# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 11:51:08 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: (2~{S},3~{S})-2-azanyl-3-[(2-nitrophenyl)methoxy]butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H](OCc1ccccc1[N](=O)=O)C(O)=O)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
 QJW  QJW  '(2~{S},3~{S})-2-azanyl-3-[(2-nitrophenyl)methoxy]butanedioic acid'  ligand  32  20  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QJW
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
 QJW  N1   N  NH2   0  -0.795  40.3982  16.0993  26.3948
 QJW  C4   C  CR16  0  -0.248  46.4609  13.9734  25.8399
 QJW  C5   C  CR6   0   0.183  45.1704  14.3884  26.1402
 QJW  C6   C  CR6   0   0.099  44.8664  15.6954  26.5095
 QJW  C7   C  CH2   0  -0.255  43.4817  16.2463  26.7168
 QJW  C8   C  CH1   0  -0.075  42.0227  17.7428  25.4757
 QJW  C10  C  CH1   0  -0.242  40.8494  16.7775  25.1979
 QJW  C1   C  CR16  0  -0.277  45.9348  16.5877  26.5784
 QJW  C11  C  C     0   0.555  41.3470  15.8311  24.1168
 QJW  C2   C  CR16  0  -0.219  47.2348  16.1905  26.3150
 QJW  C3   C  CR16  0  -0.267  47.5002  14.8797  25.9414
 QJW  C9   C  C     0   0.522  41.7438  18.7352  26.5972
 QJW  O1   O  O2    0  -0.484  43.2631  17.1196  25.6125
 QJW  O2   O  O     0  -0.418  42.5595  19.0932  27.4042
 QJW  O3   O  OH1   0  -0.589  40.5083  19.2079  26.5283
 QJW  O4   O  O     0  -0.443  41.5914  16.2067  22.9980
 QJW  O5   O  OH1   0  -0.575  41.4844  14.5789  24.5170
 QJW  O6   O  O     0  -0.367  43.3872  13.2552  27.0163
 QJW  O7   O  O     0  -0.370  44.1109  12.6586  25.0952
 QJW  H1   H  HNH2  0   0.364  39.8877  16.7538  26.9740
 QJW  H2   H  HNH2  0   0.365  39.7288  15.3776  26.1592
 QJW  H4   H  HCR6  0   0.295  46.6568  12.9487  25.5558
 QJW  H5   H  HCH2  0   0.246  43.4613  16.7916  27.6633
 QJW  H6   H  HCH2  0   0.265  42.7176  15.4784  26.7726
 QJW  H7   H  HCH1  0   0.318  42.1220  18.3626  24.5757
 QJW  H8   H  HCH1  0   0.289  40.0630  17.3705  24.7102
 QJW  H9   H  HCR6  0   0.272  45.7358  17.6169  26.8499
 QJW  H10  H  HCR6  0   0.276  48.0420  16.9056  26.3967
 QJW  H11  H  HCR6  0   0.279  48.5117  14.5606  25.7326
 QJW  H12  H  HOH1  0   0.491  40.3620  19.8784  27.2136
 QJW  H13  H  HOH1  0   0.484  41.7935  14.0315  23.7785
 QJW  N2   N  N     0   0.322  44.1368  13.3642  26.0755

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
 QJW  O4   C11  double    1.205  0.020  1.205
 QJW  O5   C11  single    1.322  0.020  1.322
 QJW  C11  C10  single    1.521  0.020  1.521
 QJW  C10  C8   single    1.544  0.020  1.544
 QJW  C10  N1   single    1.448  0.020  1.448
 QJW  O7   N2   double    1.208  0.020  1.208
 QJW  C8   O1   single    1.395  0.020  1.395
 QJW  C8   C9   single    1.523  0.020  1.523
 QJW  O1   C7   single    1.425  0.020  1.425
 QJW  C4   C3   aromatic  1.383  0.020  1.383
 QJW  C4   C5   aromatic  1.388  0.020  1.388
 QJW  C3   C2   aromatic  1.389  0.020  1.389
 QJW  N2   C5   single    1.457  0.020  1.457
 QJW  N2   O6   double    1.208  0.020  1.208
 QJW  C5   C6   aromatic  1.392  0.020  1.392
 QJW  C2   C1   aromatic  1.385  0.020  1.385
 QJW  O2   C9   double    1.202  0.020  1.202
 QJW  C6   C1   aromatic  1.394  0.020  1.394
 QJW  C6   C7   single    1.505  0.020  1.505
 QJW  C9   O3   single    1.325  0.020  1.325
 QJW  N1   H1   single    0.890  0.020  1.040
 QJW  N1   H2   single    0.890  0.020  1.040
 QJW  C4   H4   single    0.930  0.020  1.080
 QJW  C7   H5   single    0.970  0.020  1.090
 QJW  C7   H6   single    0.970  0.020  1.090
 QJW  C8   H7   single    0.970  0.020  1.090
 QJW  C10  H8   single    0.970  0.020  1.090
 QJW  C1   H9   single    0.930  0.020  1.080
 QJW  C2   H10  single    0.930  0.020  1.080
