Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
23.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.53, Jaccard 0.43, H-bond role recall 0.60
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.641 kcal/mol/HA)
✓ Good fit quality (FQ -13.45)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (23.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-31.179
kcal/mol
LE
-1.641
kcal/mol/HA
Fit Quality
-13.45
FQ (Leeson)
HAC
19
heavy atoms
MW
320
Da
LogP
2.49
cLogP
Interaction summary
HB 6
HY 24
PI 2
CLASH 5
Interaction summary
HB 6
HY 24
PI 2
CLASH 5
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 | 1.299 | Score | -31.179 |
|---|---|---|---|
| Inter norm | -1.685 | Intra norm | 0.044 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 23.1 | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
LEU208
LEU209
MET163
NAP301
PHE171
PHE97
PRO167
PRO210
TYR174
VAL164
| ||
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 | 0.43 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 582 | 1.2991898533552129 | -1.68528 | -31.179 | 6 | 14 | 10 | 0.53 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.179kcal/mol
Ligand efficiency (LE)
-1.6410kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.451
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
320.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.49
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
117.69kcal/mol
Minimised FF energy
94.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
506.4Ų
Total solvent-accessible surface area of free ligand
BSA total
482.5Ų
Buried surface area upon binding
BSA apolar
398.9Ų
Hydrophobic contacts buried
BSA polar
83.5Ų
Polar contacts buried
Fraction buried
95.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1524.6Ų
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
942.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)