# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 01:11:49 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-(4-methoxyphenyl)-N-(pyridin-3-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(=O)Nc2cccnc2)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
 H2Y  H2Y  2-(4-methoxyphenyl)-N-(pyridin-3-yl)acetamide  ligand  32  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H2Y
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
 H2Y  N1   N  NH1   0  -0.744  -2.0642  -0.7732  -0.2731
 H2Y  C4   C  CR16  0  -0.279   2.2203  -0.6017   1.2186
 H2Y  C5   C  CR6   0   0.131   1.6427  -0.8191  -0.0318
 H2Y  C6   C  CH2   0  -0.702   0.2588  -1.3778  -0.1550
 H2Y  C7   C  C     0   0.559  -0.8209  -0.3279   0.0532
 H2Y  C8   C  CR6   0   0.289  -3.2858  -0.1145  -0.1644
 H2Y  C10  C  CR16  0  -0.312  -4.7616   1.6742   0.3974
 H2Y  C13  C  CR16  0  -0.291   2.3848  -0.4855  -1.1546
 H2Y  C1   C  CH3   0  -0.436   6.2477   1.1026  -0.7115
 H2Y  C2   C  CR6   0   0.368   4.2268   0.2609   0.2008
 H2Y  C3   C  CR16  0  -0.332   3.4904  -0.0718   1.3407
 H2Y  C9   C  CR16  0  -0.213  -3.4722   1.1656   0.3542
 H2Y  C11  C  CR16  0  -0.087  -5.8174   0.9105  -0.0695
 H2Y  N2   N  N     0  -0.388  -5.6454  -0.3105  -0.5652
 H2Y  C12  C  CR16  0  -0.146  -4.4208  -0.8016  -0.6095
 H2Y  O2   O  O     0  -0.450  -0.5918   0.7833   0.4858
 H2Y  C14  C  CR16  0  -0.370   3.6660   0.0481  -1.0548
 H2Y  H1   H  HNH1  0   0.420  -2.1171  -1.7128  -0.6388
 H2Y  H2   H  HCR6  0   0.250   1.6721  -0.8562   2.1178
 H2Y  H3   H  HCH2  0   0.294   0.1191  -1.8502  -1.1309
 H2Y  H4   H  HCH2  0   0.303   0.0937  -2.1658   0.5870
 H2Y  H5   H  HCR6  0   0.274  -4.9414   2.6637   0.7950
 H2Y  H6   H  HCR6  0   0.253   1.9668  -0.6463  -2.1414
 H2Y  H7   H  HCH3  0   0.227   5.7755   1.8662  -1.3355
 H2Y  H8   H  HCH3  0   0.259   7.1839   1.4982  -0.3254
 H2Y  H9   H  HCH3  0   0.227   6.4645   0.2279  -1.3307
 H2Y  H10  H  HCR6  0   0.261   3.9234   0.0887   2.3203
 H2Y  H11  H  HCR6  0   0.293  -2.6456   1.7544   0.7158
 H2Y  H12  H  HCR6  0   0.263  -6.8316   1.2913  -0.0444
 H2Y  H13  H  HCR6  0   0.272  -4.3123  -1.8018  -1.0211
 H2Y  H14  H  HCR6  0   0.277   4.2023   0.2845  -1.9636
 H2Y  O1   O  O2    0  -0.471   5.4559   0.7718   0.4111

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
 H2Y  C10  C9   aromatic  1.387  0.020  1.387
 H2Y  C10  C11  aromatic  1.384  0.020  1.384
 H2Y  C9   C8   aromatic  1.394  0.020  1.394
 H2Y  O2   C7   double    1.214  0.020  1.214
 H2Y  C1   O1   single    1.413  0.020  1.413
 H2Y  C14  C13  aromatic  1.391  0.020  1.391
 H2Y  C14  C2   aromatic  1.392  0.020  1.392
 H2Y  C13  C5   aromatic  1.387  0.020  1.387
 H2Y  C11  N2   aromatic  1.329  0.020  1.329
 H2Y  C7   N1   single    1.360  0.020  1.360
