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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.026 kcal/mol/HA)
✓ Good fit quality (FQ -9.45)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (19.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.663
kcal/mol
LE
-1.026
kcal/mol/HA
Fit Quality
-9.45
FQ (Leeson)
HAC
26
heavy atoms
MW
378
Da
LogP
0.79
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 19.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 21
π–π 2
Clashes 3
Severe clashes 0
| Final rank | 2.5673725468482207 | Score | -26.6627 |
|---|---|---|---|
| Inter norm | -1.04069 | Intra norm | 0.0151978 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 6 clashes; 3 protein contact clashes; high strain Δ 31.3 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE97;A:PRO210;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 | 0.52 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1878 | 2.5673725468482207 | -1.04069 | -26.6627 | 8 | 13 | 11 | 0.58 | 0.20 | - | no | Current |
| 1630 | 2.8646362119362876 | -0.876983 | -23.486 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1628 | 3.160807105405868 | -0.821395 | -21.6585 | 0 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1749 | 3.2031281884027005 | -1.10079 | -26.168 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1753 | 3.5370349532162044 | -1.1019 | -28.6565 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1876 | 3.602271624387416 | -1.01526 | -24.567 | 4 | 12 | 10 | 0.53 | 0.20 | - | no | Open |
| 1634 | 4.308853823434116 | -0.831821 | -20.3883 | 0 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2020 | 4.540457615682943 | -0.772694 | -21.0518 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2024 | 4.645488021048227 | -1.0041 | -24.7592 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3683 | 4.889509546339774 | -0.762117 | -20.6747 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2023 | 5.038567329841042 | -0.901885 | -20.3628 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1884 | 5.174087558785496 | -0.972294 | -24.2184 | 3 | 10 | 9 | 0.47 | 0.00 | - | no | Open |
| 1755 | 5.202261895618559 | -1.0684 | -25.7439 | 10 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 3679 | 5.395398835596552 | -0.806512 | -16.0008 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1632 | 5.931922806630603 | -0.838742 | -21.7639 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1879 | 7.996836347150349 | -1.26272 | -30.6511 | 10 | 18 | 14 | 0.74 | 0.40 | - | no | Open |
| 1631 | 4.581065110163575 | -0.847094 | -19.9663 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1752 | 4.679603390928872 | -1.10225 | -31.9349 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1633 | 4.68205711647097 | -0.968374 | -25.5318 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1754 | 5.4316418960406345 | -1.07022 | -30.9141 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2018 | 5.843118398036463 | -0.959981 | -21.8159 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1751 | 5.938336241589376 | -1.0707 | -31.8789 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1635 | 6.2639641148406975 | -0.901883 | -21.5477 | 2 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3684 | 6.789145518202314 | -0.913291 | -22.8232 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3680 | 6.993717038004687 | -0.854193 | -21.776 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2026 | 7.014197566396646 | -0.799127 | -20.9195 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1881 | 7.029058902909822 | -1.36446 | -36.0739 | 11 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2025 | 7.17858592300807 | -0.807372 | -22.3071 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3685 | 7.185453383215806 | -0.765194 | -19.4421 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2019 | 7.214792427196625 | -0.947007 | -23.3306 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3681 | 7.346824335394429 | -0.839172 | -22.3428 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3682 | 7.465668999074897 | -0.925279 | -23.2842 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1883 | 8.003075816102625 | -1.14362 | -27.2345 | 9 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2027 | 8.1050297008441 | -0.943152 | -24.5969 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1629 | 8.397661341319047 | -0.966135 | -22.5157 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2022 | 8.689592822263654 | -0.908625 | -22.5182 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1750 | 9.204636625975743 | -1.17622 | -26.4924 | 8 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1882 | 9.236380325365387 | -1.23634 | -30.5642 | 10 | 19 | 14 | 0.74 | 0.20 | - | yes | Open |
| 1757 | 9.24075687972623 | -1.05138 | -27.7833 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1758 | 9.257616932149118 | -1.17877 | -32.5158 | 14 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3686 | 10.203133588026066 | -1.02633 | -20.5964 | 11 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1877 | 10.383983524872384 | -1.40494 | -35.3506 | 10 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1885 | 10.662049688733653 | -1.64167 | -41.9215 | 15 | 16 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1880 | 10.969072863440623 | -1.11846 | -29.9511 | 5 | 17 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2021 | 11.033599563364259 | -0.934267 | -23.1303 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1756 | 11.675951984023836 | -1.07002 | -21.8031 | 15 | 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
-26.663kcal/mol
Ligand efficiency (LE)
-1.0255kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.448
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
378.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.79
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.62kcal/mol
Minimised FF energy
82.36kcal/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.