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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
64.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.52, H-bond role recall 0.57
Reason: strain 64.0 kcal/mol
strain ΔE 64.0 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.940 kcal/mol/HA)
✓ Good fit quality (FQ -9.16)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Extreme strain energy (64.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-29.148
kcal/mol
LE
-0.940
kcal/mol/HA
Fit Quality
-9.16
FQ (Leeson)
HAC
31
heavy atoms
MW
466
Da
LogP
2.63
cLogP
Interaction summary
HB 13
HY 10
PI 2
CLASH 3
⚠ Exposure 36%
Interaction summary
HB 13
HY 10
PI 2
CLASH 3
⚠ Exposure 36%
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
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 12
Exposed 7
LogP 2.63
H-bonds 13
Exposed fragments:
aliphatic chain/group (7 atoms exposed)
| Final rank | 5.646 | Score | -29.148 |
|---|---|---|---|
| Inter norm | -0.950 | Intra norm | 0.010 |
| Top1000 | no | Excluded | no |
| Contacts | 25 | H-bonds | 13 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes; high strain Δ 63.9 | ||
| Residues |
ALA111
ALA67
ALA90
ARG154
ARG277
ASN112
ASP233
ASP88
CYS70
GLU274
GLY235
GLY236
GLY237
GLY276
HIS197
LYS169
LYS69
PHE170
PHE196
PHE238
PRO113
SER195
SER200
THR132
TYR389
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 15 | Native recall | 0.79 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 6 | Strict recall | 0.67 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 4 | HB residue recall | 0.57 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2 | 4.911502377844317 | -1.17128 | -33.06 | 12 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 1 | 5.6464844105289425 | -0.950163 | -29.1483 | 13 | 25 | 15 | 0.79 | 0.57 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.148kcal/mol
Ligand efficiency (LE)
-0.9403kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.160
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
466.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.63
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
64.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-24.24kcal/mol
Minimised FF energy
-88.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
721.6Ų
Total solvent-accessible surface area of free ligand
BSA total
615.6Ų
Buried surface area upon binding
BSA apolar
405.3Ų
Hydrophobic contacts buried
BSA polar
210.4Ų
Polar contacts buried
Fraction buried
85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2572.2Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1377.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)