# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:16:04 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: N-(2-methoxy-5-methylphenyl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C)cc1NC(=O)CN
#
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
 NY7  NY7  N-(2-methoxy-5-methylphenyl)glycinamide  ligand  28  14  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NY7
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
 NY7  N1   N  NH1   0  -0.730   1.0143   0.5027   0.3620
 NY7  C4   C  CR16  0  -0.307  -2.7661  -1.2186  -0.0963
 NY7  C5   C  CR6   0   0.080  -1.6828  -2.0585   0.1093
 NY7  C6   C  CH3   0  -0.721  -1.8454  -3.5506   0.1651
 NY7  C7   C  CR16  0  -0.337  -0.4201  -1.4841   0.2616
 NY7  C8   C  CR6   0   0.286  -0.2346  -0.1108   0.1955
 NY7  C10  C  CH2   0  -0.416   3.3520   1.0182   0.1988
 NY7  C1   C  CH3   0  -0.434  -2.1729   2.9475  -0.1658
 NY7  C2   C  CR6   0   0.318  -1.3472   0.7254  -0.0137
 NY7  C3   C  CR16  0  -0.370  -2.6061   0.1625  -0.1519
 NY7  C9   C  C     0   0.514   2.2207   0.0350  -0.0525
 NY7  N2   N  NH2   0  -0.790   4.6261   0.4723  -0.2042
 NY7  O1   O  O2    0  -0.477  -1.0877   2.0490  -0.0514
 NY7  O2   O  O     0  -0.466   2.3865  -1.0439  -0.5865
 NY7  H1   H  HNH1  0   0.408   0.9960   1.4489   0.7127
 NY7  H2   H  HCR6  0   0.249  -3.7600  -1.6337  -0.2112
 NY7  H3   H  HCH3  0   0.244  -1.5397  -4.0196  -0.7726
 NY7  H4   H  HCH3  0   0.241  -1.2361  -3.9891   0.9559
 NY7  H5   H  HCH3  0   0.242  -2.8820  -3.8312   0.3481
 NY7  H6   H  HCR6  0   0.259   0.4284  -2.1261   0.4495
 NY7  H7   H  HCH2  0   0.240   3.0799   1.9659  -0.2895
 NY7  H8   H  HCH2  0   0.266   3.3803   1.2345   1.2705
 NY7  H9   H  HCH3  0   0.229  -2.7013   2.8299  -1.1153
 NY7  H10  H  HCH3  0   0.230  -2.8868   2.8284   0.6529
 NY7  H11  H  HCH3  0   0.262  -1.7506   3.9482  -0.1235
 NY7  H12  H  HCR6  0   0.279  -3.4772   0.7841  -0.3089
 NY7  H13  H  HNH2  0   0.346   4.6570   0.3761  -1.2107
 NY7  H14  H  HNH2  0   0.356   5.3516   1.1358   0.0329

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
 NY7  C10  N2   single    1.444  0.020  1.444
 NY7  C10  C9   single    1.520  0.020  1.520
 NY7  C9   O2   double    1.215  0.020  1.215
 NY7  C9   N1   single    1.359  0.020  1.359
 NY7  N1   C8   single    1.401  0.020  1.401
 NY7  C1   O1   single    1.414  0.020  1.414
 NY7  O1   C2   single    1.349  0.020  1.349
 NY7  C8   C2   aromatic  1.407  0.020  1.407
 NY7  C8   C7   aromatic  1.387  0.020  1.387
 NY7  C2   C3   aromatic  1.386  0.020  1.386
 NY7  C7   C5   aromatic  1.396  0.020  1.396
 NY7  C3   C4   aromatic  1.391  0.020  1.391
 NY7  C5   C4   aromatic  1.386  0.020  1.386
 NY7  C5   C6   single    1.502  0.020  1.502
 NY7  N1   H1   single    0.860  0.020  1.020
 NY7  C4   H2   single    0.930  0.020  1.080
 NY7  C6   H3   single    0.970  0.020  1.090
 NY7  C6   H4   single    0.970  0.020  1.090
 NY7  C6   H5   single    0.970  0.020  1.090
 NY7  C7   H6   single    0.930  0.020  1.080
 NY7  C10  H7   single    0.970  0.020  1.090
 NY7  C10  H8   single    0.970  0.020  1.090
 NY7  C1   H9   single    0.970  0.020  1.090
 NY7  C1   H10  single    0.970  0.020  1.090
 NY7  C1   H11  single    0.970  0.020  1.090
 NY7  C3   H12  single    0.930  0.020  1.080
 NY7  N2   H13  single    0.890  0.020  1.040
