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
14.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.35, H-bond role recall 0.40
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
57% of hydrophobic surface appears solvent-exposed (16/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.675 kcal/mol/HA)
✓ Good fit quality (FQ -6.76)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ Moderate strain (14.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-22.955
kcal/mol
LE
-0.675
kcal/mol/HA
Fit Quality
-6.76
FQ (Leeson)
HAC
34
heavy atoms
MW
449
Da
LogP
4.59
cLogP
Interaction summary
HB 3
HY 3
PI 0
CLASH 3
⚠ Exposure 57%
Interaction summary
HB 3
HY 3
PI 0
CLASH 3
⚠ Exposure 57%
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (16/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 28
Buried (contacted) 12
Exposed 16
LogP 4.59
H-bonds 3
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.019 | Score | -22.955 |
|---|---|---|---|
| Inter norm | -0.670 | Intra norm | -0.006 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 3 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
ASP47
GLU384
GLY240
LEU339
LYS51
PHE284
PHE383
SER282
THR21
THR241
THR285
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 | 0.35 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 174 | 1.5953454974067567 | -1.04275 | -30.9105 | 6 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 1.8086522717655165 | -0.657332 | -21.5359 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 323 | 2.4019885584747827 | -0.689268 | -19.4794 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 315 | 2.403157705090617 | -0.684753 | -21.7406 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 203 | 3.019473352449312 | -0.669603 | -22.9554 | 3 | 16 | 8 | 0.53 | 0.40 | - | no | Current |
| 325 | 3.239213976956587 | -0.705168 | -21.9124 | 3 | 13 | 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
-22.955kcal/mol
Ligand efficiency (LE)
-0.6752kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.756
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
448.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.59
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.99kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
10.38kcal/mol
Minimised FF energy
-3.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
749.5Ų
Total solvent-accessible surface area of free ligand
BSA total
573.6Ų
Buried surface area upon binding
BSA apolar
539.9Ų
Hydrophobic contacts buried
BSA polar
33.8Ų
Polar contacts buried
Fraction buried
76.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2637.2Ų
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
1380.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)