# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:17:42 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: N-(4-methoxyphenyl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)CN)cc1
#
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
 WZY  WZY  N-(4-methoxyphenyl)glycinamide  ligand  25  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WZY
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
 WZY  N1   N  NH1   0  -0.741  18.5404  60.1534  -10.2954
 WZY  C4   C  CR16  0  -0.369  20.4489  57.6254   -8.3203
 WZY  C5   C  CR16  0  -0.305  20.0171  58.3725   -9.4133
 WZY  C6   C  CR6   0   0.351  19.0345  59.3460   -9.2625
 WZY  C7   C  CH3   0  -0.434  21.2769  56.1777   -6.0524
 WZY  C8   C  C     0   0.513  18.7943  60.1025  -11.6277
 WZY  C1   C  CR16  0  -0.332  18.4972  59.5477   -7.9867
 WZY  C2   C  CR16  0  -0.326  18.9242  58.8089   -6.9034
 WZY  C3   C  CR6   0   0.366  19.9102  57.8329   -7.0565
 WZY  C9   C  CH2   0  -0.417  18.0269  61.1609  -12.4098
 WZY  N2   N  NH2   0  -0.787  18.3234  61.1017  -13.8210
 WZY  O1   O  O2    0  -0.470  20.2662  57.1572   -5.9443
 WZY  O2   O  O     0  -0.461  19.5549  59.3110  -12.1506
 WZY  H8   H  HNH1  0   0.413  17.8842  60.8613   -9.9991
 WZY  H3   H  HCR6  0   0.277  21.2155  56.8813   -8.4900
 WZY  H4   H  HCR6  0   0.278  20.4626  58.1793  -10.3751
 WZY  H7   H  HCH3  0   0.256  21.4152  55.7620   -5.0572
 WZY  H5   H  HCH3  0   0.225  20.9949  55.3698   -6.7334
 WZY  H6   H  HCH3  0   0.225  22.2263  56.6036   -6.3896
 WZY  H1   H  HCR6  0   0.268  17.7277  60.2969   -7.8386
 WZY  H2   H  HCR6  0   0.262  18.4906  58.9855   -5.9268
 WZY  H10  H  HCH2  0   0.239  18.2242  62.1347  -11.9378
 WZY  H9   H  HCH2  0   0.266  16.9586  60.9744  -12.2659
 WZY  H12  H  HNH2  0   0.355  17.7065  61.7365  -14.3100
 WZY  H13  H  HNH2  0   0.346  19.2624  61.4369  -13.9925

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
 WZY  N2  C9   single    1.443  0.020  1.443
 WZY  C9  C8   single    1.523  0.020  1.523
 WZY  O2  C8   double    1.216  0.020  1.216
 WZY  C8  N1   single    1.357  0.020  1.357
 WZY  N1  C6   single    1.401  0.020  1.401
 WZY  C5  C6   aromatic  1.391  0.020  1.391
 WZY  C5  C4   aromatic  1.393  0.020  1.393
 WZY  C6  C1   aromatic  1.399  0.020  1.399
 WZY  C4  C3   aromatic  1.389  0.020  1.389
 WZY  C1  C2   aromatic  1.379  0.020  1.379
 WZY  C3  C2   aromatic  1.396  0.020  1.396
 WZY  C3  O1   single    1.349  0.020  1.349
 WZY  C7  O1   single    1.412  0.020  1.412
 WZY  N1  H8   single    0.860  0.020  1.020
 WZY  C4  H3   single    0.930  0.020  1.080
 WZY  C5  H4   single    0.930  0.020  1.080
 WZY  C7  H7   single    0.970  0.020  1.090
 WZY  C7  H5   single    0.970  0.020  1.090
 WZY  C7  H6   single    0.970  0.020  1.090
 WZY  C1  H1   single    0.930  0.020  1.080
 WZY  C2  H2   single    0.930  0.020  1.080
 WZY  C9  H10  single    0.970  0.020  1.090
 WZY  C9  H9   single    0.970  0.020  1.090
 WZY  N2  H12  single    0.890  0.020  1.040
 WZY  N2  H13  single    0.890  0.020  1.040