 NY7  N2   H14  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
 NY7  H1   N1   C9   116.41  3.000
 NY7  H1   N1   C8   115.82  3.000
 NY7  C9   N1   C8   127.19  3.000
 NY7  H2   C4   C3   118.79  3.000
 NY7  H2   C4   C5   120.04  3.000
 NY7  C3   C4   C5   121.17  3.000
 NY7  C7   C5   C6   120.19  3.000
 NY7  C6   C5   C4   121.53  3.000
 NY7  C7   C5   C4   118.29  3.000
 NY7  H5   C6   H4   107.84  3.000
 NY7  H5   C6   H3   107.45  3.000
 NY7  H4   C6   H3   107.07  3.000
 NY7  H5   C6   C5   111.42  3.000
 NY7  H4   C6   C5   111.47  3.000
 NY7  H3   C6   C5   111.38  3.000
 NY7  H6   C7   C8   119.44  3.000
 NY7  H6   C7   C5   119.01  3.000
 NY7  C8   C7   C5   121.55  3.000
 NY7  C2   C8   C7   119.31  3.000
 NY7  C7   C8   N1   123.15  3.000
 NY7  C2   C8   N1   117.52  3.000
 NY7  H8   C10  H7   105.72  3.000
 NY7  H8   C10  N2   108.99  3.000
 NY7  H7   C10  N2   114.84  3.000
 NY7  H8   C10  C9   108.02  3.000
 NY7  H7   C10  C9   107.44  3.000
 NY7  N2   C10  C9   111.48  3.000
 NY7  H11  C1   H10  108.96  3.000
 NY7  H11  C1   H9   108.71  3.000
 NY7  H10  C1   H9   108.86  3.000
 NY7  H11  C1   O1   106.49  3.000
 NY7  H10  C1   O1   111.82  3.000
 NY7  H9   C1   O1   111.90  3.000
 NY7  O1   C2   C3   124.78  3.000
 NY7  C3   C2   C8   119.44  3.000
 NY7  O1   C2   C8   115.78  3.000
 NY7  H12  C3   C2   120.84  3.000
 NY7  H12  C3   C4   118.92  3.000
 NY7  C2   C3   C4   120.24  3.000
 NY7  O2   C9   C10  123.06  3.000
 NY7  O2   C9   N1   124.11  3.000
 NY7  C10  C9   N1   112.82  3.000
 NY7  H14  N2   H13  105.89  3.000
 NY7  H14  N2   C10  108.64  3.000
 NY7  H13  N2   C10  109.92  3.000
 NY7  C2   O1   C1   118.56  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
 NY7  CONST_01  C8   C2   C3   C4    0.00   0.0  0
 NY7  CONST_02  C8   C7   C5   C4    0.00   0.0  0
 NY7  CONST_03  C2   C8   C7   C5    0.00   0.0  0
 NY7  CONST_04  C2   C3   C4   C5    0.00   0.0  0
 NY7  CONST_05  C3   C2   C8   C7    0.00   0.0  0
 NY7  CONST_06  C3   C4   C5   C7    0.00   0.0  0
 NY7  CONST_07  C3   C2   C8   N1  180.00   0.0  0
 NY7  CONST_08  C5   C7   C8   N1  180.00   0.0  0
 NY7  CONST_09  O1   C2   C3   C4  180.00   0.0  0
 NY7  CONST_10  C8   C7   C5   C6  180.00   0.0  0
 NY7  CONST_11  C3   C4   C5   C6  180.00   0.0  0
 NY7  CONST_12  O1   C2   C8   C7  180.00   0.0  0
 NY7  CONST_13  H6   C7   C5   C4  180.00   0.0  0
 NY7  CONST_14  H12  C3   C4   C5  180.00   0.0  0
 NY7  CONST_15  H2   C4   C5   C7  180.00   0.0  0
 NY7  CONST_19  C10  C9   N1   C8  180.00   0.0  0
 NY7  CONST_20  O2   C9   N1   C8    0.00   0.0  0
 NY7  Var_01    C3   C2   O1   C1    3.69  30.0  2
 NY7  Var_02    H3   C6   C5   C4  101.71  30.0  2
 NY7  Var_03    H9   C1   O1   C2  -64.36  30.0  3
 NY7  Var_04    N2   C10  C9   N1  177.76  30.0  2
 NY7  Var_05    H13  N2   C10  C9   67.98  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
 NY7  plan-1  N1   0.020
 NY7  plan-1  C4   0.020
 NY7  plan-1  C5   0.020
 NY7  plan-1  C6   0.020
 NY7  plan-1  C7   0.020
 NY7  plan-1  C8   0.020
 NY7  plan-1  C2   0.020
 NY7  plan-1  C3   0.020
 NY7  plan-1  O1   0.020
 NY7  plan-1  H2   0.020
 NY7  plan-1  H6   0.020
 NY7  plan-1  H12  0.020
 NY7  plan-2  N1   0.020
 NY7  plan-2  C8   0.020
 NY7  plan-2  C10  0.020
 NY7  plan-2  C9   0.020
 NY7  plan-2  O2   0.020
 NY7  plan-2  H1   0.020

