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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
61.6 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.40
Reason: 16 internal clashes, strain 61.6 kcal/mol
strain ΔE 61.6 kcal/mol
16 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.474 kcal/mol/HA)
✓ Good fit quality (FQ -4.98)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Extreme strain energy (61.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-19.430
kcal/mol
LE
-0.474
kcal/mol/HA
Fit Quality
-4.98
FQ (Leeson)
HAC
41
heavy atoms
MW
560
Da
LogP
3.95
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 0
Interaction summary
HB 4
HY 24
PI 3
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 | 1.189 | Score | -19.430 |
|---|---|---|---|
| Inter norm | -0.739 | Intra norm | 0.265 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 16 clashes; 1 protein contact clash; 1 severe cofactor-context clash; high strain Δ 56.5 | ||
| Residues |
ALA212
ARG14
GLU217
GLY214
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER95
TRP221
TYR174
TYR98
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 239 | 1.188821352848611 | -0.738794 | -19.4295 | 4 | 18 | 15 | 0.79 | 0.40 | - | no | Current |
| 307 | 2.736456701881956 | -0.641307 | -21.6716 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 236 | 4.049159380435853 | -0.620236 | -20.8061 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 173 | 7.228239214845638 | -0.663494 | -18.6148 | 16 | 19 | 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
-19.430kcal/mol
Ligand efficiency (LE)
-0.4739kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.979
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
559.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.95
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
61.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.37kcal/mol
Minimised FF energy
76.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
891.8Ų
Total solvent-accessible surface area of free ligand
BSA total
633.8Ų
Buried surface area upon binding
BSA apolar
520.4Ų
Hydrophobic contacts buried
BSA polar
113.4Ų
Polar contacts buried
Fraction buried
71.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1851.5Ų
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
958.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)