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
 WZY  H8   N1  C8   115.84  3.000
 WZY  H8   N1  C6   114.64  3.000
 WZY  C8   N1  C6   129.50  3.000
 WZY  H3   C4  C3   121.35  3.000
 WZY  H3   C4  C5   117.75  3.000
 WZY  C3   C4  C5   120.90  3.000
 WZY  H4   C5  C6   120.95  3.000
 WZY  H4   C5  C4   118.44  3.000
 WZY  C6   C5  C4   120.61  3.000
 WZY  C1   C6  C5   118.10  3.000
 WZY  C1   C6  N1   116.99  3.000
 WZY  C5   C6  N1   124.91  3.000
 WZY  H6   C7  H5   108.63  3.000
 WZY  H6   C7  H7   108.70  3.000
 WZY  H5   C7  H7   108.68  3.000
 WZY  H6   C7  O1   112.02  3.000
 WZY  H5   C7  O1   112.06  3.000
 WZY  H7   C7  O1   106.64  3.000
 WZY  O2   C8  C9   123.13  3.000
 WZY  O2   C8  N1   124.31  3.000
 WZY  C9   C8  N1   112.57  3.000
 WZY  H1   C1  C2   118.86  3.000
 WZY  H1   C1  C6   119.79  3.000
 WZY  C2   C1  C6   121.35  3.000
 WZY  H2   C2  C3   119.72  3.000
 WZY  H2   C2  C1   119.80  3.000
 WZY  C3   C2  C1   120.47  3.000
 WZY  O1   C3  C2   116.50  3.000
 WZY  O1   C3  C4   124.94  3.000
 WZY  C2   C3  C4   118.56  3.000
 WZY  H9   C9  H10  105.64  3.000
 WZY  H9   C9  N2   108.80  3.000
 WZY  H10  C9  N2   114.78  3.000
 WZY  H9   C9  C8   107.81  3.000
 WZY  H10  C9  C8   107.72  3.000
 WZY  N2   C9  C8   111.72  3.000
 WZY  H13  N2  H12  106.04  3.000
 WZY  H13  N2  C9   110.05  3.000
 WZY  H12  N2  C9   108.76  3.000
 WZY  C3   O1  C7   118.25  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
 WZY  CONST_01  C1   C6  C5  C4     0.00   0.0  0
 WZY  CONST_02  C1   C2  C3  C4     0.00   0.0  0
 WZY  CONST_03  C2   C1  C6  C5     0.00   0.0  0
 WZY  CONST_04  C2   C3  C4  C5     0.00   0.0  0
 WZY  CONST_05  C3   C4  C5  C6     0.00   0.0  0
 WZY  CONST_06  C3   C2  C1  C6     0.00   0.0  0
 WZY  CONST_07  C4   C5  C6  N1   180.00   0.0  0
 WZY  CONST_08  C2   C1  C6  N1   180.00   0.0  0
 WZY  CONST_09  O1   C3  C4  C5   180.00   0.0  0
 WZY  CONST_10  O1   C3  C2  C1   180.00   0.0  0
 WZY  CONST_11  H2   C2  C3  C4   180.00   0.0  0
 WZY  CONST_12  H1   C1  C6  C5   180.00   0.0  0
 WZY  CONST_13  H3   C4  C5  C6   180.00   0.0  0
 WZY  CONST_14  H4   C5  C6  C1   180.00   0.0  0
 WZY  CONST_15  C8   N1  C6  C5     0.00   0.0  0
 WZY  CONST_16  C1   C6  N1  C8   180.00   0.0  0
 WZY  CONST_17  H8   N1  C6  C5   180.00   0.0  0
 WZY  CONST_18  C9   C8  N1  C6   180.00   0.0  0
 WZY  CONST_19  O2   C8  N1  C6     0.00   0.0  0
 WZY  Var_01    C2   C3  O1  C7  -178.91  30.0  1
 WZY  Var_02    H7   C7  O1  C3   179.67  30.0  3
 WZY  Var_03    N2   C9  C8  N1   179.25  30.0  2
 WZY  Var_04    H12  N2  C9  C8   172.76  30.0  3

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
 WZY  plan-1  N1  0.020
 WZY  plan-1  C4  0.020
 WZY  plan-1  C5  0.020
 WZY  plan-1  C6  0.020
 WZY  plan-1  C1  0.020
 WZY  plan-1  C2  0.020
 WZY  plan-1  C3  0.020
 WZY  plan-1  O1  0.020
 WZY  plan-1  H3  0.020
 WZY  plan-1  H4  0.020
 WZY  plan-1  H1  0.020
 WZY  plan-1  H2  0.020
 WZY  plan-2  N1  0.020
 WZY  plan-2  C6  0.020
 WZY  plan-2  C8  0.020
 WZY  plan-2  C9  0.020
 WZY  plan-2  O2  0.020
 WZY  plan-2  H8  0.020

