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 mixed
SASA done
Strain ΔE
12.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.20
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.819 kcal/mol/HA)
✓ Good fit quality (FQ -7.55)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (12.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-21.299
kcal/mol
LE
-0.819
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
26
heavy atoms
MW
371
Da
LogP
2.53
cLogP
Interaction summary
HB 6
HY 1
PI 0
CLASH 4
⚠ Exposure 68%
Interaction summary
HB 6
HY 1
PI 0
CLASH 4
⚠ Exposure 68%
Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 19
Buried (contacted) 6
Exposed 13
LogP 2.53
H-bonds 6
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.916 | Score | -21.299 |
|---|---|---|---|
| Inter norm | -0.859 | Intra norm | 0.040 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
ASP47
GLU384
GLY240
LEU339
LYS51
PHE383
PRO338
SER282
THR241
VAL335
VAL336
| ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 8 | Native recall | 0.53 |
| Jaccard | 0.36 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 46 | 0.5040962761140213 | -1.37861 | -35.266 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 1.4965351920943302 | -1.08707 | -27.6415 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 2.446473056600728 | -0.905597 | -22.4709 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 52 | 2.916497224455439 | -0.858929 | -21.299 | 6 | 15 | 8 | 0.53 | 0.20 | - | no | Current |
| 46 | 3.4883448942087782 | -0.875418 | -19.1176 | 8 | 18 | 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
-21.299kcal/mol
Ligand efficiency (LE)
-0.8192kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.547
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.53
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.09kcal/mol
Minimised FF energy
65.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
632.5Ų
Total solvent-accessible surface area of free ligand
BSA total
479.3Ų
Buried surface area upon binding
BSA apolar
364.6Ų
Hydrophobic contacts buried
BSA polar
114.7Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2456.9Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1389.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)