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
32.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.88, Jaccard 0.75, H-bond role recall 0.36
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (9/21 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 (-1.017 kcal/mol/HA)
✓ Good fit quality (FQ -9.60)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-28.466
kcal/mol
LE
-1.017
kcal/mol/HA
Fit Quality
-9.60
FQ (Leeson)
HAC
28
heavy atoms
MW
393
Da
LogP
3.58
cLogP
Interaction summary
HB 9
HY 6
PI 2
CLASH 4
⚠ Exposure 42%
Interaction summary
HB 9
HY 6
PI 2
CLASH 4
⚠ Exposure 42%
Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 12
Exposed 9
LogP 3.58
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.244 | Score | -28.466 |
|---|---|---|---|
| Inter norm | -0.958 | Intra norm | -0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; high strain Δ 31.1 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
LEU101
SER46
THR117
THR74
TYR49
VAL97
| ||
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 15 | Native recall | 0.88 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 43 | 1.1728836106535168 | -1.15406 | -31.1202 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 1.5080412680464408 | -1.19861 | -29.6204 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 33 | 1.565675456546163 | -0.805172 | -22.1294 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 47 | 2.257128692601215 | -1.14501 | -33.9816 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 34 | 2.4507228953981053 | -0.956091 | -24.0652 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 34 | 2.9344294306635303 | -1.03576 | -26.0298 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 21 | 3.244451123765894 | -0.958338 | -28.4656 | 9 | 18 | 15 | 0.88 | 0.36 | - | no | Current |
| 37 | 3.2541776923072754 | -0.94766 | -25.8329 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 33 | 3.3373689399605038 | -1.06988 | -32.9082 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 24 | 3.5583407345718885 | -1.08027 | -29.9241 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 42 | 3.6105363889928936 | -0.880375 | -23.1448 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 3.6772301933141605 | -0.886989 | -25.4605 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 22 | 3.9398829104489517 | -0.820834 | -22.4978 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 35 | 5.976485328510418 | -1.13445 | -27.9224 | 13 | 16 | 5 | 0.29 | 0.36 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.466kcal/mol
Ligand efficiency (LE)
-1.0166kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.597
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
393.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.58
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
25.87kcal/mol
Minimised FF energy
-6.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
700.5Ų
Total solvent-accessible surface area of free ligand
BSA total
495.2Ų
Buried surface area upon binding
BSA apolar
353.8Ų
Hydrophobic contacts buried
BSA polar
141.4Ų
Polar contacts buried
Fraction buried
70.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2260.6Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
688.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)