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 (-1.232 kcal/mol/HA)
✓ Good fit quality (FQ -11.35)
✓ Strong H-bond network (7 bonds)
✗ High strain energy (17.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-32.028
kcal/mol
LE
-1.232
kcal/mol/HA
Fit Quality
-11.35
FQ (Leeson)
HAC
26
heavy atoms
MW
349
Da
LogP
2.66
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 17.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 5
Severe clashes 0
| Final rank | 3.360779007337855 | Score | -32.028 |
|---|---|---|---|
| Inter norm | -1.21674 | Intra norm | -0.0151033 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 13 clashes; 5 protein contact clashes; moderate strain Δ 18.0 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;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 | 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 | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 111 | 3.360779007337855 | -1.21674 | -32.028 | 7 | 15 | 14 | 0.74 | 0.40 | - | no | Current |
| 110 | 3.442122624019677 | -1.21522 | -31.9059 | 7 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 93 | 3.699891532165524 | -0.996357 | -27.5408 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 112 | 3.8145373961952544 | -1.09529 | -28.7447 | 9 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 92 | 3.894791390276917 | -1.09051 | -30.1724 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 94 | 4.117158662979138 | -1.06014 | -24.3512 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 4.323370650410053 | -0.760687 | -17.7451 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 4.537151348789815 | -0.97357 | -25.402 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 68 | 4.76876667974091 | -0.719336 | -20.7661 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 5.020995352586303 | -0.804207 | -18.2131 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 78 | 5.844625676418907 | -0.834551 | -20.0158 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 116 | 6.943216971288747 | -1.08568 | -25.0988 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 69 | 7.1954168182638885 | -0.812568 | -20.336 | 5 | 10 | 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
-32.028kcal/mol
Ligand efficiency (LE)
-1.2318kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.349
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
349.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-125.78kcal/mol
Minimised FF energy
-143.05kcal/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.