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
42.7 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.20
Reason: strain 42.7 kcal/mol
strain ΔE 42.7 kcal/mol
1 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.549 kcal/mol/HA)
✓ Good fit quality (FQ -5.58)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Extreme strain energy (42.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-19.771
kcal/mol
LE
-0.549
kcal/mol/HA
Fit Quality
-5.58
FQ (Leeson)
HAC
36
heavy atoms
MW
480
Da
LogP
3.99
cLogP
Interaction summary
HB 6
HY 12
PI 4
CLASH 3
Interaction summary
HB 6
HY 12
PI 4
CLASH 3
| Final rank | 2.357 | Score | -19.771 |
|---|---|---|---|
| Inter norm | -0.675 | Intra norm | 0.126 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; 1 severe cofactor-context clash; high strain Δ 42.7 | ||
| Residues |
ARG17
HIS241
LEU188
LEU229
MET233
NDP302
PHE113
SER111
TYR191
TYR194
TYR283
VAL230
ALA288
ARG287
| ||
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
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 354 | 2.3571217579682013 | -0.675425 | -19.7712 | 6 | 14 | 12 | 0.63 | 0.20 | - | no | Current |
| 389 | 3.5785822705287464 | -0.77347 | -21.3242 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 423 | 3.651966678010715 | -0.661393 | -19.5496 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 460 | 3.7545924671768027 | -0.689627 | -26.031 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 3.9939126117944443 | -0.63276 | -15.1147 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 4.416801981477295 | -0.677978 | -20.5428 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 352 | 4.91609811747713 | -0.805784 | -21.2247 | 10 | 19 | 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
-19.771kcal/mol
Ligand efficiency (LE)
-0.5492kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.582
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.99
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
42.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.91kcal/mol
Minimised FF energy
96.21kcal/mol
SASA & burial
✓ computed
SASA (unbound)
765.2Ų
Total solvent-accessible surface area of free ligand
BSA total
556.4Ų
Buried surface area upon binding
BSA apolar
415.1Ų
Hydrophobic contacts buried
BSA polar
141.2Ų
Polar contacts buried
Fraction buried
72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1718.6Ų
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
1049.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)