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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
12.1 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.60, Jaccard 0.41, H-bond role recall 0.20
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
77% of hydrophobic surface is solvent-exposed (20/26 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 (-0.592 kcal/mol/HA)
✓ Good fit quality (FQ -5.82)
✓ Good H-bonds (3 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ Moderate strain (12.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (21)
Score
-18.936
kcal/mol
LE
-0.592
kcal/mol/HA
Fit Quality
-5.82
FQ (Leeson)
HAC
32
heavy atoms
MW
488
Da
LogP
5.33
cLogP
Interaction summary
HB 3
HY 8
PI 0
CLASH 8
⚠ Exposure 76%
Interaction summary
HB 3
HY 8
PI 0
CLASH 8
⚠ Exposure 76%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
77% of hydrophobic surface is solvent-exposed (20/26 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 26
Buried (contacted) 6
Exposed 20
LogP 5.33
H-bonds 3
Exposed fragments:
phenyl (5/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 5.396 | Score | -18.936 |
|---|---|---|---|
| Inter norm | -0.695 | Intra norm | 0.103 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 21 clashes; 2 protein clashes | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
ASP47
GLU384
LEU339
LEU382
LYS51
MET386
PHE383
PRO338
SER282
THR241
VAL335
VAL336
| ||
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 | 9 | Native recall | 0.60 |
| Jaccard | 0.41 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 632 | 1.243029950327408 | -0.715524 | -23.1313 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 635 | 1.4623639465361715 | -0.810768 | -24.5451 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 655 | 3.2994755327115124 | -0.702435 | -21.7347 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 650 | 3.6866953484990788 | -0.880427 | -27.0054 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 5.395951478542988 | -0.694543 | -18.9361 | 3 | 16 | 9 | 0.60 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.936kcal/mol
Ligand efficiency (LE)
-0.5918kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.819
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
488.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.33
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
131.25kcal/mol
Minimised FF energy
119.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
718.4Ų
Total solvent-accessible surface area of free ligand
BSA total
530.5Ų
Buried surface area upon binding
BSA apolar
496.2Ų
Hydrophobic contacts buried
BSA polar
34.2Ų
Polar contacts buried
Fraction buried
73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2587.0Ų
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
1420.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)