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
46.6 kcal/mol
Protein clashes
5
Internal clashes
7
Native overlap
contact recall 0.53, Jaccard 0.37, H-bond role recall 0.80
Reason: 7 internal clashes, strain 46.6 kcal/mol
strain ΔE 46.6 kcal/mol
5 protein-contact clashes
7 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.044 kcal/mol/HA)
✓ Good fit quality (FQ -10.36)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Extreme strain energy (46.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-34.463
kcal/mol
LE
-1.044
kcal/mol/HA
Fit Quality
-10.36
FQ (Leeson)
HAC
33
heavy atoms
MW
478
Da
LogP
1.61
cLogP
Interaction summary
HB 10
HY 24
PI 2
CLASH 7
Interaction summary
HB 10
HY 24
PI 2
CLASH 7
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
| Final rank | 3.959 | Score | -34.463 |
|---|---|---|---|
| Inter norm | -1.197 | Intra norm | 0.153 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 10 |
| Artifact reason | geometry warning; 15 clashes; 2 protein clashes; 3 cofactor-context clashes; high strain Δ 46.6 | ||
| Residues |
ARG14
ASN175
ASP161
ASP165
CYS168
GLN166
LEU208
LEU209
LYS13
MET163
NAP301
PHE171
PHE97
PRO167
PRO210
TYR174
VAL164
VAL211
| ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.37 | RMSD | - |
| HB strict | 5 | Strict recall | 0.83 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 331 | 1.7902700583309057 | -0.915236 | -24.1392 | 6 | 17 | 14 | 0.74 | 0.20 | - | no | Open |
| 451 | 2.876644440223795 | -0.83621 | -21.5131 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 454 | 3.68647256374911 | -0.738459 | -19.964 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 3.872969880470129 | -0.923897 | -27.655 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 3.959392997784092 | -1.19748 | -34.4628 | 10 | 18 | 10 | 0.53 | 0.80 | - | no | Current |
| 323 | 3.962161196702303 | -0.853485 | -19.9813 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 4.044111887372217 | -0.685336 | -18.0096 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 346 | 4.164560827014589 | -1.06742 | -25.3382 | 10 | 16 | 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
-34.463kcal/mol
Ligand efficiency (LE)
-1.0443kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.362
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
477.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.61
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
46.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
175.35kcal/mol
Minimised FF energy
128.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
724.9Ų
Total solvent-accessible surface area of free ligand
BSA total
633.5Ų
Buried surface area upon binding
BSA apolar
530.4Ų
Hydrophobic contacts buried
BSA polar
103.1Ų
Polar contacts buried
Fraction buried
87.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1665.3Ų
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
994.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)