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 (-0.669 kcal/mol/HA)
✓ Good fit quality (FQ -6.69)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (61.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-22.745
kcal/mol
LE
-0.669
kcal/mol/HA
Fit Quality
-6.69
FQ (Leeson)
HAC
34
heavy atoms
MW
481
Da
LogP
4.53
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 61.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 5
Clashes 16
Severe clashes 1
| Final rank | 11.59640554655577 | Score | -22.7449 |
|---|---|---|---|
| Inter norm | -0.746348 | Intra norm | 0.0773802 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 61.8 | ||
| Residues | A:ARG14;A:ASP161;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:SER95;A:TRP221;A:TYR174;A:TYR98;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 | 17 | Native recall | 0.89 |
| Jaccard | 0.89 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3178 | 8.561225452286191 | -0.597946 | -15.6921 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3181 | 9.178150742018827 | -0.6968 | -22.311 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 3176 | 9.273427524404912 | -0.730579 | -13.7786 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 2208 | 9.332053475094035 | -0.736386 | -19.1927 | 0 | 16 | 14 | 0.74 | 0.00 | - | no | Open |
| 2890 | 9.351777890041042 | -0.684534 | -18.706 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2884 | 9.695369144262646 | -0.55047 | -14.5265 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2330 | 10.075589793746309 | -0.816482 | -25.0979 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2171 | 10.34880812517319 | -0.939239 | -28.1464 | 11 | 15 | 13 | 0.68 | 0.60 | - | no | Open |
| 2174 | 10.544682831572473 | -0.77176 | -22.7559 | 6 | 11 | 8 | 0.42 | 0.20 | - | no | Open |
| 2326 | 9.179645142698693 | -0.663474 | -17.5578 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2325 | 10.22054777738333 | -0.717665 | -21.9072 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2329 | 10.580682134405247 | -0.739363 | -24.0846 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2207 | 10.594814460347544 | -0.556055 | -6.93792 | 4 | 17 | 16 | 0.84 | 0.20 | - | yes | Open |
| 2328 | 10.648916877177417 | -0.637867 | -17.8702 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2887 | 10.712734239227101 | -0.636859 | -18.0653 | 11 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2210 | 10.97681039861124 | -0.851627 | -19.6831 | 4 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 3177 | 11.008975613395442 | -0.668741 | -20.0653 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2331 | 11.017205893859852 | -0.765682 | -21.5174 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2173 | 11.038656642582188 | -0.789011 | -28.5754 | 8 | 17 | 17 | 0.89 | 0.60 | - | yes | Open |
| 3183 | 11.16436584579619 | -0.646548 | -16.6086 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2206 | 11.203053045338944 | -0.735342 | -14.6301 | 1 | 14 | 14 | 0.74 | 0.00 | - | yes | Open |
| 2211 | 11.59640554655577 | -0.746348 | -22.7449 | 3 | 17 | 17 | 0.89 | 0.20 | - | yes | Current |
| 2175 | 11.611438314020434 | -0.778434 | -17.8094 | 13 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 3182 | 11.635782916121967 | -0.704824 | -20.8652 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3184 | 11.675325310296653 | -0.602876 | -11.5392 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2169 | 11.796479552715045 | -0.78653 | -16.841 | 10 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2168 | 11.805667118246944 | -0.923673 | -25.9456 | 9 | 16 | 14 | 0.74 | 0.80 | - | yes | Open |
| 2332 | 11.806130018933356 | -0.711398 | -19.8184 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2888 | 11.866923259069576 | -0.727557 | -22.9649 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2327 | 11.88393810217282 | -0.75158 | -20.667 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2881 | 11.985767806692772 | -0.688236 | -20.3951 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2170 | 12.024862324890075 | -0.847577 | -27.4326 | 7 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2883 | 12.448929720311018 | -0.63381 | -20.5646 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2886 | 12.883497375178285 | -0.722445 | -21.2426 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2212 | 12.961329528483635 | -0.749899 | -18.6328 | 1 | 14 | 14 | 0.74 | 0.20 | - | yes | Open |
| 2882 | 13.1402612192278 | -0.595169 | -7.89714 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2885 | 13.202474894798751 | -0.68163 | -22.734 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2889 | 13.228627783853733 | -0.760975 | -21.4321 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3180 | 13.337831595790384 | -0.705517 | -17.5048 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2172 | 13.641360761219438 | -0.910092 | -28.0326 | 7 | 15 | 14 | 0.74 | 0.60 | - | yes | Open |
| 3179 | 13.78453648987174 | -0.780503 | -24.7605 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3175 | 14.759476767944397 | -0.678912 | -19.8678 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2209 | 15.542191551637483 | -0.691434 | -20.8054 | 4 | 16 | 16 | 0.84 | 0.40 | - | yes | Open |
| 2205 | 16.369266440136705 | -0.589797 | -8.40918 | 6 | 18 | 12 | 0.63 | 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
-22.745kcal/mol
Ligand efficiency (LE)
-0.6690kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.694
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.53
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
61.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.99kcal/mol
Minimised FF energy
52.61kcal/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.