# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:40:15 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2R)-2-amino-3-(naphthalen-2-yl)propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc2ccccc2c1)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 4J2  4J2  '(2R)-2-amino-3-(naphthalen-2-yl)propanoic acid (non-preferred name)'  D-peptide  28  16  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_4J2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 4J2  N     N  NH2    0  -0.809  -1.5370  3.1235  -0.5790
 4J2  CA    C  CH1    0  -0.205  -2.7543  2.5969   0.0148
 4J2  CB    C  CH2    0  -0.491  -2.4547  1.9886   1.3922
 4J2  CG    C  CR6    0   0.133  -1.8874  2.9973   2.3488
 4J2  CD1   C  CR16   0  -0.298  -0.4883  3.2040   2.4378
 4J2  CD2   C  CR16   0  -0.387  -2.7119  3.7721   3.1262
 4J2  CE1   C  CR16   0  -0.299   0.0394  4.1478   3.2750
 4J2  CZ1   C  CR66   0   0.093  -0.7995  4.9541   4.0790
 4J2  CZ2   C  CR16   0  -0.308  -0.2889  5.9395   4.9564
 4J2  CZ3   C  CR16   0  -0.262  -1.1322  6.6994   5.7208
 4J2  CE2   C  CR66   0   0.141  -2.2026  4.7591   4.0005
 4J2  CE3   C  CR16   0  -0.316  -3.0497  5.5594   4.8043
 4J2  CE4   C  CR16   0  -0.259  -2.5285  6.5066   5.6432
 4J2  HE1   H  HCR6   0   0.248   1.1127  4.2881   3.3313
 4J2  HE3   H  HCR6   0   0.249  -4.1215  5.4101   4.7451
 4J2  HE4   H  HCR6   0   0.253  -3.1865  7.1126   6.2527
 4J2  C     C  C      0   0.410  -3.4373  1.5634  -0.9212
 4J2  O     O  O      0  -0.605  -4.3570  0.8896  -0.4177
 4J2  H     H  HNH2   0   0.334  -1.6750  3.1807  -1.5790
 4J2  H1    H  HNH2   0   0.333  -1.3606  4.0617  -0.2457
 4J2  HA    H  HCH1   0   0.202  -3.5098  3.3852   0.1772
 4J2  HB2   H  HCH2   0   0.232  -3.3759  1.5731   1.8002
 4J2  HB1   H  HCH2   0   0.224  -1.7502  1.1617   1.2656
 4J2  HD1   H  HCR6   0   0.241   0.1704  2.5957   1.8306
 4J2  HD2   H  HCR6   0   0.239  -3.7867  3.6290   3.0776
 4J2  HZ2   H  HCR6   0   0.250   0.7835  6.0849   5.0142
 4J2  HZ23  H  HCR6   0   0.253  -0.7321  7.4515   6.3883
 4J2  OXT   O  OC    -1  -0.596  -3.0402  1.5207  -2.1023

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 4J2  N    CA    single    1.458  0.019  1.458
 4J2  CA   CB    single    1.521  0.033  1.521
 4J2  CA   C     single    1.525  0.021  1.525
 4J2  CB   CG    single    1.501  0.020  1.501
 4J2  CG   CD1   aromatic  1.417  0.020  1.417
 4J2  CG   CD2   aromatic  1.373  0.020  1.373
 4J2  CD1  CE1   aromatic  1.368  0.020  1.368
 4J2  CD2  CE2   aromatic  1.414  0.020  1.414
 4J2  CE1  CZ1   aromatic  1.414  0.020  1.414
 4J2  CE1  HE1   single    0.930  0.020  1.080
 4J2  CZ1  CZ2   aromatic  1.415  0.020  1.415
 4J2  CZ1  CE2   aromatic  1.419  0.020  1.419
 4J2  CZ2  CZ3   aromatic  1.369  0.020  1.369
 4J2  CZ3  CE4   aromatic  1.412  0.020  1.412
 4J2  CE2  CE3   aromatic  1.416  0.020  1.416
 4J2  CE3  CE4   aromatic  1.368  0.020  1.368
 4J2  CE3  HE3   single    0.930  0.020  1.080
 4J2  CE4  HE4   single    0.930  0.020  1.080
 4J2  C    O     deloc     1.231  0.020  1.231
 4J2  N    H     single    0.860  0.020  0.860
 4J2  N    H1    single    0.890  0.020  1.040
 4J2  CA   HA    single    0.970  0.020  0.970
 4J2  CB   HB2   single    0.970  0.020  1.090
 4J2  CB   HB1   single    0.970  0.020  1.090
 4J2  CD1  HD1   single    0.930  0.020  1.080
 4J2  CD2  HD2   single    0.930  0.020  1.080
 4J2  CZ2  HZ2   single    0.930  0.020  1.080
 4J2  CZ3  HZ23  single    0.930  0.020  1.080
 4J2  C    OXT   deloc     1.247  0.020  1.247

