# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 07:26:32 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: (4R)-4-({[(E)-(3,4-dimethoxyphenyl)methylidene]amino}oxy)-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(/C=N/O[C@H]2CN[C@@H](C2)C(O)=O)cc1OC
#
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
 ZYJ  ZYJ  (4R)-4-({[(E)-(3,4-dimethoxyphenyl)methylidene]amino}oxy)-L-proline  L-peptide  38  21  .  2019-03-22  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_ZYJ
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
 ZYJ  C     C  C      0   0.427   0.1401   4.3047   0.5965
 ZYJ  N     N  NH1    0  -0.584  -2.1742   3.5031   0.5845
 ZYJ  O     O  O      0  -0.599   0.9470   3.4577   0.1586
 ZYJ  N1    N  N      0  -0.086  -1.6605  -0.5285   2.5289
 ZYJ  O2    O  O2     0  -0.399  -2.0878   0.4171   1.6709
 ZYJ  C4    C  CH3    0  -0.439   4.0216  -1.7200   5.0266
 ZYJ  C6    C  CR6    0   0.260   0.9538  -3.5957   5.5603
 ZYJ  C7    C  CR6    0   0.351   1.8267  -2.6112   5.0717
 ZYJ  C9    C  CR16   0  -0.306  -0.3737  -3.5919   5.1641
 ZYJ  CA    C  CH1    0  -0.261  -1.0290   3.7777   1.4621
 ZYJ  CB    C  CH2    0  -0.467  -0.7313   2.4415   2.1558
 ZYJ  CD    C  CH2    0  -0.338  -1.9285   2.1678   0.0609
 ZYJ  CG    C  CH1    0  -0.013  -1.1610   1.3744   1.1374
 ZYJ  C10   C  CR16   0  -0.455   1.3364  -1.6447   4.2020
 ZYJ  C11   C  CR16   0  -0.322  -0.8614  -2.6250   4.2988
 ZYJ  C12   C  CR6    0   0.114  -0.0044  -1.6441   3.8098
 ZYJ  C13   C  C1     0  -0.130  -0.4426  -0.5877   2.8920
 ZYJ  C14   C  CH3    0  -0.408   1.9976  -5.6705   5.8170
 ZYJ  O51   O  OC    -1  -0.610   0.1566   5.5327   0.3840
 ZYJ  HN    H  HNH1   0   0.344  -3.0119   3.4758   1.1546
 ZYJ  H4    H  HCH3   0   0.261   4.9799  -1.9660   5.4772
 ZYJ  H4A   H  HCH3   0   0.229   4.1251  -1.7568   3.9389
 ZYJ  H4B   H  HCH3   0   0.230   3.7445  -0.7042   5.3202
 ZYJ  H9    H  HCR6   0   0.265  -1.0356  -4.3565   5.5522
 ZYJ  HA    H  HCH1   0   0.225  -1.3142   4.5482   2.1818
 ZYJ  HB    H  HCH2   0   0.237   0.3079   2.3453   2.4679
 ZYJ  HBA   H  HCH2   0   0.237  -1.3516   2.3545   3.0526
 ZYJ  HD    H  HCH2   0   0.243  -2.8626   1.6793  -0.2190
 ZYJ  HDA   H  HCH2   0   0.234  -1.3161   2.2273  -0.8394
 ZYJ  HG    H  HCH1   0   0.240  -0.3100   0.8434   0.6998
 ZYJ  H10   H  HCR6   0   0.282   1.9892  -0.8727   3.8136
 ZYJ  H11   H  HCR6   0   0.250  -1.9022  -2.6395   4.0064
 ZYJ  H13   H  H      0   0.253   0.3286   0.1064   2.5670
 ZYJ  H14   H  HCH3   0   0.238   2.3423  -6.3265   6.6141
 ZYJ  H14A  H  HCH3   0   0.220   1.2697  -6.2118   5.2064
 ZYJ  H14B  H  HCH3   0   0.223   2.8507  -5.4035   5.1889
 ZYJ  O5    O  O2     0  -0.485   1.4115  -4.5319   6.4335
 ZYJ  O4    O  O2     0  -0.461   3.0974  -2.6781   5.5024

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
 ZYJ  C    O     deloc     1.231  0.020  1.231
 ZYJ  C    CA    single    1.525  0.021  1.525
 ZYJ  C    O51   deloc     1.246  0.020  1.246
