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
24.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (12/20 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 (-0.981 kcal/mol/HA)
✓ Good fit quality (FQ -8.92)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (24.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-24.526
kcal/mol
LE
-0.981
kcal/mol/HA
Fit Quality
-8.92
FQ (Leeson)
HAC
25
heavy atoms
MW
340
Da
LogP
3.91
cLogP
Interaction summary
HB 11
HY 5
PI 1
CLASH 5
⚠ Exposure 60%
Interaction summary
HB 11
HY 5
PI 1
CLASH 5
⚠ Exposure 60%
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (12/20 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 20
Buried (contacted) 8
Exposed 12
LogP 3.91
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 2.600 | Score | -24.526 |
|---|---|---|---|
| Inter norm | -1.018 | Intra norm | 0.037 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; moderate strain Δ 24.6 | ||
| Residues |
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU136
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 | 14 | Native recall | 0.82 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 5 | Strict recall | 0.38 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 8 | HB residue recall | 0.73 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 66 | 0.8305093453479375 | -0.860099 | -15.002 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 74 | 2.1373659912864653 | -0.970433 | -20.7683 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 2.600107939307177 | -1.01846 | -24.5258 | 11 | 15 | 14 | 0.82 | 0.45 | - | no | Current |
| 65 | 2.6022736026417634 | -0.939392 | -18.7025 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 3.0349276914671437 | -1.1562 | -26.1336 | 11 | 17 | 5 | 0.29 | 0.18 | - | no | Open |
| 43 | 3.222270151018671 | -1.10798 | -20.2889 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 3.5206894931967216 | -1.022 | -18.8867 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 3.7209462673393525 | -1.01938 | -22.3114 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 4.14130884921673 | -1.0316 | -21.4621 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 4.326743905642506 | -0.753896 | -17.6426 | 7 | 12 | 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
-24.526kcal/mol
Ligand efficiency (LE)
-0.9810kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.918
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.91
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
83.64kcal/mol
Minimised FF energy
59.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
626.4Ų
Total solvent-accessible surface area of free ligand
BSA total
436.2Ų
Buried surface area upon binding
BSA apolar
339.5Ų
Hydrophobic contacts buried
BSA polar
96.7Ų
Polar contacts buried
Fraction buried
69.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2252.8Ų
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
671.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)