# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 13:12:45 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: (4R)-4-{[(3,4-dimethoxybenzoyl)amino]oxy}-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)C(=O)NO[C@H]2CN[C@@H](C2)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
 ZYK  ZYK  (4R)-4-{[(3,4-dimethoxybenzoyl)amino]oxy}-L-proline  L-peptide  39  22  .  2019-03-22  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZYK
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
 ZYK  C    C  C      0   0.389   4.1035  -1.2170  -0.9337
 ZYK  N    N  NH1    0  -0.613   2.4891  -1.6316   0.9606
 ZYK  O    O  O      0  -0.613   4.4965  -0.3972  -1.7899
 ZYK  C1   C  C      0   0.508  -1.2237   1.2318   2.4829
 ZYK  N1   N  NH1    0  -0.395   0.0978   1.5113   2.6146
 ZYK  O1   O  O2     0  -0.388   0.8821   1.4955   1.4977
 ZYK  C2   C  CR6    0  -0.057  -2.0146   1.4511   3.7255
 ZYK  O2   O  O      0  -0.457  -1.7229   0.8181   1.4523
 ZYK  C3   C  CR16   0  -0.409  -3.3888   1.6797   3.5877
 ZYK  C4   C  CR16   0  -0.297  -1.4580   1.4056   4.9926
 ZYK  C5   C  CR16   0  -0.371  -2.2525   1.6097   6.1165
 ZYK  C6   C  CR6    0   0.320  -3.6090   1.8598   5.9859
 ZYK  C7   C  CH3    0  -0.438  -3.9307   2.0801   8.3185
 ZYK  C8   C  CR6    0   0.332  -4.1861   1.8903   4.6953
 ZYK  C9   C  CH3    0  -0.439  -6.1453   2.1625   3.3990
 ZYK  CA   C  CH1    0  -0.186   2.8098  -0.8230  -0.2049
 ZYK  CB   C  CH2    0  -0.486   2.8239   0.5947   0.3843
 ZYK  CD   C  CH2    0  -0.308   1.3916  -0.9352   1.5999
 ZYK  CG   C  CH1    0   0.058   1.9073   0.5090   1.6128
 ZYK  O6   O  OC    -1  -0.600   4.6264  -2.3073  -0.6391
 ZYK  HN   H  HNH1   0   0.339   2.2489  -2.5814   0.7120
 ZYK  HN1  H  HNH1   0   0.412   0.4107   2.1749   3.3121
 ZYK  H3   H  HCR6   0   0.284  -3.8140   1.6986   2.5935
 ZYK  H4   H  HCR6   0   0.262  -0.4077   1.1907   5.1394
 ZYK  H5   H  HCR6   0   0.288  -1.7909   1.5622   7.0931
 ZYK  H7   H  HCH3   0   0.261  -4.7686   2.2812   8.9809
 ZYK  H7A  H  HCH3   0   0.231  -3.4920   1.1154   8.5860
 ZYK  H7B  H  HCH3   0   0.231  -3.1774   2.8604   8.4544
 ZYK  H9   H  HCH3   0   0.261  -7.1946   2.3737   3.5894
 ZYK  H9A  H  HCH3   0   0.229  -5.7383   2.9480   2.7568
 ZYK  H9B  H  HCH3   0   0.229  -6.0688   1.2052   2.8762
 ZYK  HA   H  HCH1   0   0.201   1.9952  -0.8625  -0.9521
 ZYK  HB   H  HCH2   0   0.240   3.8303   0.8859   0.6864
 ZYK  HBA  H  HCH2   0   0.239   2.4730   1.3397  -0.3296
 ZYK  HD   H  HCH2   0   0.197   0.4550  -0.9710   1.0221
 ZYK  HDA  H  HCH2   0   0.230   1.1893  -1.3289   2.5977
 ZYK  HG   H  HCH1   0   0.230   2.4752   0.7000   2.5294
 ZYK  O3   O  O2     0  -0.453  -4.4520   2.0757   7.0040
 ZYK  O4   O  O2     0  -0.460  -5.5083   2.1292   4.6596

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
 ZYK  C   O    deloc     1.231  0.020  1.231
 ZYK  C   CA   single    1.525  0.021  1.525
 ZYK  C   O6   deloc     1.245  0.020  1.245