 ZYJ  N    CA    single    1.466  0.015  1.466
 ZYJ  N    CD    single    1.473  0.014  1.473
 ZYJ  N    HN    single    0.890  0.020  1.040
 ZYJ  N1   O2    single    1.346  0.020  1.346
 ZYJ  N1   C13   double    1.272  0.020  1.272
 ZYJ  O2   CG    single    1.435  0.020  1.435
 ZYJ  C4   O4    single    1.414  0.020  1.414
 ZYJ  C4   H4    single    0.970  0.020  1.090
 ZYJ  C4   H4A   single    0.970  0.020  1.090
 ZYJ  C4   H4B   single    0.970  0.020  1.090
 ZYJ  O4   C7    single    1.343  0.020  1.343
 ZYJ  O5   C6    single    1.360  0.020  1.360
 ZYJ  O5   C14   single    1.421  0.020  1.421
 ZYJ  C6   C7    aromatic  1.404  0.020  1.404
 ZYJ  C6   C9    aromatic  1.385  0.020  1.385
 ZYJ  C7   C10   aromatic  1.390  0.020  1.390
 ZYJ  C9   C11   aromatic  1.386  0.020  1.386
 ZYJ  C9   H9    single    0.930  0.020  1.080
 ZYJ  CA   CB    single    1.530  0.020  1.530
 ZYJ  CA   HA    single    0.970  0.020  0.970
 ZYJ  CB   CG    single    1.536  0.020  1.536
 ZYJ  CB   HB    single    0.970  0.020  1.090
 ZYJ  CB   HBA   single    0.970  0.020  1.090
 ZYJ  CD   CG    single    1.542  0.020  1.542
 ZYJ  CD   HD    single    0.970  0.020  1.090
 ZYJ  CD   HDA   single    0.970  0.020  1.090
 ZYJ  CG   HG    single    0.970  0.020  1.090
 ZYJ  C10  C12   aromatic  1.397  0.020  1.397
 ZYJ  C10  H10   single    0.930  0.020  1.080
 ZYJ  C11  C12   aromatic  1.391  0.020  1.391
 ZYJ  C11  H11   single    0.930  0.020  1.080
 ZYJ  C12  C13   single    1.466  0.020  1.466
 ZYJ  C13  H13   single    0.930  0.020  1.080
 ZYJ  C14  H14   single    0.970  0.020  1.090
 ZYJ  C14  H14A  single    0.970  0.020  1.090
 ZYJ  C14  H14B  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
 ZYJ  O51   C    CA    116.17  3.000
 ZYJ  O51   C    O     126.86  3.000
 ZYJ  CA    C    O     119.00  3.000
 ZYJ  HN    N    CD    108.50  3.000
 ZYJ  HN    N    CA    108.26  3.000
 ZYJ  CD    N    CA    104.77  3.000
 ZYJ  C13   N1   O2    121.22  3.000
 ZYJ  CG    O2   N1    120.02  3.000
 ZYJ  H4B   C4   H4A   108.81  3.000
 ZYJ  H4B   C4   H4    108.81  3.000
 ZYJ  H4A   C4   H4    108.75  3.000
 ZYJ  H4B   C4   O4    111.94  3.000
 ZYJ  H4A   C4   O4    111.96  3.000
 ZYJ  H4    C4   O4    106.46  3.000
 ZYJ  C9    C6   C7    119.64  3.000
 ZYJ  C9    C6   O5    120.54  3.000
 ZYJ  C7    C6   O5    119.81  3.000
 ZYJ  C10   C7   C6    119.10  3.000
 ZYJ  C10   C7   O4    124.69  3.000
 ZYJ  C6    C7   O4    116.22  3.000
 ZYJ  H9    C9   C11   120.07  3.000
 ZYJ  H9    C9   C6    118.76  3.000
 ZYJ  C11   C9   C6    121.17  3.000
 ZYJ  HA    CA   CB    109.00  3.000
 ZYJ  HA    CA   N     110.00  3.000
 ZYJ  CB    CA   N     103.00  1.100
 ZYJ  HA    CA   C     109.00  3.000
 ZYJ  CB    CA   C     110.10  1.900
 ZYJ  N     CA   C     112.10  2.500
 ZYJ  HBA   CB   HB    107.40  3.000
 ZYJ  HBA   CB   CG    109.24  3.000
 ZYJ  HB    CB   CG    113.28  3.000
 ZYJ  HBA   CB   CA    109.26  3.000
 ZYJ  HB    CB   CA    113.05  3.000
 ZYJ  CG    CB   CA    104.53  3.000
 ZYJ  HDA   CD   HD    107.07  3.000
