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
11.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (15/23 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 (-1.128 kcal/mol/HA)
✓ Good fit quality (FQ -10.88)
✓ Strong H-bond network (13 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (11.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-33.841
kcal/mol
LE
-1.128
kcal/mol/HA
Fit Quality
-10.88
FQ (Leeson)
HAC
30
heavy atoms
MW
410
Da
LogP
4.14
cLogP
Interaction summary
HB 13
HY 6
PI 3
CLASH 3
⚠ Exposure 65%
Interaction summary
HB 13
HY 6
PI 3
CLASH 3
⚠ Exposure 65%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (15/23 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 23
Buried (contacted) 8
Exposed 15
LogP 4.14
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.981 | Score | -33.841 |
|---|---|---|---|
| Inter norm | -1.156 | Intra norm | 0.028 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 13 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
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 | 17 | Native recall | 1.00 |
| Jaccard | 1.00 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 327 | 0.8171546905266917 | -0.881496 | -24.9437 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 252 | 1.25262528314132 | -0.815055 | -21.9899 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 190 | 2.393610264960986 | -1.01227 | -27.9274 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 274 | 2.6728153685243323 | -0.971128 | -26.73 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 3.509170011564179 | -0.852226 | -22.326 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 296 | 3.6097912474495737 | -0.80505 | -19.7428 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 294 | 3.8954333947123394 | -0.850379 | -23.5994 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 204 | 3.980686356420171 | -1.15557 | -33.8409 | 13 | 17 | 17 | 1.00 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-33.841kcal/mol
Ligand efficiency (LE)
-1.1280kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.881
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
410.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.14
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
58.56kcal/mol
Minimised FF energy
46.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
701.2Ų
Total solvent-accessible surface area of free ligand
BSA total
428.9Ų
Buried surface area upon binding
BSA apolar
320.1Ų
Hydrophobic contacts buried
BSA polar
108.8Ų
Polar contacts buried
Fraction buried
61.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2312.8Ų
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
675.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)