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
36.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.63, H-bond role recall 0.36
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
62% of hydrophobic surface is solvent-exposed (13/21 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 (-0.887 kcal/mol/HA)
✓ Good fit quality (FQ -8.64)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (36.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.499
kcal/mol
LE
-0.887
kcal/mol/HA
Fit Quality
-8.64
FQ (Leeson)
HAC
31
heavy atoms
MW
465
Da
LogP
5.67
cLogP
Interaction summary
HB 11
HY 3
PI 2
CLASH 4
⚠ Exposure 61%
Interaction summary
HB 11
HY 3
PI 2
CLASH 4
⚠ Exposure 61%
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
62% of hydrophobic surface is solvent-exposed (13/21 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 21
Buried (contacted) 8
Exposed 13
LogP 5.67
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 5.461 | Score | -27.499 |
|---|---|---|---|
| Inter norm | -0.778 | Intra norm | -0.109 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 11 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; high strain Δ 36.4 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASP13
ASP44
CYS72
GLY73
HIS105
HIS14
HIS141
SER46
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.63 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 445 | 0.794847904014074 | -0.865717 | -26.5077 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 433 | 2.1134409178227136 | -0.842731 | -25.6964 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 2.2343133209621033 | -1.05016 | -31.7644 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 463 | 2.8406508519396483 | -0.715929 | -21.1612 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 421 | 3.406317180187885 | -0.697704 | -23.1971 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 394 | 4.01505079065604 | -0.939961 | -29.2802 | 7 | 18 | 5 | 0.29 | 0.27 | - | no | Open |
| 413 | 4.212330441451837 | -1.16321 | -34.6908 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 389 | 5.46063911248349 | -0.777983 | -27.4987 | 11 | 14 | 12 | 0.71 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.499kcal/mol
Ligand efficiency (LE)
-0.8871kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.642
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
464.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.67
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.23kcal/mol
Minimised FF energy
29.81kcal/mol
SASA & burial
✓ computed
SASA (unbound)
661.2Ų
Total solvent-accessible surface area of free ligand
BSA total
474.7Ų
Buried surface area upon binding
BSA apolar
375.8Ų
Hydrophobic contacts buried
BSA polar
98.8Ų
Polar contacts buried
Fraction buried
71.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2210.7Ų
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
680.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)