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
18.8 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.082 kcal/mol/HA)
✓ Good fit quality (FQ -10.10)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (18.8 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (13)
Score
-29.223
kcal/mol
LE
-1.082
kcal/mol/HA
Fit Quality
-10.10
FQ (Leeson)
HAC
27
heavy atoms
MW
404
Da
LogP
3.94
cLogP
Interaction summary
HB 2
HY 24
PI 2
CLASH 3
Interaction summary
HB 2
HY 24
PI 2
CLASH 3
| Final rank | 0.603 | Score | -29.223 |
|---|---|---|---|
| Inter norm | -1.200 | Intra norm | 0.117 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 2 |
| Artifact reason | geometry warning; 13 clashes; 2 protein contact clashes; 2 cofactor-context clashes | ||
| Residues |
ARG14
ASP161
CYS168
GLU217
LEU208
LEU209
LYS220
MET213
NAP301
PHE171
PHE97
PRO210
TRP221
TYR174
| ||
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
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 539 | 0.6027912714060862 | -1.19966 | -29.2226 | 2 | 14 | 12 | 0.63 | 0.00 | - | no | Current |
| 541 | 1.4498956315614218 | -0.810314 | -20.4761 | 2 | 12 | 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
-29.223kcal/mol
Ligand efficiency (LE)
-1.0823kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.098
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
404.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.94
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
158.25kcal/mol
Minimised FF energy
139.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.4Ų
Total solvent-accessible surface area of free ligand
BSA total
538.7Ų
Buried surface area upon binding
BSA apolar
488.2Ų
Hydrophobic contacts buried
BSA polar
50.5Ų
Polar contacts buried
Fraction buried
85.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1703.5Ų
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
915.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)