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
32.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.94, Jaccard 0.94, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.302 kcal/mol/HA)
✓ Good fit quality (FQ -11.67)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Very high strain energy (32.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-31.255
kcal/mol
LE
-1.302
kcal/mol/HA
Fit Quality
-11.67
FQ (Leeson)
HAC
24
heavy atoms
MW
409
Da
LogP
4.56
cLogP
Interaction summary
HB 12
HY 5
PI 1
CLASH 1
⚠ Exposure 64%
Interaction summary
HB 12
HY 5
PI 1
CLASH 1
⚠ Exposure 64%
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 6
Exposed 11
LogP 4.56
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 1.889 | Score | -31.255 |
|---|---|---|---|
| Inter norm | -1.456 | Intra norm | 0.154 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 12 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; high strain Δ 32.8 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
THR74
TYR49
| ||
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.94 | RMSD | - |
| HB strict | 6 | Strict recall | 0.46 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 437 | 1.0622373773057405 | -1.14598 | -24.2338 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 384 | 1.6543390194869305 | -1.30146 | -32.1781 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 1.8894308683503533 | -1.45598 | -31.2552 | 12 | 16 | 16 | 0.94 | 0.45 | - | no | Current |
| 417 | 2.420917382962812 | -1.29827 | -28.0042 | 14 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 427 | 2.9718852536009854 | -0.815124 | -17.3361 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 421 | 4.01819321477796 | -0.930807 | -22.6703 | 10 | 13 | 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
-31.255kcal/mol
Ligand efficiency (LE)
-1.3023kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.671
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
409.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
110.18kcal/mol
Minimised FF energy
77.35kcal/mol
SASA & burial
✓ computed
SASA (unbound)
623.2Ų
Total solvent-accessible surface area of free ligand
BSA total
426.6Ų
Buried surface area upon binding
BSA apolar
320.3Ų
Hydrophobic contacts buried
BSA polar
106.2Ų
Polar contacts buried
Fraction buried
68.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2206.2Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
714.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)