 H2Y  C7   C6   single    1.520  0.020  1.520
 H2Y  C8   N1   single    1.392  0.020  1.392
 H2Y  C8   C12  aromatic  1.399  0.020  1.399
 H2Y  O1   C2   single    1.348  0.020  1.348
 H2Y  C2   C3   aromatic  1.397  0.020  1.397
 H2Y  C5   C6   single    1.497  0.020  1.497
 H2Y  C5   C4   aromatic  1.394  0.020  1.394
 H2Y  N2   C12  aromatic  1.320  0.020  1.320
 H2Y  C3   C4   aromatic  1.382  0.020  1.382
 H2Y  N1   H1   single    0.860  0.020  1.020
 H2Y  C4   H2   single    0.930  0.020  1.080
 H2Y  C6   H3   single    0.970  0.020  1.090
 H2Y  C6   H4   single    0.970  0.020  1.090
 H2Y  C10  H5   single    0.930  0.020  1.080
 H2Y  C13  H6   single    0.930  0.020  1.080
 H2Y  C1   H7   single    0.970  0.020  1.090
 H2Y  C1   H8   single    0.970  0.020  1.090
 H2Y  C1   H9   single    0.970  0.020  1.090
 H2Y  C3   H10  single    0.930  0.020  1.080
 H2Y  C9   H11  single    0.930  0.020  1.080
 H2Y  C11  H12  single    0.930  0.020  1.080
 H2Y  C12  H13  single    0.930  0.020  1.080
 H2Y  C14  H14  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
 H2Y  H1   N1   C8   115.00  3.000
 H2Y  H1   N1   C7   116.06  3.000
 H2Y  C8   N1   C7   128.93  3.000
 H2Y  H2   C4   C3   118.80  3.000
 H2Y  H2   C4   C5   119.87  3.000
 H2Y  C3   C4   C5   121.32  3.000
 H2Y  C13  C5   C6   121.18  3.000
 H2Y  C6   C5   C4   120.98  3.000
 H2Y  C13  C5   C4   117.84  3.000
 H2Y  H4   C6   H3   105.94  3.000
 H2Y  H4   C6   C7   107.28  3.000
 H2Y  H3   C6   C7   109.26  3.000
 H2Y  H4   C6   C5   110.62  3.000
 H2Y  H3   C6   C5   110.66  3.000
 H2Y  C7   C6   C5   112.80  3.000
 H2Y  O2   C7   C6   123.14  3.000
 H2Y  C6   C7   N1   112.97  3.000
 H2Y  O2   C7   N1   123.88  3.000
 H2Y  C12  C8   C9   117.44  3.000
 H2Y  C12  C8   N1   117.04  3.000
 H2Y  C9   C8   N1   125.52  3.000
 H2Y  H5   C10  C11  120.13  3.000
 H2Y  H5   C10  C9   120.11  3.000
 H2Y  C11  C10  C9   119.76  3.000
 H2Y  H6   C13  C14  118.52  3.000
 H2Y  H6   C13  C5   119.68  3.000
 H2Y  C14  C13  C5   121.80  3.000
 H2Y  H9   C1   H8   108.75  3.000
 H2Y  H9   C1   H7   108.73  3.000
 H2Y  H8   C1   H7   108.69  3.000
 H2Y  H9   C1   O1   111.95  3.000
 H2Y  H8   C1   O1   106.59  3.000
 H2Y  H7   C1   O1   112.01  3.000
 H2Y  C14  C2   C3   119.17  3.000
 H2Y  C3   C2   O1   116.34  3.000
 H2Y  C14  C2   O1   124.50  3.000
 H2Y  H10  C3   C2   119.47  3.000
 H2Y  H10  C3   C4   120.29  3.000
 H2Y  C2   C3   C4   120.24  3.000
 H2Y  H11  C9   C10  120.17  3.000
 H2Y  H11  C9   C8   121.61  3.000
 H2Y  C10  C9   C8   118.22  3.000
 H2Y  H12  C11  N2   116.92  3.000
 H2Y  H12  C11  C10  120.81  3.000
 H2Y  N2   C11  C10  122.27  3.000
 H2Y  C12  N2   C11  118.32  3.000
 H2Y  H13  C12  N2   116.59  3.000
 H2Y  H13  C12  C8   119.42  3.000
 H2Y  N2   C12  C8   123.99  3.000
