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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
41.5 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.65, Jaccard 0.55, H-bond role recall 0.50
Reason: 1 severe internal clashes
1 severe internal clashes
2 protein-contact clashes
4 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.201 kcal/mol/HA)
✓ Good fit quality (FQ -12.11)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Extreme strain energy (41.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Many internal clashes (15)
Score
-42.033
kcal/mol
LE
-1.201
kcal/mol/HA
Fit Quality
-12.11
FQ (Leeson)
HAC
35
heavy atoms
MW
553
Da
LogP
5.83
cLogP
Interaction summary
HB 7
HY 24
PI 2
CLASH 4
Severe 1
Interaction summary
HB 7
HY 24
PI 2
CLASH 4
Severe 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 | 1.321 | Score | -42.033 |
|---|---|---|---|
| Inter norm | -0.922 | Intra norm | -0.279 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 15 clashes; 3 protein contact clashes; 2 severe cofactor-context clashes; high strain Δ 41.0 | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
MET183
NDP302
PHE113
SER111
SER112
TYR194
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 | 0.55 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 576 | 1.321147178710912 | -0.922248 | -42.0326 | 7 | 14 | 11 | 0.65 | 0.50 | - | no | Current |
| 590 | 1.7976173245508116 | -0.760813 | -30.967 | 3 | 14 | 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
-42.033kcal/mol
Ligand efficiency (LE)
-1.2009kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.113
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
553.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.83
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
143.50kcal/mol
Minimised FF energy
102.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
731.4Ų
Total solvent-accessible surface area of free ligand
BSA total
592.4Ų
Buried surface area upon binding
BSA apolar
489.5Ų
Hydrophobic contacts buried
BSA polar
102.9Ų
Polar contacts buried
Fraction buried
81.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1724.3Ų
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
1080.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)