Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
19.7 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.35, Jaccard 0.30, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
37% of hydrophobic surface appears solvent-exposed (7/19 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 (-1.126 kcal/mol/HA)
✓ Good fit quality (FQ -10.24)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (19.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (10)
Score
-28.158
kcal/mol
LE
-1.126
kcal/mol/HA
Fit Quality
-10.24
FQ (Leeson)
HAC
25
heavy atoms
MW
337
Da
LogP
3.83
cLogP
Interaction summary
HB 5
HY 14
PI 3
CLASH 2
⚠ Exposure 36%
Interaction summary
HB 5
HY 14
PI 3
CLASH 2
⚠ Exposure 36%
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (7/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 12
Exposed 7
LogP 3.83
H-bonds 5
Exposed fragments:
phenyl (5/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.144 | Score | -28.158 |
|---|---|---|---|
| Inter norm | -1.178 | Intra norm | 0.052 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 7 protein contact clashes; 3 cofactor-context clashes | ||
| Residues |
ARG17
ARG39
NDP302
PHE113
SER111
SER112
TYR114
TYR194
VAL230
| ||
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 | 6 | Native recall | 0.35 |
| Jaccard | 0.30 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 84 | 1.1444723794799883 | -1.17822 | -28.1582 | 5 | 9 | 6 | 0.35 | 0.50 | - | no | Current |
| 131 | 3.189362755779069 | -0.882345 | -18.7913 | 6 | 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
-28.158kcal/mol
Ligand efficiency (LE)
-1.1263kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.239
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
337.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.83
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
12.89kcal/mol
Minimised FF energy
-6.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
586.6Ų
Total solvent-accessible surface area of free ligand
BSA total
468.1Ų
Buried surface area upon binding
BSA apolar
376.9Ų
Hydrophobic contacts buried
BSA polar
91.3Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1612.4Ų
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
1044.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)