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 (-1.234 kcal/mol/HA)
✓ Good fit quality (FQ -11.22)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (59.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.851
kcal/mol
LE
-1.234
kcal/mol/HA
Fit Quality
-11.22
FQ (Leeson)
HAC
25
heavy atoms
MW
366
Da
LogP
1.82
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 59.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 3
Clashes 3
Severe clashes 0
| Final rank | 4.754404343219468 | Score | -30.8509 |
|---|---|---|---|
| Inter norm | -1.23447 | Intra norm | 0.000428488 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 3 protein contact clashes; high strain Δ 60.4 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;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 | 0.70 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1715 | 4.754404343219468 | -1.23447 | -30.8509 | 6 | 15 | 14 | 0.74 | 0.40 | - | no | Current |
| 1717 | 5.415580592656754 | -0.983976 | -27.4278 | 6 | 14 | 14 | 0.74 | 0.20 | - | no | Open |
| 1718 | 5.9714215141263045 | -1.07911 | -23.9288 | 4 | 18 | 16 | 0.84 | 0.40 | - | no | Open |
| 2465 | 7.519309608485525 | -0.897139 | -20.9851 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2064 | 7.715096032417254 | -0.987865 | -20.7635 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2470 | 7.721786756161238 | -0.953253 | -23.1038 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2065 | 7.742346601665181 | -0.808067 | -20.5623 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2068 | 7.925436660903836 | -1.02181 | -26.26 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1716 | 9.269707568857488 | -0.940801 | -23.4818 | 11 | 14 | 13 | 0.68 | 0.80 | - | yes | Open |
| 2468 | 9.563296130458863 | -0.821577 | -22.6843 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2466 | 9.7363230121066 | -0.85673 | -19.3996 | 14 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2067 | 10.378140319525615 | -0.783147 | -22.5962 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2467 | 10.511009171598115 | -0.769221 | -18.4055 | 13 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2469 | 10.780032313639396 | -0.944222 | -22.2685 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1714 | 11.134586279400969 | -1.07146 | -22.9122 | 9 | 14 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2066 | 11.594586677080748 | -0.895448 | -21.2236 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2069 | 12.21701713827499 | -0.947578 | -20.8787 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1719 | 13.276212413431605 | -1.04776 | -22.2405 | 7 | 18 | 16 | 0.84 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.851kcal/mol
Ligand efficiency (LE)
-1.2340kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.219
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.82
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
59.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
156.43kcal/mol
Minimised FF energy
96.77kcal/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.