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 medium
Native strong
SASA done
Strain ΔE
34.7 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.68, Jaccard 0.62, H-bond role recall 0.57
Reason: no major geometry red flags detected
5 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (5/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.257 kcal/mol/HA)
✓ Good fit quality (FQ -10.52)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Very high strain energy (34.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-25.135
kcal/mol
LE
-1.257
kcal/mol/HA
Fit Quality
-10.52
FQ (Leeson)
HAC
20
heavy atoms
MW
305
Da
LogP
-2.11
cLogP
Interaction summary
HB 13
HY 3
PI 2
CLASH 0
⚠ Exposure 50%
Interaction summary
HB 13
HY 3
PI 2
CLASH 0
⚠ Exposure 50%
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
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (5/10 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 10
Buried (contacted) 5
Exposed 5
LogP -2.11
H-bonds 13
Exposed fragments:
aliphatic chain/group (5 atoms exposed)
| Final rank | 3.122 | Score | -25.135 |
|---|---|---|---|
| Inter norm | -1.451 | Intra norm | 0.194 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 13 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes; high strain Δ 34.7 | ||
| Residues |
ALA67
ARG277
ASP332
ASP88
GLU274
GLY199
GLY201
GLY236
GLY237
GLY276
HIS197
LYS69
PRO275
SER200
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 92 | -0.27488169405600155 | -1.23978 | -26.4643 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 136 | 2.6826692841091115 | -1.97334 | -36.3274 | 16 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 133 | 2.8727048910606037 | -1.53924 | -31.1406 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 207 | 3.038856002369936 | -1.16176 | -18.4277 | 9 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 117 | 3.1221365776763337 | -1.4511 | -25.135 | 13 | 15 | 13 | 0.68 | 0.57 | - | no | Current |
| 124 | 3.1723629671495166 | -1.40024 | -20.1365 | 15 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 3.7635505504674556 | -1.53162 | -25.3456 | 16 | 19 | 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
-25.135kcal/mol
Ligand efficiency (LE)
-1.2568kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.517
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
304.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.11
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
117.06kcal/mol
Minimised FF energy
82.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
475.9Ų
Total solvent-accessible surface area of free ligand
BSA total
368.0Ų
Buried surface area upon binding
BSA apolar
246.5Ų
Hydrophobic contacts buried
BSA polar
121.5Ų
Polar contacts buried
Fraction buried
77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2386.1Ų
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
1384.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)