# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:57:40 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{S},3~{R})-2-azanyl-3-phenyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H](N)C(O)=O)c1ccccc1
#
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
 JCX  JCX  "(2S,3R)-2-azanyl-3-phenyl-butanoic acid"  ligand  25  13  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JCX
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
 JCX  C10  C  CR16   0  -0.313  12.9539  38.8817  129.4278
 JCX  C02  C  CH1    0  -0.146  13.1167  40.6880  126.8912
 JCX  C03  C  CH1    0  -0.302  11.9692  39.7299  127.2531
 JCX  C06  C  CR16   0  -0.326  12.3601  37.2892  127.7476
 JCX  C09  C  CR16   0  -0.239  13.3775  37.8524  130.2569
 JCX  C04  C  CH3    0  -0.661  10.7825  40.4643  127.8810
 JCX  C05  C  CR6    0   0.160  12.4404  38.6177  128.1576
 JCX  C07  C  CR16   0  -0.238  12.7786  36.2536  128.5741
 JCX  C08  C  CR16   0  -0.276  13.2928  36.5317  129.8327
 JCX  N01  N  NH2    0  -0.813  12.6434  41.6579  125.9035
 JCX  H1   H  HCR6   0   0.242  13.0252  39.9053  129.7771
 JCX  H2   H  HCH1   0   0.173  13.4511  41.1789  127.8178
 JCX  H3   H  HCH1   0   0.222  11.6331  39.2771  126.3158
 JCX  H4   H  HCR6   0   0.241  11.9624  37.0604  126.7656
 JCX  H5   H  HCR6   0   0.246  13.7770  38.0818  131.2368
 JCX  H6   H  HCH3   0   0.232   9.9896  39.7648  128.1487
 JCX  H7   H  HCH3   0   0.218  11.0784  40.9948  128.7886
 JCX  H8   H  HCH3   0   0.227  10.3493  41.1923  127.1940
 JCX  H9   H  HCR6   0   0.246  12.7039  35.2289  128.2321
 JCX  H10  H  HCR6   0   0.247  13.6233  35.7281  130.4784
 JCX  H11  H  HNH2   0   0.338  12.0213  42.3181  126.3535
 JCX  H12  H  HNH2   0   0.338  13.4249  42.2171  125.5831
 JCX  C11  C  C      0   0.393  14.3161  39.8995  126.3089
 JCX  O12  O  OC    -1  -0.605  15.3942  39.9772  126.9316
 JCX  O13  O  O      0  -0.604  14.1022  39.2575  125.2618

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
 JCX  N01  C02  single    1.463  0.020  1.463
 JCX  O13  C11  deloc     1.247  0.020  1.247
 JCX  C11  O12  deloc     1.247  0.020  1.247
 JCX  C11  C02  single    1.549  0.020  1.549
 JCX  C02  C03  single    1.538  0.020  1.538
 JCX  C03  C04  single    1.530  0.020  1.530
 JCX  C03  C05  single    1.509  0.020  1.509
 JCX  C06  C05  aromatic  1.393  0.020  1.393
 JCX  C06  C07  aromatic  1.389  0.020  1.389
 JCX  C05  C10  aromatic  1.395  0.020  1.395
 JCX  C07  C08  aromatic  1.388  0.020  1.388
 JCX  C10  C09  aromatic  1.388  0.020  1.388
 JCX  C08  C09  aromatic  1.390  0.020  1.390
 JCX  C10  H1   single    0.930  0.020  1.080
 JCX  C02  H2   single    0.970  0.020  1.090
 JCX  C03  H3   single    0.970  0.020  1.090
 JCX  C06  H4   single    0.930  0.020  1.080
 JCX  C09  H5   single    0.930  0.020  1.080
 JCX  C04  H6   single    0.970  0.020  1.090
 JCX  C04  H7   single    0.970  0.020  1.090
 JCX  C04  H8   single    0.970  0.020  1.090
 JCX  C07  H9   single    0.930  0.020  1.080
 JCX  C08  H10  single    0.930  0.020  1.080
 JCX  N01  H11  single    0.890  0.020  1.040
 JCX  N01  H12  single    0.890  0.020  1.040

