Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
22.0 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.38, H-bond role recall 0.40
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.391 kcal/mol/HA)
✓ Good fit quality (FQ -12.65)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (22.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-34.782
kcal/mol
LE
-1.391
kcal/mol/HA
Fit Quality
-12.65
FQ (Leeson)
HAC
25
heavy atoms
MW
339
Da
LogP
1.73
cLogP
Interaction summary
HB 9
HY 11
PI 1
CLASH 1
Interaction summary
HB 9
HY 11
PI 1
CLASH 1
| Final rank | 2.318 | Score | -34.782 |
|---|---|---|---|
| Inter norm | -1.317 | Intra norm | -0.074 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 9 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; 4 cofactor-context clashes; moderate strain Δ 22.0 | ||
| Residues |
ALA96
ARG14
ASP161
LYS13
NAP301
PHE97
PRO210
SER95
TYR174
TYR98
| ||
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 | 8 | Native recall | 0.42 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 533 | 1.3842393497320211 | -1.10561 | -24.9518 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 534 | 1.4161180290319177 | -0.989145 | -24.122 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 535 | 2.3183982255942754 | -1.31713 | -34.7821 | 9 | 10 | 8 | 0.42 | 0.40 | - | no | Current |
| 543 | 2.358570273815441 | -1.29787 | -36.8733 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 2.3614780804753868 | -1.05293 | -26.4844 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 2.9003254481956033 | -1.26056 | -33.7209 | 4 | 15 | 12 | 0.63 | 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
-34.782kcal/mol
Ligand efficiency (LE)
-1.3913kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.648
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
339.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.73
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-52.97kcal/mol
Minimised FF energy
-74.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
565.9Ų
Total solvent-accessible surface area of free ligand
BSA total
472.8Ų
Buried surface area upon binding
BSA apolar
379.5Ų
Hydrophobic contacts buried
BSA polar
93.3Ų
Polar contacts buried
Fraction buried
83.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1538.9Ų
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
969.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)