 5.495517280677142 | -0.804662 | -20.0098 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3222 | 6.537342022383261 | -0.830924 | -30.3003 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1127 | 6.709009201969063 | -0.995902 | -28.253 | 4 | 16 | 14 | 0.74 | 0.20 | - | no | Current |
| 1399 | 7.62006595412909 | -0.96383 | -31.6017 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1089 | 7.6984814651196185 | -0.818645 | -26.6835 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1090 | 7.497082335438109 | -0.724689 | -23.3311 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1125 | 7.8030714914072625 | -1.02904 | -33.082 | 6 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1529 | 8.182983638868611 | -0.769449 | -19.8324 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3223 | 8.19092049036176 | -0.698686 | -22.1781 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3221 | 9.548514152466478 | -0.863483 | -22.5455 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1536 | 9.690789504027954 | -0.8747 | -28.2335 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1535 | 9.770765721051635 | -0.756297 | -23.3441 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1397 | 10.147541912645721 | -0.990361 | -24.2501 | 9 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1403 | 11.003232429246697 | -0.920543 | -27.907 | 8 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1091 | 11.071375581393362 | -0.757091 | -19.9934 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1401 | 11.174887562347209 | -0.884581 | -24.5527 | 6 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3224 | 11.212594506355108 | -0.709155 | -24.1587 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1122 | 11.46340833119197 | -1.27557 | -33.6293 | 6 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1128 | 11.488107004820021 | -1.23343 | -38.4147 | 8 | 18 | 14 | 0.74 | 0.80 | - | yes | Open |
| 1396 | 11.963498025998048 | -0.924728 | -23.7154 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1088 | 11.978308355620037 | -0.699765 | -22.2108 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1534 | 12.217372798123625 | -0.919535 | -26.0195 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1400 | 12.259932483171232 | -0.870616 | -21.0829 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1124 | 12.371108479274021 | -1.16653 | -31.6339 | 5 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1402 | 13.01271359088762 | -0.903003 | -23.1355 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1398 | 13.288316598777456 | -0.953562 | -27.4265 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1126 | 14.408097668142403 | -1.20945 | -15.7096 | 9 | 19 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1531 | 14.578053305973047 | -0.871169 | -27.0713 | 8 | 12 | 0 | 0.00 | 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
-28.253kcal/mol
Ligand efficiency (LE)
-1.0090kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.526
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
414.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.40kcal/mol
Minimised FF energy
56.17kcal/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.