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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
28.6 kcal/mol
Protein clashes
3
Internal clashes
6
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.40
Reason: 6 internal clashes
3 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.048 kcal/mol/HA)
✓ Good fit quality (FQ -10.65)
✓ Good H-bonds (4 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (28.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-37.730
kcal/mol
LE
-1.048
kcal/mol/HA
Fit Quality
-10.65
FQ (Leeson)
HAC
36
heavy atoms
MW
519
Da
LogP
4.37
cLogP
Interaction summary
HB 4
HY 24
PI 5
CLASH 6
Interaction summary
HB 4
HY 24
PI 5
CLASH 6
| Final rank | 2.349 | Score | -37.730 |
|---|---|---|---|
| Inter norm | -1.028 | Intra norm | -0.020 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; 3 cofactor-context clashes; moderate strain Δ 28.6 | ||
| Residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS13
MET163
MET213
NAP301
PHE97
PRO210
TRP221
TYR174
VAL206
VAL211
| ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.59 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 669 | 2.242959162236587 | -0.630998 | -24.4217 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 658 | 2.348686823393062 | -1.02818 | -37.7301 | 4 | 16 | 13 | 0.68 | 0.40 | - | no | Current |
| 666 | 2.6812968608128886 | -0.619624 | -21.6677 | 4 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 647 | 2.681307657453689 | -0.654945 | -24.3869 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 2.976194309743088 | -0.539639 | -21.2114 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 3.703549043285708 | -0.923151 | -32.1561 | 6 | 23 | 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
-37.730kcal/mol
Ligand efficiency (LE)
-1.0481kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.652
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
518.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
39.68kcal/mol
Minimised FF energy
11.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
783.2Ų
Total solvent-accessible surface area of free ligand
BSA total
688.9Ų
Buried surface area upon binding
BSA apolar
565.9Ų
Hydrophobic contacts buried
BSA polar
123.0Ų
Polar contacts buried
Fraction buried
88.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1758.9Ų
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
930.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)