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
26.1 kcal/mol
Protein clashes
3
Internal clashes
4
Native overlap
contact recall 0.74, Jaccard 0.58, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.893 kcal/mol/HA)
✓ Good fit quality (FQ -9.01)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (26.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-31.264
kcal/mol
LE
-0.893
kcal/mol/HA
Fit Quality
-9.01
FQ (Leeson)
HAC
35
heavy atoms
MW
486
Da
LogP
4.87
cLogP
Interaction summary
HB 8
HY 24
PI 5
CLASH 4
Interaction summary
HB 8
HY 24
PI 5
CLASH 4
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
| Final rank | 2.221 | Score | -31.264 |
|---|---|---|---|
| Inter norm | -0.859 | Intra norm | -0.034 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 8 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; 3 cofactor-context clashes; moderate strain Δ 26.1 | ||
| Residues |
ALA170
ARG14
CYS168
GLU217
GLY205
LEU208
LEU209
LEU263
LYS220
MET169
MET213
NAP301
PHE171
PHE97
PRO210
SER207
TRP221
TYR174
VAL206
| ||
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 | 0.58 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 1.9271579709132454 | -0.992974 | -32.066 | 9 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 408 | 2.220985624121666 | -0.859212 | -31.2638 | 8 | 19 | 14 | 0.74 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.264kcal/mol
Ligand efficiency (LE)
-0.8933kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.010
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
485.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.68kcal/mol
Minimised FF energy
115.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
764.8Ų
Total solvent-accessible surface area of free ligand
BSA total
618.1Ų
Buried surface area upon binding
BSA apolar
514.2Ų
Hydrophobic contacts buried
BSA polar
103.9Ų
Polar contacts buried
Fraction buried
80.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1752.3Ų
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
933.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)