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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.65, Jaccard 0.50, H-bond role recall 0.17
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.495 kcal/mol/HA)
✓ Good fit quality (FQ -12.25)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (17.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-28.404
kcal/mol
LE
-1.495
kcal/mol/HA
Fit Quality
-12.25
FQ (Leeson)
HAC
19
heavy atoms
MW
263
Da
LogP
0.28
cLogP
Interaction summary
HB 8
HY 16
PI 3
CLASH 1
Interaction summary
HB 8
HY 16
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 | 3.275 | Score | -28.404 |
|---|---|---|---|
| Inter norm | -1.601 | Intra norm | 0.106 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ARG17
ASP181
LEU188
LEU226
LEU229
LYS198
MET183
NDP302
PHE113
PRO187
THR184
THR195
TYR191
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 | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 1 | HB role recall | 0.17 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 269 | 1.9744945659750004 | -1.07862 | -18.0223 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 238 | 2.100724177218206 | -1.53049 | -25.0062 | 5 | 10 | 10 | 0.59 | 0.33 | - | no | Open |
| 225 | 3.2749514114110547 | -1.60122 | -28.4044 | 8 | 16 | 11 | 0.65 | 0.17 | - | no | Current |
| 354 | 3.339664030123585 | -1.4508 | -24.8462 | 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
-28.404kcal/mol
Ligand efficiency (LE)
-1.4950kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.254
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
263.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.28
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.54kcal/mol
Minimised FF energy
18.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
541.9Ų
Total solvent-accessible surface area of free ligand
BSA total
530.0Ų
Buried surface area upon binding
BSA apolar
455.8Ų
Hydrophobic contacts buried
BSA polar
74.2Ų
Polar contacts buried
Fraction buried
97.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1623.6Ų
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
1021.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)