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 medium
Native strong
SASA done
Strain ΔE
36.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.55, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.293 kcal/mol/HA)
✓ Good fit quality (FQ -11.75)
✓ Good H-bonds (3 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Very high strain energy (36.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-32.324
kcal/mol
LE
-1.293
kcal/mol/HA
Fit Quality
-11.75
FQ (Leeson)
HAC
25
heavy atoms
MW
349
Da
LogP
2.82
cLogP
Interaction summary
HB 3
HY 20
PI 3
CLASH 2
Interaction summary
HB 3
HY 20
PI 3
CLASH 2
| Final rank | 2.665 | Score | -32.324 |
|---|---|---|---|
| Inter norm | -1.033 | Intra norm | -0.260 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 3 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; 1 cofactor-context clash; high strain Δ 36.7 | ||
| Residues |
ASP232
GLY225
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
TYR194
VAL230
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 655 | 2.297298822677387 | -1.11574 | -21.8348 | 16 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 647 | 2.664669471635406 | -1.03291 | -32.3238 | 3 | 12 | 11 | 0.58 | 0.20 | - | no | Current |
| 630 | 3.413208291730832 | -1.06105 | -23.2911 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 647 | 3.4491358016340006 | -1.13398 | -28.6141 | 10 | 14 | 11 | 0.58 | 0.20 | - | no | Open |
| 637 | 4.194231666647193 | -1.27092 | -24.8645 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 4.214149267054125 | -0.836819 | -15.4094 | 10 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 4.602546806562358 | -1.02704 | -25.7758 | 14 | 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
-32.324kcal/mol
Ligand efficiency (LE)
-1.2930kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.754
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
349.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.82
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.46kcal/mol
Minimised FF energy
44.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
578.5Ų
Total solvent-accessible surface area of free ligand
BSA total
414.6Ų
Buried surface area upon binding
BSA apolar
261.3Ų
Hydrophobic contacts buried
BSA polar
153.2Ų
Polar contacts buried
Fraction buried
71.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1505.7Ų
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
1068.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)