# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 09:01:40 2022
#   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  30  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.809  40.4827  16.9284  26.8630
 QJW  C4   C  CR16   0  -0.249  46.7069  14.3693  25.6928
 QJW  C5   C  CR6    0   0.192  45.3611  14.6972  25.7053
 QJW  C6   C  CR6    0   0.098  44.8177  15.6399  26.5745
 QJW  C7   C  CH2    0  -0.173  43.3765  16.0747  26.5296
 QJW  C8   C  CH1    0  -0.076  41.9911  17.2582  24.9353
 QJW  C10  C  CH1    0  -0.243  40.6355  16.7441  25.4274
 QJW  C1   C  CR16   0  -0.321  45.7012  16.2436  27.4628
 QJW  C11  C  C      0   0.416  40.4008  15.2781  24.9881
 QJW  C2   C  CR16   0  -0.217  47.0472  15.9058  27.4985
 QJW  C3   C  CR16   0  -0.273  47.5540  14.9695  26.6101
 QJW  C9   C  C      0   0.385  42.2558  18.7220  25.3753
 QJW  O1   O  O2     0  -0.504  43.0768  16.3874  25.1935
 QJW  O2   O  O      0  -0.592  43.3947  19.0175  25.7799
 QJW  O3   O  OC    -1  -0.611  41.2879  19.4990  25.2319
 QJW  O4   O  O      0  -0.612  40.5300  15.0527  23.7685
 QJW  O5   O  OC    -1  -0.603  40.0657  14.4555  25.8649
 QJW  O6   O  O      0  -0.367  43.5398  13.4113  25.2106
 QJW  O7   O  O      0  -0.374  44.8533  13.9452  23.6105
 QJW  H1   H  HNH2   0   0.328  40.0820  17.8370  27.0495
 QJW  H2   H  HNH2   0   0.329  39.8373  16.2315  27.2093
 QJW  H4   H  HCR6   0   0.288  47.0896  13.6368  24.9948
 QJW  H5   H  HCH2   0   0.221  43.2547  16.9290  27.1965
 QJW  H6   H  HCH2   0   0.210  42.7298  15.2811  26.9166
 QJW  H7   H  HCH1   0   0.216  41.9354  17.2732  23.8407
 QJW  H8   H  HCH1   0   0.202  39.8877  17.3274  24.8708
 QJW  H9   H  HCR6   0   0.267  45.3226  17.0027  28.1355
 QJW  H10  H  HCR6   0   0.269  47.7024  16.3890  28.2111
 QJW  H11  H  HCR6   0   0.271  48.6031  14.7077  26.6233
 QJW  N2   N  N      0   0.331  44.5100  13.9753  24.7679

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  deloc     1.247  0.020  1.247
 QJW  O5   C11  deloc     1.248  0.020  1.248
 QJW  C11  C10  single    1.548  0.020  1.548
 QJW  C10  C8   single    1.531  0.020  1.531
 QJW  C10  N1   single    1.455  0.020  1.455
 QJW  O7   N2   double    1.208  0.020  1.208
 QJW  C8   O1   single    1.416  0.020  1.416
 QJW  C8   C9   single    1.551  0.020  1.551
 QJW  O1   C7   single    1.405  0.020  1.405
 QJW  C4   C3   aromatic  1.385  0.020  1.385
 QJW  C4   C5   aromatic  1.385  0.020  1.385
 QJW  C3   C2   aromatic  1.387  0.020  1.387
 QJW  N2   C5   single    1.457  0.020  1.457
 QJW  N2   O6   double    1.206  0.020  1.206
 QJW  C5   C6   aromatic  1.393  0.020  1.393
 QJW  C2   C1   aromatic  1.388  0.020  1.388
 QJW  O2   C9   deloc     1.244  0.020  1.244
 QJW  C6   C1   aromatic  1.391  0.020  1.391
 QJW  C6   C7   single    1.506  0.020  1.506
 QJW  C9   O3   deloc     1.249  0.020  1.249
 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

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   107.66  3.000
 QJW  H2   N1   C10  108.52  3.000
 QJW  H1   N1   C10  109.73  3.000
 QJW  H4   C4   C3   120.28  3.000
 QJW  H4   C4   C5   120.65  3.000
 QJW  C3   C4   C5   119.05  3.000
 QJW  N2   C5   C6   120.59  3.000
 QJW  C6   C5   C4   123.02  3.000
 QJW  N2   C5   C4   116.38  3.000
 QJW  C1   C6   C7   120.11  3.000
 QJW  C7   C6   C5   123.38  3.000
 QJW  C1   C6   C5   116.40  3.000
 QJW  H6   C7   H5   106.61  3.000
 QJW  H6   C7   O1   111.82  3.000
 QJW  H5   C7   O1   112.55  3.000
 QJW  H6   C7   C6   110.22  3.000
 QJW  H5   C7   C6   108.35  3.000
 QJW  O1   C7   C6   107.26  3.000
 QJW  H7   C8   O1   103.27  3.000
 QJW  H7   C8   C9   106.20  3.000
 QJW  O1   C8   C9   113.44  3.000
 QJW  H7   C8   C10  106.29  3.000
 QJW  C9   C8   C10  112.14  3.000
 QJW  O1   C8   C10  114.45  3.000
 QJW  H8   C10  C11  104.81  3.000
 QJW  H8   C10  C8   105.15  3.000
 QJW  C11  C10  C8   111.16  3.000
 QJW  H8   C10  N1   111.14  3.000
 QJW  C8   C10  N1   111.56  3.000
 QJW  C11  C10  N1   112.57  3.000
 QJW  H9   C1   C2   119.58  3.000
 QJW  H9   C1   C6   118.63  3.000
 QJW  C2   C1   C6   121.79  3.000
 QJW  O5   C11  O4   126.57  3.000
 QJW  O5   C11  C10  117.74  3.000
 QJW  O4   C11  C10  115.66  3.000
 QJW  H10  C2   C3   120.14  3.000
 QJW  H10  C2   C1   119.70  3.000
 QJW  C3   C2   C1   120.15  3.000
 QJW  H11  C3   C2   120.68  3.000
 QJW  H11  C3   C4   119.76  3.000
 QJW  C2   C3   C4   119.56  3.000
 QJW  O3   C9   O2   126.78  3.000
 QJW  O3   C9   C8   114.96  3.000
 QJW  O2   C9   C8   118.20  3.000
 QJW  C8   O1   C7   118.30  3.000
 QJW  O7   N2   O6   124.66  3.000
 QJW  O6   N2   C5   117.71  3.000
 QJW  O7   N2   C5   117.57  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  Var_01    O1   C7  C6  C5  -49.01  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-4  C8   0.020
 QJW  plan-4  C9   0.020
 QJW  plan-4  O2   0.020
 QJW  plan-4  O3   0.020

