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
38.7 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (9/24 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 (-0.840 kcal/mol/HA)
✓ Good fit quality (FQ -8.40)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (12)
Score
-28.543
kcal/mol
LE
-0.840
kcal/mol/HA
Fit Quality
-8.40
FQ (Leeson)
HAC
34
heavy atoms
MW
490
Da
LogP
2.10
cLogP
Interaction summary
HB 7
HY 24
PI 3
CLASH 3
⚠ Exposure 37%
Interaction summary
HB 7
HY 24
PI 3
CLASH 3
⚠ Exposure 37%
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 15
Exposed 9
LogP 2.1
H-bonds 7
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 0.741 | Score | -28.543 |
|---|---|---|---|
| Inter norm | -1.001 | Intra norm | 0.140 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 2 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 38.7 | ||
| Residues |
ARG14
CYS168
GLY205
LEU208
LEU209
LYS13
MET213
NAP301
PHE171
PHE97
PRO210
SER37
TRP221
VAL206
| ||
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 | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 131 | 0.741389635545671 | -1.00078 | -28.5431 | 7 | 14 | 12 | 0.63 | 0.40 | - | no | Current |
| 126 | 1.3797833655969036 | -0.827691 | -22.9203 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 108 | 1.5551227982840858 | -0.612014 | -16.5936 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 107 | 1.8269898376243545 | -0.6882 | -16.6942 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 107 | 2.5779596116192525 | -0.715894 | -19.7387 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 103 | 2.627717269226338 | -0.70053 | -19.5816 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 3.037984985392039 | -0.854469 | -21.9956 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 3.453230294175056 | -0.941129 | -26.7094 | 10 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 3.735174048928779 | -0.68683 | -14.5077 | 5 | 14 | 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
-28.543kcal/mol
Ligand efficiency (LE)
-0.8395kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.400
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
489.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.10
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
160.28kcal/mol
Minimised FF energy
121.58kcal/mol
SASA & burial
✓ computed
SASA (unbound)
763.8Ų
Total solvent-accessible surface area of free ligand
BSA total
618.3Ų
Buried surface area upon binding
BSA apolar
504.2Ų
Hydrophobic contacts buried
BSA polar
114.1Ų
Polar contacts buried
Fraction buried
81.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1732.0Ų
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
938.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)