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 high
Native strong
SASA done
Strain ΔE
26.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.484 kcal/mol/HA)
✓ Good fit quality (FQ -13.49)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ High strain energy (26.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-37.094
kcal/mol
LE
-1.484
kcal/mol/HA
Fit Quality
-13.49
FQ (Leeson)
HAC
25
heavy atoms
MW
361
Da
LogP
2.50
cLogP
Interaction summary
HB 7
HY 24
PI 3
CLASH 1
Interaction summary
HB 7
HY 24
PI 3
CLASH 1
| Final rank | 1.564 | Score | -37.094 |
|---|---|---|---|
| Inter norm | -1.439 | Intra norm | -0.045 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 26.6 | ||
| Residues |
ALA96
ARG14
ASP161
CYS168
LEU208
LEU209
LYS178
MET213
NAP301
PHE97
PRO210
SER95
TRP221
TYR174
VAL206
| ||
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
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 47 | 0.5239177324356373 | -1.45605 | -36.1942 | 6 | 19 | 16 | 0.84 | 0.60 | - | no | Open |
| 37 | 1.564295037877516 | -1.43855 | -37.0939 | 7 | 15 | 14 | 0.74 | 0.60 | - | no | Current |
| 54 | 1.9683045743388685 | -1.03179 | -26.1007 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 44 | 2.072174738895213 | -1.11322 | -27.8978 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 43 | 2.507509878719639 | -1.15696 | -29.4478 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 3.060926401421796 | -1.13474 | -27.1771 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 53 | 3.6625414032485835 | -0.910007 | -21.8572 | 6 | 13 | 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
-37.094kcal/mol
Ligand efficiency (LE)
-1.4838kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.489
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
360.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.50
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
15.01kcal/mol
Minimised FF energy
-11.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
570.9Ų
Total solvent-accessible surface area of free ligand
BSA total
527.8Ų
Buried surface area upon binding
BSA apolar
454.1Ų
Hydrophobic contacts buried
BSA polar
73.7Ų
Polar contacts buried
Fraction buried
92.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1642.7Ų
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
906.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)