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
 JCX  H1   C10  C05  119.75  3.000
 JCX  H1   C10  C09  119.20  3.000
 JCX  C05  C10  C09  121.05  3.000
 JCX  H2   C02  N01  111.78  3.000
 JCX  H2   C02  C11  107.95  3.000
 JCX  N01  C02  C11  109.52  3.000
 JCX  H2   C02  C03  107.84  3.000
 JCX  C11  C02  C03  110.43  3.000
 JCX  N01  C02  C03  109.30  3.000
 JCX  H3   C03  C05  107.72  3.000
 JCX  H3   C03  C04  108.18  3.000
 JCX  C05  C03  C04  110.48  3.000
 JCX  H3   C03  C02  106.59  3.000
 JCX  C05  C03  C02  111.54  3.000
 JCX  C04  C03  C02  112.09  3.000
 JCX  H4   C06  C07  119.48  3.000
 JCX  H4   C06  C05  119.28  3.000
 JCX  C07  C06  C05  121.23  3.000
 JCX  H5   C09  C08  120.00  3.000
 JCX  H5   C09  C10  119.74  3.000
 JCX  C08  C09  C10  120.26  3.000
 JCX  H8   C04  H7   107.87  3.000
 JCX  H8   C04  H6   107.09  3.000
 JCX  H7   C04  H6   107.73  3.000
 JCX  H8   C04  C03  111.71  3.000
 JCX  H7   C04  C03  111.35  3.000
 JCX  H6   C04  C03  110.89  3.000
 JCX  C06  C05  C03  120.58  3.000
 JCX  C06  C05  C10  118.02  3.000
 JCX  C03  C05  C10  121.40  3.000
 JCX  H9   C07  C08  120.10  3.000
 JCX  H9   C07  C06  119.78  3.000
 JCX  C08  C07  C06  120.12  3.000
 JCX  H10  C08  C07  120.35  3.000
 JCX  H10  C08  C09  120.32  3.000
 JCX  C07  C08  C09  119.33  3.000
 JCX  H12  N01  H11  104.75  3.000
 JCX  H12  N01  C02  109.27  3.000
 JCX  H11  N01  C02  109.33  3.000
 JCX  O13  C11  O12  126.84  3.000
 JCX  O12  C11  C02  116.74  3.000
 JCX  O13  C11  C02  116.42  3.000

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
 JCX  CONST_01  C07  C06  C05  C10    0.00  0.0  0
 JCX  CONST_02  C07  C08  C09  C10    0.00  0.0  0
 JCX  CONST_03  C09  C10  C05  C06    0.00  0.0  0
 JCX  CONST_04  C09  C08  C07  C06    0.00  0.0  0
 JCX  CONST_05  C08  C07  C06  C05    0.00  0.0  0
 JCX  CONST_06  C08  C09  C10  C05    0.00  0.0  0
 JCX  CONST_07  C07  C06  C05  C03  180.00  0.0  0
 JCX  CONST_08  C09  C10  C05  C03  180.00  0.0  0
 JCX  CONST_09  H4   C06  C05  C10  180.00  0.0  0
 JCX  CONST_10  H10  C08  C09  C10  180.00  0.0  0
 JCX  CONST_11  H1   C10  C05  C06  180.00  0.0  0
 JCX  CONST_12  H10  C08  C07  C06  180.00  0.0  0
 JCX  CONST_13  H9   C07  C08  C09  180.00  0.0  0
 JCX  CONST_14  H9   C07  C06  C05  180.00  0.0  0
 JCX  CONST_15  H5   C09  C10  C05  180.00  0.0  0
 JCX  CONST_16  H5   C09  C08  C07  180.00  0.0  0
 JCX  CONST_17  H4   C06  C07  C08  180.00  0.0  0
 JCX  CONST_18  H1   C10  C09  C08  180.00  0.0  0

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
 JCX  chir_01  C02  N01  C11  C03  positiv
 JCX  chir_02  C03  C02  C04  C05  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
 JCX  plan-1  C10  0.020
 JCX  plan-1  C03  0.020
 JCX  plan-1  C06  0.020
 JCX  plan-1  C09  0.020
 JCX  plan-1  C05  0.020
 JCX  plan-1  C07  0.020
 JCX  plan-1  C08  0.020
 JCX  plan-1  H1   0.020
 JCX  plan-1  H4   0.020
 JCX  plan-1  H5   0.020
 JCX  plan-1  H9   0.020
 JCX  plan-1  H10  0.020
 JCX  plan-2  C02  0.020
 JCX  plan-2  C11  0.020
 JCX  plan-2  O12  0.020
 JCX  plan-2  O13  0.020

