Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
18.5 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.74, Jaccard 0.64, H-bond role recall 0.00
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.082 kcal/mol/HA)
✓ Good fit quality (FQ -10.33)
✓ Good H-bonds (3 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (18.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-31.388
kcal/mol
LE
-1.082
kcal/mol/HA
Fit Quality
-10.33
FQ (Leeson)
HAC
29
heavy atoms
MW
410
Da
LogP
2.78
cLogP
Interaction summary
HB 3
HY 24
PI 4
CLASH 0
Interaction summary
HB 3
HY 24
PI 4
CLASH 0
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
| Final rank | 0.262 | Score | -31.388 |
|---|---|---|---|
| Inter norm | -1.102 | Intra norm | 0.020 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | geometry warning; 11 clashes; 1 protein contact clash | ||
| Residues |
ARG14
ASP161
CYS168
GLU217
LEU208
LEU209
LYS220
MET169
MET213
NAP301
PHE171
PHE97
PRO210
SER207
TRP221
TYR174
VAL206
| ||
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 | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 14 | Native recall | 0.74 |
| Jaccard | 0.64 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NAP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 633 | 0.2617411494880156 | -1.10204 | -31.388 | 3 | 17 | 14 | 0.74 | 0.00 | - | no | Current |
| 623 | 0.7630253132284526 | -0.957756 | -25.8221 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 1.1076329238342517 | -0.820794 | -23.2766 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 1.4223813885356413 | -0.871795 | -21.9547 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 652 | 1.929780656881121 | -1.08923 | -28.9651 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 2.1407979593867883 | -1.03918 | -26.9312 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 638 | 2.582980298651682 | -0.930167 | -25.6601 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.388kcal/mol
Ligand efficiency (LE)
-1.0823kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.332
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
410.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.83kcal/mol
Minimised FF energy
5.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
638.8Ų
Total solvent-accessible surface area of free ligand
BSA total
571.3Ų
Buried surface area upon binding
BSA apolar
463.5Ų
Hydrophobic contacts buried
BSA polar
107.8Ų
Polar contacts buried
Fraction buried
89.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1636.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
924.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)