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 4J2  H1    N    H    107.30  3.000
 4J2  H1    N    CA   110.35  3.000
 4J2  H     N    CA   114.00  3.000
 4J2  HA    CA   C    110.00  3.000
 4J2  HA    CA   CB   109.00  3.000
 4J2  C     CA   CB   110.50  1.500
 4J2  HA    CA   N    110.00  3.000
 4J2  C     CA   N    111.00  2.800
 4J2  CB    CA   N    110.40  1.500
 4J2  HB1   CB   HB2  107.43  3.000
 4J2  HB1   CB   CG   109.77  3.000
 4J2  HB2   CB   CG   109.70  3.000
 4J2  HB1   CB   CA   108.75  3.000
 4J2  HB2   CB   CA   108.78  3.000
 4J2  CG    CB   CA   112.28  3.000
 4J2  CD2   CG   CD1  118.36  3.000
 4J2  CD2   CG   CB   120.87  3.000
 4J2  CD1   CG   CB   120.74  3.000
 4J2  HD1   CD1  CE1  119.75  3.000
 4J2  HD1   CD1  CG   118.91  3.000
 4J2  CE1   CD1  CG   121.34  3.000
 4J2  HD2   CD2  CE2  118.46  3.000
 4J2  HD2   CD2  CG   119.67  3.000
 4J2  CE2   CD2  CG   121.87  3.000
 4J2  HE1   CE1  CZ1  118.95  3.000
 4J2  HE1   CE1  CD1  120.22  3.000
 4J2  CZ1   CE1  CD1  120.83  3.000
 4J2  CE2   CZ1  CZ2  119.14  3.000
 4J2  CE2   CZ1  CE1  118.48  3.000
 4J2  CZ2   CZ1  CE1  122.38  3.000
 4J2  HZ2   CZ2  CZ3  120.36  3.000
 4J2  HZ2   CZ2  CZ1  118.92  3.000
 4J2  CZ3   CZ2  CZ1  120.71  3.000
 4J2  HZ23  CZ3  CE4  119.63  3.000
 4J2  HZ23  CZ3  CZ2  120.17  3.000
 4J2  CE4   CZ3  CZ2  120.20  3.000
 4J2  CE3   CE2  CZ1  118.86  3.000
 4J2  CE3   CE2  CD2  122.03  3.000
 4J2  CZ1   CE2  CD2  119.11  3.000
 4J2  HE3   CE3  CE4  120.37  3.000
 4J2  HE3   CE3  CE2  118.87  3.000
 4J2  CE4   CE3  CE2  120.76  3.000
 4J2  HE4   CE4  CE3  120.08  3.000
 4J2  HE4   CE4  CZ3  119.60  3.000
 4J2  CE3   CE4  CZ3  120.33  3.000
 4J2  OXT   C    O    126.81  3.000
 4J2  OXT   C    CA   120.80  1.700
 4J2  O     C    CA   120.80  1.700

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 4J2  CONST_01  CZ1   CE1  CD1  CG     0.00   0.0  0
 4J2  CONST_02  CZ1   CE2  CD2  CG     0.00   0.0  0
 4J2  CONST_03  CE3   CE2  CD2  CG   180.00   0.0  0
 4J2  CONST_04  CE2   CD2  CG   CD1    0.00   0.0  0
 4J2  CONST_05  CZ2   CZ1  CE1  CD1  180.00   0.0  0
 4J2  CONST_06  CE2   CZ1  CE1  CD1    0.00   0.0  0
 4J2  CONST_07  CE1   CD1  CG   CD2    0.00   0.0  0
 4J2  CONST_08  CE1   CZ1  CE2  CD2    0.00   0.0  0
 4J2  CONST_09  CZ2   CZ1  CE2  CD2  180.00   0.0  0
 4J2  CONST_10  CE4   CE3  CE2  CD2  180.00   0.0  0
 4J2  CONST_11  CZ3   CZ2  CZ1  CE1  180.00   0.0  0
 4J2  CONST_12  CE3   CE2  CZ1  CE1  180.00   0.0  0
 4J2  CONST_13  CE4   CZ3  CZ2  CZ1    0.00   0.0  0
 4J2  CONST_14  CE4   CE3  CE2  CZ1    0.00   0.0  0
 4J2  CONST_15  CE3   CE2  CZ1  CZ2    0.00   0.0  0
 4J2  CONST_16  CE3   CE4  CZ3  CZ2    0.00   0.0  0
 4J2  CONST_17  CE2   CZ1  CZ2  CZ3    0.00   0.0  0
 4J2  CONST_18  CE2   CE3  CE4  CZ3    0.00   0.0  0
 4J2  CONST_19  CE1   CD1  CG   CB   180.00   0.0  0
 4J2  CONST_20  CE2   CD2  CG   CB   180.00   0.0  0
 4J2  CONST_21  HE1   CE1  CD1  CG   180.00   0.0  0
 4J2  CONST_22  HD2   CD2  CG   CD1  180.00   0.0  0
 4J2  CONST_23  HD1   CD1  CG   CD2  180.00   0.0  0
 4J2  CONST_24  HE3   CE3  CE2  CD2    0.00   0.0  0
 4J2  CONST_25  HZ2   CZ2  CZ1  CE1    0.00   0.0  0
 4J2  CONST_26  HZ23  CZ3  CZ2  CZ1  180.00   0.0  0
 4J2  CONST_27  HE4   CE4  CZ3  CZ2  180.00   0.0  0
 4J2  Var_01    CD1   CG   CB   CA   -89.81  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 4J2  chir_01  CA  N  CB  C  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 4J2  plan-1  CB    0.020
 4J2  plan-1  CG    0.020
 4J2  plan-1  CD1   0.020
 4J2  plan-1  CD2   0.020
 4J2  plan-1  CE1   0.020
 4J2  plan-1  CZ1   0.020
 4J2  plan-1  CZ2   0.020
 4J2  plan-1  CZ3   0.020
 4J2  plan-1  CE2   0.020
 4J2  plan-1  CE3   0.020
 4J2  plan-1  CE4   0.020
 4J2  plan-1  HE1   0.020
 4J2  plan-1  HE3   0.020
 4J2  plan-1  HE4   0.020
 4J2  plan-1  HD1   0.020
 4J2  plan-1  HD2   0.020
 4J2  plan-1  HZ2   0.020
 4J2  plan-1  HZ23  0.020
 4J2  plan-2  CA    0.020
 4J2  plan-2  C     0.020
 4J2  plan-2  O     0.020
 4J2  plan-2  OXT   0.020

