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
17.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.025 kcal/mol/HA)
✓ Good fit quality (FQ -9.56)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (17.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-27.677
kcal/mol
LE
-1.025
kcal/mol/HA
Fit Quality
-9.56
FQ (Leeson)
HAC
27
heavy atoms
MW
375
Da
LogP
4.61
cLogP
Interaction summary
HB 6
HY 23
PI 3
CLASH 1
Interaction summary
HB 6
HY 23
PI 3
CLASH 1
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
| Final rank | 3.019 | Score | -27.677 |
|---|---|---|---|
| Inter norm | -1.039 | Intra norm | 0.014 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes | ||
| Residues |
ARG17
GLY225
LEU226
LEU229
NDP302
PHE113
PRO115
TYR114
TYR191
TYR194
VAL228
VAL230
ARG287
| ||
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.58 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 565 | 3.018843044563312 | -1.03927 | -27.6768 | 6 | 13 | 11 | 0.65 | 0.50 | - | no | Current |
| 582 | 3.657711068170762 | -1.01793 | -22.7233 | 10 | 18 | 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
-27.677kcal/mol
Ligand efficiency (LE)
-1.0251kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.564
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
375.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
46.92kcal/mol
Minimised FF energy
29.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
604.6Ų
Total solvent-accessible surface area of free ligand
BSA total
489.5Ų
Buried surface area upon binding
BSA apolar
407.0Ų
Hydrophobic contacts buried
BSA polar
82.5Ų
Polar contacts buried
Fraction buried
81.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1636.8Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1055.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)