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
16.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.047 kcal/mol/HA)
✓ Good fit quality (FQ -9.64)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (9)
Score
-27.211
kcal/mol
LE
-1.047
kcal/mol/HA
Fit Quality
-9.64
FQ (Leeson)
HAC
26
heavy atoms
MW
351
Da
LogP
0.96
cLogP
Interaction summary
HB 8
HY 19
PI 5
CLASH 1
Interaction summary
HB 8
HY 19
PI 5
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 | 0.375 | Score | -27.211 |
|---|---|---|---|
| Inter norm | -1.104 | Intra norm | 0.057 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
PRO115
TYR191
TYR194
ARG287
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 11 | Native recall | 0.58 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 246 | 0.05212297211422521 | -1.26728 | -31.9198 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 245 | 0.15333775693127674 | -1.28287 | -31.1967 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 0.375190949082224 | -1.10388 | -27.2108 | 8 | 11 | 11 | 0.58 | 0.80 | - | no | Current |
| 269 | 2.030229846488461 | -0.847474 | -16.4266 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 2.036323288363696 | -1.19848 | -25.4194 | 11 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 239 | 3.0498119327730224 | -1.07349 | -27.244 | 9 | 20 | 16 | 0.84 | 0.60 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.211kcal/mol
Ligand efficiency (LE)
-1.0466kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.642
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
351.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.96
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.05kcal/mol
Minimised FF energy
84.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
612.1Ų
Total solvent-accessible surface area of free ligand
BSA total
442.4Ų
Buried surface area upon binding
BSA apolar
323.2Ų
Hydrophobic contacts buried
BSA polar
119.1Ų
Polar contacts buried
Fraction buried
72.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1625.6Ų
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
1030.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)