 QJW  C3   H11  single    0.930  0.020  1.080
 QJW  O3   H12  single    0.850  0.020  0.980
 QJW  O5   H13  single    0.850  0.020  0.980

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
 QJW  H2   N1   H1   105.11  3.000
 QJW  H2   N1   C10  110.35  3.000
 QJW  H1   N1   C10  109.11  3.000
 QJW  H4   C4   C3   120.28  3.000
 QJW  H4   C4   C5   120.56  3.000
 QJW  C3   C4   C5   119.13  3.000
 QJW  N2   C5   C6   121.14  3.000
 QJW  C6   C5   C4   122.76  3.000
 QJW  N2   C5   C4   116.09  3.000
 QJW  C1   C6   C7   117.66  3.000
 QJW  C7   C6   C5   125.55  3.000
 QJW  C1   C6   C5   116.55  3.000
 QJW  H6   C7   H5   107.19  3.000
 QJW  H6   C7   O1   111.45  3.000
 QJW  H5   C7   O1   111.26  3.000
 QJW  H6   C7   C6   113.34  3.000
 QJW  H5   C7   C6   108.62  3.000
 QJW  O1   C7   C6   105.00  3.000
 QJW  H7   C8   O1   104.62  3.000
 QJW  H7   C8   C9   104.62  3.000
 QJW  O1   C8   C9   112.43  3.000
 QJW  H7   C8   C10  105.92  3.000
 QJW  C9   C8   C10  113.61  3.000
 QJW  O1   C8   C10  114.46  3.000
 QJW  H8   C10  C11  104.74  3.000
 QJW  H8   C10  C8   106.63  3.000
 QJW  C11  C10  C8   105.56  3.000
 QJW  H8   C10  N1   113.37  3.000
 QJW  C8   C10  N1   112.39  3.000
 QJW  C11  C10  N1   113.46  3.000
 QJW  H9   C1   C2   119.52  3.000
 QJW  H9   C1   C6   118.69  3.000
 QJW  C2   C1   C6   121.78  3.000
 QJW  O5   C11  O4   123.72  3.000
 QJW  O5   C11  C10  114.11  3.000
 QJW  O4   C11  C10  122.17  3.000
 QJW  H10  C2   C3   120.12  3.000
 QJW  H10  C2   C1   119.79  3.000
 QJW  C3   C2   C1   120.09  3.000
 QJW  H11  C3   C2   120.62  3.000
 QJW  H11  C3   C4   119.71  3.000
 QJW  C2   C3   C4   119.66  3.000
 QJW  O3   C9   O2   124.17  3.000
 QJW  O3   C9   C8   111.40  3.000
 QJW  O2   C9   C8   124.34  3.000
 QJW  C8   O1   C7   119.10  3.000
 QJW  H12  O3   C9   110.52  3.000
 QJW  H13  O5   C11  109.71  3.000
 QJW  O7   N2   O6   124.47  3.000
 QJW  O6   N2   C5   117.99  3.000
 QJW  O7   N2   C5   117.51  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
 QJW  CONST_01  C1   C2  C3   C4      0.00   0.0  0
 QJW  CONST_02  C1   C6  C5   C4      0.00   0.0  0
 QJW  CONST_03  C2   C3  C4   C5      0.00   0.0  0
 QJW  CONST_04  C2   C1  C6   C5      0.00   0.0  0
 QJW  CONST_05  C3   C4  C5   C6      0.00   0.0  0
 QJW  CONST_06  C3   C2  C1   C6      0.00   0.0  0
 QJW  CONST_07  C7   C6  C5   C4    180.00   0.0  0
 QJW  CONST_08  C2   C1  C6   C7    180.00   0.0  0
 QJW  CONST_09  N2   C5  C6   C1    180.00   0.0  0
 QJW  CONST_10  N2   C5  C4   C3    180.00   0.0  0
 QJW  CONST_11  H10  C2  C3   C4    180.00   0.0  0
 QJW  CONST_12  H11  C3  C4   C5    180.00   0.0  0
 QJW  CONST_13  H9   C1  C6   C5    180.00   0.0  0
 QJW  CONST_14  H4   C4  C5   C6    180.00   0.0  0
 QJW  CONST_19  H12  O3  C9   C8    180.00   0.0  0
 QJW  CONST_20  H13  O5  C11  C10   180.00   0.0  0
 QJW  Var_01    O1   C7  C6   C5   -108.78  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
 QJW  chir_01  C8   C10  O1  C9   positiv
 QJW  chir_02  C10  N1   C8  C11  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
 QJW  plan-1  C4   0.020
 QJW  plan-1  C5   0.020
 QJW  plan-1  C6   0.020
 QJW  plan-1  C7   0.020
 QJW  plan-1  C1   0.020
 QJW  plan-1  C2   0.020
 QJW  plan-1  C3   0.020
 QJW  plan-1  H4   0.020
 QJW  plan-1  H9   0.020
 QJW  plan-1  H10  0.020
 QJW  plan-1  H11  0.020
 QJW  plan-1  N2   0.020
 QJW  plan-2  C5   0.020
 QJW  plan-2  O6   0.020
 QJW  plan-2  O7   0.020
 QJW  plan-2  N2   0.020
 QJW  plan-3  C10  0.020
 QJW  plan-3  C11  0.020
 QJW  plan-3  O4   0.020
 QJW  plan-3  O5   0.020
 QJW  plan-3  H13  0.020
 QJW  plan-4  C8   0.020
 QJW  plan-4  C9   0.020
 QJW  plan-4  O2   0.020
 QJW  plan-4  O3   0.020
 QJW  plan-4  H12  0.020

