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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
66.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.56
Reason: strain 66.1 kcal/mol
strain ΔE 66.1 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (9/22 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 (-0.618 kcal/mol/HA)
✓ Good fit quality (FQ -6.08)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Extreme strain energy (66.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-19.788
kcal/mol
LE
-0.618
kcal/mol/HA
Fit Quality
-6.08
FQ (Leeson)
HAC
32
heavy atoms
MW
433
Da
LogP
-0.00
cLogP
Interaction summary
HB 13
HY 10
PI 3
CLASH 3
⚠ Exposure 40%
Interaction summary
HB 13
HY 10
PI 3
CLASH 3
⚠ Exposure 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
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (9/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 13
Exposed 9
LogP -0.0
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.879 | Score | -19.788 |
|---|---|---|---|
| Inter norm | -0.818 | Intra norm | 0.200 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 13 |
| Artifact reason | geometry warning; 14 clashes; 1 protein clash; high strain Δ 66.1 | ||
| Residues |
ARG137
ARG140
ARG141
ASN103
HIS102
ASP10
ASP45
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER43
SER71
TYR46
VAL44
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 6 | HB residue recall | 0.75 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 359 | 2.244470784373827 | -0.798467 | -14.7208 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 2.8793379368286023 | -0.818089 | -19.7883 | 13 | 18 | 13 | 0.93 | 0.56 | - | no | Current |
| 339 | 4.037169782378875 | -1.25769 | -31.2658 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 303 | 4.54368954996928 | -0.824304 | -21.8567 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 4.921780442364073 | -1.03614 | -25.2784 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 4.964586519044101 | -0.839228 | -19.9991 | 7 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 5.335617475749751 | -0.879574 | -24.4531 | 11 | 20 | 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
-19.788kcal/mol
Ligand efficiency (LE)
-0.6184kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.081
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
433.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.00
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
66.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
188.52kcal/mol
Minimised FF energy
122.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
746.8Ų
Total solvent-accessible surface area of free ligand
BSA total
529.8Ų
Buried surface area upon binding
BSA apolar
422.5Ų
Hydrophobic contacts buried
BSA polar
107.2Ų
Polar contacts buried
Fraction buried
70.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2333.3Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
775.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)