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 high
Native strong
SASA done
Strain ΔE
19.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.75, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.159 kcal/mol/HA)
✓ Good fit quality (FQ -11.40)
✓ Good H-bonds (5 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (19.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-37.093
kcal/mol
LE
-1.159
kcal/mol/HA
Fit Quality
-11.40
FQ (Leeson)
HAC
32
heavy atoms
MW
455
Da
LogP
1.30
cLogP
Interaction summary
HB 5
HY 22
PI 4
CLASH 1
Interaction summary
HB 5
HY 22
PI 4
CLASH 1
| Final rank | 3.208 | Score | -37.093 |
|---|---|---|---|
| Inter norm | -1.209 | Intra norm | 0.050 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 17 clashes; 2 protein clashes; 2 cofactor-context clashes | ||
| Residues |
ARG17
ASP232
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
SER111
TYR191
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 9 | 1.7359748197207696 | -0.702858 | -20.101 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 11 | 2.345239731061546 | -0.832378 | -24.7526 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 8 | 2.5166177658116644 | -0.900904 | -26.4385 | 6 | 15 | 15 | 0.79 | 0.80 | - | no | Open |
| 9 | 2.799838389457709 | -0.852745 | -25.4636 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 5 | 3.1171657565070787 | -0.913652 | -17.4952 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 5 | 3.2083135537940506 | -1.20929 | -37.0925 | 5 | 16 | 15 | 0.79 | 0.80 | - | no | Current |
| 7 | 3.2558005905835374 | -0.870375 | -27.8055 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 4.25676227034814 | -0.89215 | -26.2924 | 12 | 20 | 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
-37.093kcal/mol
Ligand efficiency (LE)
-1.1591kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.399
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.30
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-32.16kcal/mol
Minimised FF energy
-51.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
730.1Ų
Total solvent-accessible surface area of free ligand
BSA total
546.6Ų
Buried surface area upon binding
BSA apolar
362.1Ų
Hydrophobic contacts buried
BSA polar
184.5Ų
Polar contacts buried
Fraction buried
74.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1669.3Ų
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
1023.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)