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
28.3 kcal/mol
Protein clashes
3
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.50, H-bond role recall 0.60
Reason: no major geometry red flags detected
3 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.851 kcal/mol/HA)
✓ Good fit quality (FQ -15.18)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (96% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (28.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (7)
Score
-35.179
kcal/mol
LE
-1.851
kcal/mol/HA
Fit Quality
-15.18
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
1.69
cLogP
Interaction summary
HB 12
HY 20
PI 4
CLASH 2
Interaction summary
HB 12
HY 20
PI 4
CLASH 2
| Final rank | -0.462 | Score | -35.179 |
|---|---|---|---|
| Inter norm | -1.926 | Intra norm | 0.075 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 12 |
| Artifact reason | geometry warning; 7 clashes; 3 protein contact clashes; 2 severe cofactor-context clashes; moderate strain Δ 28.3 | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
GLY205
LEU208
LYS178
MET163
NAP301
PHE171
PHE97
PRO167
SER95
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 536 | -1.2117718742022974 | -2.27302 | -41.2505 | 13 | 13 | 10 | 0.53 | 0.60 | - | no | Open |
| 543 | -0.4617272198664007 | -1.92622 | -35.1793 | 12 | 14 | 11 | 0.58 | 0.60 | - | no | Current |
| 553 | 0.7901052041183204 | -1.64895 | -25.0906 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 1.9197835489469466 | -1.27997 | -22.0242 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 2.834875949212269 | -1.96567 | -32.6489 | 13 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.938359789590277 | -1.13258 | -19.6979 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 542 | 3.36456591187264 | -1.66906 | -29.2551 | 16 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 544 | 3.597282871221922 | -1.55687 | -25.5432 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 546 | 3.9655058659124927 | -1.52952 | -21.6706 | 9 | 11 | 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
-35.179kcal/mol
Ligand efficiency (LE)
-1.8515kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-15.177
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
107.25kcal/mol
Minimised FF energy
78.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
487.4Ų
Total solvent-accessible surface area of free ligand
BSA total
470.4Ų
Buried surface area upon binding
BSA apolar
332.7Ų
Hydrophobic contacts buried
BSA polar
137.7Ų
Polar contacts buried
Fraction buried
96.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1462.8Ų
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
929.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)