# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:04:32 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: (1R,2R)-2-aminocyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCC[C@H]1C(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
 XZP  XZP  '(1R,2R)-2-aminocyclopentane-1-carboxylic acid'  ligand  19  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XZP
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
 XZP  O    O  O      0  -0.618  -1.9155  -0.1812  -0.9858
 XZP  C    C  C      0   0.410  -1.5386  -0.1465   0.2048
 XZP  CA   C  CH1    0  -0.343  -0.0714   0.2296   0.4492
 XZP  CB   C  CH1    0  -0.072   0.9214  -0.7241  -0.2153
 XZP  N    N  NH2    0  -0.794   0.8769  -2.0615   0.3467
 XZP  CG   C  CH2    0  -0.450   2.2447   0.0398  -0.1031
 XZP  CD   C  CH2    0  -0.447   1.8691   1.5020  -0.3786
 XZP  CE   C  CH2    0  -0.440   0.3448   1.5922  -0.1161
 XZP  O1   O  OC    -1  -0.622  -2.2472  -0.3876   1.2047
 XZP  H1   H  HCH1   0   0.192   0.1320   0.2156   1.5285
 XZP  H2   H  HCH1   0   0.206   0.6489  -0.8014  -1.2745
 XZP  H3   H  HNH2   0   0.338   1.5699  -2.6437  -0.1083
 XZP  H4   H  HNH2   0   0.328   1.1560  -2.0209   1.3210
 XZP  H6   H  HCH2   0   0.208   2.6259  -0.0729   0.9173
 XZP  H7   H  HCH2   0   0.222   3.0143  -0.3440  -0.7767
 XZP  H8   H  HCH2   0   0.223   2.4340   2.1873   0.2543
 XZP  H9   H  HCH2   0   0.220   2.0977   1.7779  -1.4093
 XZP  H10  H  HCH2   0   0.216  -0.1880   1.7731  -1.0514
 XZP  H11  H  HCH2   0   0.222   0.0866   2.4117   0.5569

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
 XZP  O   C    deloc   1.249  0.020  1.249
 XZP  C   CA   single  1.534  0.020  1.534
 XZP  N   CB   single  1.451  0.020  1.451
 XZP  CB  CA   single  1.529  0.020  1.529
 XZP  CB  CG   single  1.532  0.020  1.532
 XZP  CA  CE   single  1.533  0.020  1.533
 XZP  CG  CD   single  1.535  0.020  1.535
 XZP  CE  CD   single  1.549  0.020  1.549
 XZP  C   O1   deloc   1.249  0.020  1.249
 XZP  CA  H1   single  0.970  0.020  1.090
 XZP  CB  H2   single  0.970  0.020  1.090
 XZP  N   H3   single  0.890  0.020  1.040
 XZP  N   H4   single  0.890  0.020  1.040
 XZP  CG  H6   single  0.970  0.020  1.090
 XZP  CG  H7   single  0.970  0.020  1.090
 XZP  CD  H8   single  0.970  0.020  1.090
 XZP  CD  H9   single  0.970  0.020  1.090
 XZP  CE  H10  single  0.970  0.020  1.090
 XZP  CE  H11  single  0.970  0.020  1.090

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
 XZP  O1   C   CA   117.54  3.000
 XZP  O1   C   O    125.91  3.000
 XZP  CA   C   O    116.56  3.000
 XZP  H1   CA  CE   108.87  3.000
 XZP  H1   CA  CB   107.39  3.000
 XZP  CE   CA  CB   102.59  3.000
 XZP  H1   CA  C    109.30  3.000
 XZP  CE   CA  C    114.76  3.000
 XZP  CB   CA  C    113.51  3.000
 XZP  H2   CB  CG   108.70  3.000
 XZP  H2   CB  N    107.54  3.000
 XZP  CG   CB  N    117.23  3.000
 XZP  H2   CB  CA   107.61  3.000
 XZP  CG   CB  CA   102.60  3.000
 XZP  N    CB  CA   112.75  3.000
 XZP  H4   N   H3   105.44  3.000
 XZP  H4   N   CB   109.06  3.000
 XZP  H3   N   CB   109.56  3.000
 XZP  H7   CG  H6   107.05  3.000
 XZP  H7   CG  CD   113.36  3.000
 XZP  H6   CG  CD   110.52  3.000
 XZP  H7   CG  CB   112.84  3.000
 XZP  H6   CG  CB   108.51  3.000
 XZP  CD   CG  CB   104.51  3.000
 XZP  H9   CD  H8   106.31  3.000
 XZP  H9   CD  CE   110.57  3.000
 XZP  H8   CD  CE   112.00  3.000
 XZP  H9   CD  CG   111.05  3.000
 XZP  H8   CD  CG   111.58  3.000
 XZP  CE   CD  CG   105.42  3.000
 XZP  H11  CE  H10  106.77  3.000
 XZP  H11  CE  CD   112.39  3.000
 XZP  H10  CE  CD   110.17  3.000
 XZP  H11  CE  CA   112.08  3.000
 XZP  H10  CE  CA   109.31  3.000
 XZP  CD   CE  CA   106.13  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
 XZP  Var_01  CG  CD  CE  CA   6.19  30.0  1
 XZP  Var_02  CE  CD  CG  CB  20.37  30.0  1

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
 XZP  chir_01  CA  C  CB  CE  negativ
 XZP  chir_02  CB  N  CA  CG  negativ

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
 XZP  plan-1  O   0.020
 XZP  plan-1  C   0.020
 XZP  plan-1  CA  0.020
 XZP  plan-1  O1  0.020

