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 (-1.375 kcal/mol/HA)
✓ Good fit quality (FQ -12.98)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (33.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-38.511
kcal/mol
LE
-1.375
kcal/mol/HA
Fit Quality
-12.98
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 33.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 4
Clashes 12
Severe clashes 1
| Final rank | 7.73170765426241 | Score | -38.5113 |
|---|---|---|---|
| Inter norm | -1.14684 | Intra norm | -0.228564 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 11 clashes; 1 protein clash; high strain Δ 32.8 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:TRP221;A:TYR174;A:VAL164;A:VAL206 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | 15 | Native recall | 0.79 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3046 | 3.490923664677839 | -0.823985 | -28.0144 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1162 | 4.759325631447518 | -0.759942 | -29.5411 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1209 | 4.849005780632088 | -0.929422 | -23.6948 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1207 | 5.522036292125615 | -0.94041 | -35.9841 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1206 | 6.018524377959602 | -0.945999 | -28.0195 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1208 | 6.128241424690152 | -0.905644 | -23.0788 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 927 | 6.190592186557567 | -0.834364 | -18.4219 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2932 | 6.595529750713936 | -0.862318 | -31.5771 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 942 | 6.821120114270912 | -1.0871 | -25.0164 | 14 | 14 | 11 | 0.58 | 0.40 | - | no | Open |
| 926 | 6.862765999940556 | -0.798454 | -21.0282 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 974 | 6.929475768396844 | -0.842991 | -22.1206 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2934 | 7.096800352532449 | -0.792048 | -18.471 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 929 | 7.139662786890231 | -0.878088 | -31.4505 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 939 | 4.999747684332393 | -1.18433 | -30.604 | 9 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2931 | 6.369683972769396 | -0.847027 | -28.5541 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3050 | 7.098450172668274 | -0.802973 | -27.2864 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3048 | 7.302548360895769 | -0.644105 | -21.2259 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3047 | 7.332544445716109 | -0.874696 | -33.1558 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 923 | 7.528304497507772 | -0.844355 | -27.5643 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 944 | 7.73170765426241 | -1.14684 | -38.5113 | 7 | 20 | 15 | 0.79 | 0.40 | - | yes | Current |
| 1163 | 7.752172248103994 | -0.944043 | -25.3008 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 938 | 7.820015125864169 | -1.12677 | -37.6442 | 11 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2936 | 7.975191810318751 | -0.759875 | -24.9403 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1205 | 8.031344672604394 | -0.874414 | -30.8205 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 975 | 8.39177954273392 | -0.981468 | -32.0097 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3049 | 8.512686393039127 | -0.807943 | -18.5723 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3051 | 8.923005381864684 | -0.722309 | -27.8252 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2933 | 8.995541155502092 | -0.707341 | -21.3917 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 941 | 9.161822960782839 | -1.17761 | -32.8392 | 11 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 925 | 9.961473392684617 | -0.853965 | -29.5396 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 943 | 10.370268827522315 | -1.08754 | -29.0441 | 8 | 14 | 10 | 0.53 | 0.80 | - | yes | Open |
| 940 | 10.49695750179936 | -1.16914 | -39.3369 | 10 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2935 | 11.670522812268036 | -0.937716 | -27.4849 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 924 | 11.680413858552193 | -0.820291 | -21.5552 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 928 | 12.210256193802767 | -0.838173 | -22.0462 | 7 | 18 | 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
-38.511kcal/mol
Ligand efficiency (LE)
-1.3754kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.984
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.31
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.92kcal/mol
Minimised FF energy
-10.36kcal/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.