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
Promising
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
15.5 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.20
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.663 kcal/mol/HA)
✓ Good fit quality (FQ -6.18)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (15.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-17.889
kcal/mol
LE
-0.663
kcal/mol/HA
Fit Quality
-6.18
FQ (Leeson)
HAC
27
heavy atoms
MW
401
Da
LogP
3.74
cLogP
Interaction summary
HB 7
HY 5
PI 0
CLASH 6
⚠ Exposure 57%
Interaction summary
HB 7
HY 5
PI 0
CLASH 6
⚠ Exposure 57%
Partial hydrophobic solvent exposure
58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 8
Exposed 11
LogP 3.74
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.374 | Score | -17.889 |
|---|---|---|---|
| Inter norm | -0.913 | Intra norm | 0.250 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 7 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
GLY240
LEU339
LYS51
PHE383
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 | 0.40 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 569 | 0.36532912233574083 | -1.30221 | -32.7212 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 2.3737859879803827 | -0.913048 | -17.8893 | 7 | 13 | 8 | 0.53 | 0.20 | - | no | Current |
| 589 | 2.791741137083932 | -1.08787 | -23.2147 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 3.8312358695408832 | -0.914807 | -24.99 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 562 | 3.9390179097197437 | -1.12619 | -30.2577 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 4.131557866139451 | -0.953971 | -23.907 | 11 | 15 | 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
-17.889kcal/mol
Ligand efficiency (LE)
-0.6626kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.182
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
400.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.74
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-57.56kcal/mol
Minimised FF energy
-73.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
635.3Ų
Total solvent-accessible surface area of free ligand
BSA total
500.9Ų
Buried surface area upon binding
BSA apolar
378.9Ų
Hydrophobic contacts buried
BSA polar
122.0Ų
Polar contacts buried
Fraction buried
78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2434.2Ų
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
1400.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)