 ZYK  N   CA   single    1.466  0.015  1.466
 ZYK  N   CD   single    1.473  0.014  1.473
 ZYK  N   HN   single    0.890  0.020  1.040
 ZYK  C1  N1   single    1.357  0.020  1.357
 ZYK  C1  C2   single    1.489  0.020  1.489
 ZYK  C1  O2   double    1.218  0.020  1.218
 ZYK  N1  O1   single    1.365  0.020  1.365
 ZYK  N1  HN1  single    0.890  0.020  1.040
 ZYK  O1  CG   single    1.427  0.020  1.427
 ZYK  C2  C3   aromatic  1.400  0.020  1.400
 ZYK  C2  C4   aromatic  1.385  0.020  1.385
 ZYK  C3  C8   aromatic  1.381  0.020  1.381
 ZYK  C3  H3   single    0.930  0.020  1.080
 ZYK  O3  C6   single    1.339  0.020  1.339
 ZYK  O3  C7   single    1.414  0.020  1.414
 ZYK  C4  C5   aromatic  1.391  0.020  1.391
 ZYK  C4  H4   single    0.930  0.020  1.080
 ZYK  O4  C8   single    1.344  0.020  1.344
 ZYK  O4  C9   single    1.413  0.020  1.413
 ZYK  C5  C6   aromatic  1.385  0.020  1.385
 ZYK  C5  H5   single    0.930  0.020  1.080
 ZYK  C6  C8   aromatic  1.414  0.020  1.414
 ZYK  C7  H7   single    0.970  0.020  1.090
 ZYK  C7  H7A  single    0.970  0.020  1.090
 ZYK  C7  H7B  single    0.970  0.020  1.090
 ZYK  C9  H9   single    0.970  0.020  1.090
 ZYK  C9  H9A  single    0.970  0.020  1.090
 ZYK  C9  H9B  single    0.970  0.020  1.090
 ZYK  CA  CB   single    1.530  0.020  1.530
 ZYK  CA  HA   single    0.970  0.020  0.970
 ZYK  CB  CG   single    1.535  0.020  1.535
 ZYK  CB  HB   single    0.970  0.020  1.090
 ZYK  CB  HBA  single    0.970  0.020  1.090
 ZYK  CD  CG   single    1.533  0.020  1.533
 ZYK  CD  HD   single    0.970  0.020  1.090
 ZYK  CD  HDA  single    0.970  0.020  1.090
 ZYK  CG  HG   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
 ZYK  O6   C   CA   117.79  3.000
 ZYK  O6   C   O    127.24  3.000
 ZYK  CA   C   O    119.00  3.000
 ZYK  HN   N   CD   112.35  3.000
 ZYK  HN   N   CA   112.19  3.000
 ZYK  CD   N   CA   104.68  3.000
 ZYK  O2   C1  C2   122.59  3.000
 ZYK  O2   C1  N1   123.46  3.000
 ZYK  C2   C1  N1   113.94  3.000
 ZYK  HN1  N1  O1   113.19  3.000
 ZYK  HN1  N1  C1   120.19  3.000
 ZYK  O1   N1  C1   118.54  3.000
 ZYK  CG   O1  N1   110.78  3.000
 ZYK  C4   C2  C3   119.34  3.000
 ZYK  C4   C2  C1   123.04  3.000
 ZYK  C3   C2  C1   117.60  3.000
 ZYK  H3   C3  C8   120.52  3.000
 ZYK  H3   C3  C2   118.63  3.000
 ZYK  C8   C3  C2   120.85  3.000
 ZYK  H4   C4  C5   118.28  3.000
 ZYK  H4   C4  C2   121.39  3.000
 ZYK  C5   C4  C2   120.32  3.000
 ZYK  H5   C5  C6   120.73  3.000
 ZYK  H5   C5  C4   118.65  3.000
 ZYK  C6   C5  C4   120.63  3.000
 ZYK  C8   C6  C5   119.31  3.000
 ZYK  C8   C6  O3   115.68  3.000
 ZYK  C5   C6  O3   125.01  3.000
 ZYK  H7B  C7  H7A  108.85  3.000
 ZYK  H7B  C7  H7   108.87  3.000
 ZYK  H7A  C7  H7   108.88  3.000
 ZYK  H7B  C7  O3   111.82  3.000
 ZYK  H7A  C7  O3   111.89  3.000
 ZYK  H7   C7  O3   106.43  3.000
 ZYK  C6   C8  O4   115.44  3.000
 ZYK  C6   C8  C3   119.54  3.000
 ZYK  O4   C8  C3   125.01  3.000
