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 high
Native strong
SASA done
Strain ΔE
10.4 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.47, H-bond role recall 0.50
Reason: no major geometry red flags detected
57% of hydrophobic surface appears solvent-exposed (12/21 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 (-1.063 kcal/mol/HA)
✓ Good fit quality (FQ -9.80)
✓ Good H-bonds (4 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Moderate strain (10.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-27.649
kcal/mol
LE
-1.063
kcal/mol/HA
Fit Quality
-9.80
FQ (Leeson)
HAC
26
heavy atoms
MW
345
Da
LogP
3.45
cLogP
Interaction summary
HB 4
HY 12
PI 2
CLASH 1
⚠ Exposure 57%
Interaction summary
HB 4
HY 12
PI 2
CLASH 1
⚠ Exposure 57%
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (12/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 9
Exposed 12
LogP 3.45
H-bonds 4
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.754 | Score | -27.649 |
|---|---|---|---|
| Inter norm | -1.127 | Intra norm | 0.063 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 4 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG17
LEU188
LEU226
LYS16
NDP302
PHE113
SER111
SER112
TYR194
VAL230
ARG287
| ||
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NDP302
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 9 | Native recall | 0.53 |
| Jaccard | 0.47 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 374 | 0.6079945178106212 | -0.898734 | -18.9633 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 1.7539303087813454 | -1.12654 | -27.6494 | 4 | 11 | 9 | 0.53 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.649kcal/mol
Ligand efficiency (LE)
-1.0634kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.798
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
345.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.45
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.09kcal/mol
Minimised FF energy
48.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
613.0Ų
Total solvent-accessible surface area of free ligand
BSA total
540.7Ų
Buried surface area upon binding
BSA apolar
489.8Ų
Hydrophobic contacts buried
BSA polar
50.9Ų
Polar contacts buried
Fraction buried
88.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1675.9Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1060.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)