 H2Y  H14  C14  C2   121.67  3.000
 H2Y  H14  C14  C13  118.70  3.000
 H2Y  C2   C14  C13  119.63  3.000
 H2Y  C2   O1   C1   118.41  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
 H2Y  CONST_01  C14  C13  C5   C4     0.00   0.0  0
 H2Y  CONST_02  C14  C2   C3   C4     0.00   0.0  0
 H2Y  CONST_03  C2   C14  C13  C5     0.00   0.0  0
 H2Y  CONST_04  C2   C3   C4   C5     0.00   0.0  0
 H2Y  CONST_05  C11  C10  C9   C8     0.00   0.0  0
 H2Y  CONST_06  C11  N2   C12  C8     0.00   0.0  0
 H2Y  CONST_07  C12  C8   C9   C10    0.00   0.0  0
 H2Y  CONST_08  C12  N2   C11  C10    0.00   0.0  0
 H2Y  CONST_09  C3   C2   C14  C13    0.00   0.0  0
 H2Y  CONST_10  C3   C4   C5   C13    0.00   0.0  0
 H2Y  CONST_11  N2   C11  C10  C9     0.00   0.0  0
 H2Y  CONST_12  N2   C12  C8   C9     0.00   0.0  0
 H2Y  CONST_13  C10  C9   C8   N1   180.00   0.0  0
 H2Y  CONST_14  N2   C12  C8   N1   180.00   0.0  0
 H2Y  CONST_15  O1   C2   C3   C4   180.00   0.0  0
 H2Y  CONST_16  C14  C13  C5   C6   180.00   0.0  0
 H2Y  CONST_17  C3   C4   C5   C6   180.00   0.0  0
 H2Y  CONST_18  O1   C2   C14  C13  180.00   0.0  0
 H2Y  CONST_19  H6   C13  C5   C4   180.00   0.0  0
 H2Y  CONST_20  H14  C14  C13  C5   180.00   0.0  0
 H2Y  CONST_21  H10  C3   C4   C5   180.00   0.0  0
 H2Y  CONST_22  H5   C10  C9   C8   180.00   0.0  0
 H2Y  CONST_23  H2   C4   C5   C13  180.00   0.0  0
 H2Y  CONST_24  H12  C11  C10  C9   180.00   0.0  0
 H2Y  CONST_25  H13  C12  C8   C9   180.00   0.0  0
 H2Y  CONST_26  H11  C9   C10  C11  180.00   0.0  0
 H2Y  CONST_27  C9   C8   N1   C7     0.00   0.0  0
 H2Y  CONST_28  C12  C8   N1   C7   180.00   0.0  0
 H2Y  CONST_29  H1   N1   C8   C9   180.00   0.0  0
 H2Y  CONST_30  C8   N1   C7   C6   180.00   0.0  0
 H2Y  CONST_31  O2   C7   N1   C8     0.00   0.0  0
 H2Y  Var_01    C7   C6   C5   C4    80.11  30.0  2
 H2Y  Var_02    C14  C2   O1   C1    -0.87  30.0  2
 H2Y  Var_03    C5   C6   C7   N1   169.76  30.0  3
 H2Y  Var_04    H7   C1   O1   C2    60.89  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
 H2Y  plan-1  N1   0.020
 H2Y  plan-1  C8   0.020
 H2Y  plan-1  C10  0.020
 H2Y  plan-1  C9   0.020
 H2Y  plan-1  C11  0.020
 H2Y  plan-1  N2   0.020
 H2Y  plan-1  C12  0.020
 H2Y  plan-1  H5   0.020
 H2Y  plan-1  H11  0.020
 H2Y  plan-1  H12  0.020
 H2Y  plan-1  H13  0.020
 H2Y  plan-2  C4   0.020
 H2Y  plan-2  C5   0.020
 H2Y  plan-2  C6   0.020
 H2Y  plan-2  C13  0.020
 H2Y  plan-2  C2   0.020
 H2Y  plan-2  C3   0.020
 H2Y  plan-2  C14  0.020
 H2Y  plan-2  H2   0.020
 H2Y  plan-2  H6   0.020
 H2Y  plan-2  H10  0.020
 H2Y  plan-2  H14  0.020
 H2Y  plan-2  O1   0.020
 H2Y  plan-3  N1   0.020
 H2Y  plan-3  C6   0.020
 H2Y  plan-3  C7   0.020
 H2Y  plan-3  C8   0.020
 H2Y  plan-3  O2   0.020
 H2Y  plan-3  H1   0.020