 ZYK  H9B  C9  H9A  108.79  3.000
 ZYK  H9B  C9  H9   108.75  3.000
 ZYK  H9A  C9  H9   108.83  3.000
 ZYK  H9B  C9  O4   111.99  3.000
 ZYK  H9A  C9  O4   111.92  3.000
 ZYK  H9   C9  O4   106.46  3.000
 ZYK  HA   CA  CB   109.00  3.000
 ZYK  HA   CA  N    110.00  3.000
 ZYK  CB   CA  N    103.00  1.100
 ZYK  HA   CA  C    109.00  3.000
 ZYK  CB   CA  C    110.10  1.900
 ZYK  N    CA  C    112.10  2.500
 ZYK  HBA  CB  HB   107.22  3.000
 ZYK  HBA  CB  CG   111.72  3.000
 ZYK  HB   CB  CG   110.14  3.000
 ZYK  HBA  CB  CA   112.14  3.000
 ZYK  HB   CB  CA   111.19  3.000
 ZYK  CG   CB  CA   104.48  3.000
 ZYK  HDA  CD  HD   108.08  3.000
 ZYK  HDA  CD  CG   113.22  3.000
 ZYK  HD   CD  CG   108.73  3.000
 ZYK  HDA  CD  N    111.74  3.000
 ZYK  HD   CD  N    113.41  3.000
 ZYK  CG   CD  N    103.20  1.500
 ZYK  HG   CG  CD   110.23  3.000
 ZYK  HG   CG  CB   110.51  3.000
 ZYK  CD   CG  CB   104.28  3.000
 ZYK  HG   CG  O1   108.63  3.000
 ZYK  CD   CG  O1   114.12  3.000
 ZYK  CB   CG  O1   109.01  3.000
 ZYK  C7   O3  C6   118.36  3.000
 ZYK  C9   O4  C8   118.13  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
 ZYK  CONST_01  C6  C8  C3  C2     0.00   0.0  0
 ZYK  CONST_02  C6  C5  C4  C2     0.00   0.0  0
 ZYK  CONST_03  C5  C4  C2  C3     0.00   0.0  0
 ZYK  CONST_04  C5  C6  C8  C3     0.00   0.0  0
 ZYK  CONST_05  C8  C3  C2  C4     0.00   0.0  0
 ZYK  CONST_06  C8  C6  C5  C4     0.00   0.0  0
 ZYK  CONST_07  C8  C3  C2  C1   180.00   0.0  0
 ZYK  CONST_08  C5  C4  C2  C1   180.00   0.0  0
 ZYK  CONST_09  O4  C8  C3  C2   180.00   0.0  0
 ZYK  CONST_10  O3  C6  C8  C3   180.00   0.0  0
 ZYK  CONST_11  C4  C5  C6  O3   180.00   0.0  0
 ZYK  CONST_12  C5  C6  C8  O4   180.00   0.0  0
 ZYK  CONST_13  H5  C5  C4  C2   180.00   0.0  0
 ZYK  CONST_14  H4  C4  C2  C3   180.00   0.0  0
 ZYK  CONST_15  H3  C3  C2  C4   180.00   0.0  0
 ZYK  CONST_16  C2  C1  N1  O1   180.00   0.0  0
 ZYK  CONST_18  O2  C1  N1  O1     0.00   0.0  0
 ZYK  Var_01    CG  CD  N   CA   -47.33  30.0  1
 ZYK  Var_02    C3  C2  C1  N1   156.67  30.0  2
 ZYK  Var_03    C8  C6  O3  C7  -178.96  30.0  2
 ZYK  Var_04    H7  C7  O3  C6   179.39  30.0  3
 ZYK  Var_05    H9  C9  O4  C8  -179.62  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
 ZYK  chir_01  CA  C   N   CB  negativ
 ZYK  chir_02  CG  O1  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
 ZYK  plan-1  C1   0.020
 ZYK  plan-1  C2   0.020
 ZYK  plan-1  C3   0.020
 ZYK  plan-1  C4   0.020
 ZYK  plan-1  C5   0.020
 ZYK  plan-1  C6   0.020
 ZYK  plan-1  C8   0.020
 ZYK  plan-1  H3   0.020
 ZYK  plan-1  H4   0.020
 ZYK  plan-1  H5   0.020
 ZYK  plan-1  O3   0.020
 ZYK  plan-1  O4   0.020
 ZYK  plan-2  C1   0.020
 ZYK  plan-2  N1   0.020
 ZYK  plan-2  O1   0.020
 ZYK  plan-2  C2   0.020
 ZYK  plan-2  O2   0.020
 ZYK  plan-2  HN1  0.020
 ZYK  plan-3  C    0.020
 ZYK  plan-3  O    0.020
 ZYK  plan-3  CA   0.020
 ZYK  plan-3  O6   0.020

