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 (-0.810 kcal/mol/HA)
✓ Good fit quality (FQ -7.46)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (29.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.064
kcal/mol
LE
-0.810
kcal/mol/HA
Fit Quality
-7.46
FQ (Leeson)
HAC
26
heavy atoms
MW
363
Da
LogP
4.61
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 29.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 4
Clashes 9
Severe clashes 1
| Final rank | 7.089011389910191 | Score | -21.0638 |
|---|---|---|---|
| Inter norm | -1.1163 | Intra norm | 0.306157 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 14 clashes; 1 protein clash; high strain Δ 27.7 | ||
| Residues | A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1999 | 4.83731950956685 | -1.10636 | -22.2886 | 0 | 17 | 15 | 0.79 | 0.00 | - | no | Open |
| 3605 | 4.914679292379297 | -0.776605 | -19.4335 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1880 | 5.1484444757963255 | -1.17192 | -23.9092 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 3740 | 5.189218168719204 | -0.805574 | -19.8458 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3741 | 5.201594232834019 | -0.916384 | -22.9003 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3737 | 5.4268351780334525 | -0.899263 | -23.1297 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3600 | 6.213182159782699 | -0.908652 | -20.3799 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3607 | 6.379610085203417 | -0.860634 | -21.2351 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 3739 | 5.187756743233576 | -0.808362 | -20.7532 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1878 | 5.509524402126366 | -1.22924 | -31.0162 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3601 | 5.917585356008802 | -0.812897 | -17.1631 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3604 | 5.971416899831939 | -0.858294 | -20.6792 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3738 | 6.050314402017285 | -0.907781 | -23.4759 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1872 | 6.112325330166928 | -1.23174 | -30.4383 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1874 | 6.4357760026553095 | -1.23731 | -31.0508 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1877 | 6.68661890659087 | -1.18256 | -29.3826 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1995 | 6.80039548250077 | -1.16249 | -22.3003 | 2 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 3602 | 6.9659372660389565 | -0.787414 | -19.7091 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2001 | 7.089011389910191 | -1.1163 | -21.0638 | 4 | 15 | 13 | 0.68 | 0.20 | - | yes | Current |
| 1876 | 7.2756832024672065 | -1.25442 | -31.4785 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1873 | 8.044827955135421 | -1.27102 | -31.0398 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3742 | 8.133900140334468 | -0.818218 | -18.418 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3603 | 8.392139234071568 | -0.805696 | -20.7518 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3606 | 8.43599062400888 | -0.866013 | -20.2763 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1994 | 8.553020583829618 | -1.19081 | -24.0608 | 1 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 1875 | 8.897515807926572 | -1.26205 | -32.4237 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1871 | 9.478705753645684 | -1.3034 | -31.1692 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1996 | 9.60972015633746 | -1.09001 | -22.373 | 2 | 15 | 13 | 0.68 | 0.20 | - | yes | Open |
| 1879 | 9.629279651731526 | -1.21545 | -24.2171 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1998 | 10.114937198992198 | -0.982861 | -23.1137 | 3 | 17 | 14 | 0.74 | 0.20 | - | yes | Open |
| 2000 | 10.244262570648672 | -1.13948 | -23.5593 | 2 | 15 | 13 | 0.68 | 0.20 | - | yes | Open |
| 1997 | 10.523607869661232 | -0.984782 | -24.5528 | 1 | 16 | 14 | 0.74 | 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
-21.064kcal/mol
Ligand efficiency (LE)
-0.8101kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.464
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
362.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.93kcal/mol
Minimised FF energy
35.53kcal/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.