 ZYJ  HDA   CD   CG    108.97  3.000
 ZYJ  HD    CD   CG    112.02  3.000
 ZYJ  HDA   CD   N     109.99  3.000
 ZYJ  HD    CD   N     111.02  3.000
 ZYJ  CG    CD   N     103.20  1.500
 ZYJ  HG    CG   CD    110.95  3.000
 ZYJ  HG    CG   CB    112.62  3.000
 ZYJ  CD    CG   CB    104.16  3.000
 ZYJ  HG    CG   O2    109.10  3.000
 ZYJ  CD    CG   O2    106.34  3.000
 ZYJ  CB    CG   O2    113.42  3.000
 ZYJ  H10   C10  C12   118.53  3.000
 ZYJ  H10   C10  C7    120.50  3.000
 ZYJ  C12   C10  C7    120.97  3.000
 ZYJ  H11   C11  C12   120.49  3.000
 ZYJ  H11   C11  C9    119.87  3.000
 ZYJ  C12   C11  C9    119.63  3.000
 ZYJ  C13   C12  C11   122.94  3.000
 ZYJ  C13   C12  C10   117.57  3.000
 ZYJ  C11   C12  C10   119.49  3.000
 ZYJ  H13   C13  C12   115.79  3.000
 ZYJ  H13   C13  N1    124.33  3.000
 ZYJ  C12   C13  N1    119.88  3.000
 ZYJ  H14B  C14  H14A  108.65  3.000
 ZYJ  H14B  C14  H14   108.73  3.000
 ZYJ  H14A  C14  H14   108.75  3.000
 ZYJ  H14B  C14  O5    112.06  3.000
 ZYJ  H14A  C14  O5    111.36  3.000
 ZYJ  H14   C14  O5    107.20  3.000
 ZYJ  C14   O5   C6    114.32  3.000
 ZYJ  C7    O4   C4    118.47  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
 ZYJ  CONST_01  C12  C10  C7   C6     0.00   0.0  0
 ZYJ  CONST_02  C12  C11  C9   C6     0.00   0.0  0
 ZYJ  CONST_03  C11  C9   C6   C7     0.00   0.0  0
 ZYJ  CONST_04  C11  C12  C10  C7     0.00   0.0  0
 ZYJ  CONST_05  C10  C7   C6   C9     0.00   0.0  0
 ZYJ  CONST_06  C10  C12  C11  C9     0.00   0.0  0
 ZYJ  CONST_07  C9   C6   C7   O4   180.00   0.0  0
 ZYJ  CONST_08  C12  C10  C7   O4   180.00   0.0  0
 ZYJ  CONST_09  C10  C7   C6   O5   180.00   0.0  0
 ZYJ  CONST_10  C11  C9   C6   O5   180.00   0.0  0
 ZYJ  CONST_11  C13  C12  C10  C7   180.00   0.0  0
 ZYJ  CONST_12  C13  C12  C11  C9   180.00   0.0  0
 ZYJ  CONST_13  H10  C10  C7   C6   180.00   0.0  0
 ZYJ  CONST_14  H11  C11  C9   C6   180.00   0.0  0
 ZYJ  CONST_15  H9   C9   C6   C7   180.00   0.0  0
 ZYJ  Var_01    CG   CD   N    CA    31.31  30.0  1
 ZYJ  Var_02    C10  C12  C13  N1  -178.50  30.0  2
 ZYJ  Var_03    C6   C7   O4   C4   179.19  30.0  2
 ZYJ  Var_04    C12  C13  N1   O2  -178.94   0.0  2
 ZYJ  Var_05    H14  C14  O5   C6   178.66  30.0  3
 ZYJ  Var_06    H4   C4   O4   C7  -178.85  30.0  3

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
 ZYJ  chir_01  CA  C   N   CB  negativ
 ZYJ  chir_02  CG  O2  CB  CD  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
 ZYJ  plan-1  C6   0.020
 ZYJ  plan-1  C7   0.020
 ZYJ  plan-1  C9   0.020
 ZYJ  plan-1  C10  0.020
 ZYJ  plan-1  C11  0.020
 ZYJ  plan-1  C12  0.020
 ZYJ  plan-1  C13  0.020
 ZYJ  plan-1  H9   0.020
 ZYJ  plan-1  H10  0.020
 ZYJ  plan-1  H11  0.020
 ZYJ  plan-1  O5   0.020
 ZYJ  plan-1  O4   0.020
 ZYJ  plan-2  C    0.020
 ZYJ  plan-2  O    0.020
 ZYJ  plan-2  CA   0.020
 ZYJ  plan-2  O51  0.020
 ZYJ  plan-3  N1   0.020
 ZYJ  plan-3  O2   0.020
 ZYJ  plan-3  C12  0.020
 ZYJ  plan-3  C13  0.020
 ZYJ  plan-3  H13  0.020

