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
38.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.40
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
36% of hydrophobic surface appears solvent-exposed (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.710 kcal/mol/HA)
✓ Good fit quality (FQ -6.98)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (38.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-22.724
kcal/mol
LE
-0.710
kcal/mol/HA
Fit Quality
-6.98
FQ (Leeson)
HAC
32
heavy atoms
MW
441
Da
LogP
4.21
cLogP
Interaction summary
HB 8
HY 18
PI 2
CLASH 4
⚠ Exposure 36%
Interaction summary
HB 8
HY 18
PI 2
CLASH 4
⚠ Exposure 36%
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
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 16
Exposed 9
LogP 4.21
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.909 | Score | -22.724 |
|---|---|---|---|
| Inter norm | -0.995 | Intra norm | 0.285 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 8 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 28.0 | ||
| Residues |
ALA96
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS13
MET163
NAP301
PHE97
PRO210
SER207
SER95
TRP221
TYR174
TYR98
VAL206
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 296 | 2.7732698524951354 | -0.807286 | -24.283 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 2.908685936879818 | -0.995215 | -22.7242 | 8 | 19 | 15 | 0.79 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.724kcal/mol
Ligand efficiency (LE)
-0.7101kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.983
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
440.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.21
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
135.46kcal/mol
Minimised FF energy
97.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
744.1Ų
Total solvent-accessible surface area of free ligand
BSA total
659.1Ų
Buried surface area upon binding
BSA apolar
564.5Ų
Hydrophobic contacts buried
BSA polar
94.5Ų
Polar contacts buried
Fraction buried
88.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1736.5Ų
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
944.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)