# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 00:04:58 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 3-azanyl-5-(azepan-1-yl)-~{N}-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(c(OC)n1)c2nc(c(N)nc2N3CCCCCC3)C(=O)NC(N)=N
#
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
 32I  32I  3-azanyl-5-(azepan-1-yl)-~{N}-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide  ligand  55  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_32I
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
 32I  N1   N  NT    0  -0.477  -1.4529  -2.1785   0.1001
 32I  O1   O  O     0  -0.459   4.7381  -1.4497  -0.8620
 32I  N3   N  NH1   0  -0.710   3.9877   0.6441  -0.3014
 32I  C12  C  C     0   0.578   5.1561   1.3782  -0.1834
 32I  N5   N  N     0  -0.672   6.3005   0.8186  -0.1281
 32I  N4   N  NH2   0  -0.814   4.8899   2.7165  -0.0593
 32I  C18  C  CR6   0  -0.071   2.4197  -1.1098  -0.4859
 32I  N8   N  N     0  -0.394   1.5138  -0.1624  -0.2563
 32I  C8   C  CR6   0   0.101   0.2412  -0.4317  -0.1395
 32I  C10  C  CR6   0  -0.206  -0.6887   0.7130  -0.1462
 32I  C13  C  CR16  0  -0.004  -1.5628   0.9210  -1.1881
 32I  C15  C  CR6   0   0.561  -0.6999   1.7245   0.8354
 32I  O3   O  O2    0  -0.448   0.1013   1.5799   1.8721
 32I  C17  C  CH3   0  -0.398   0.0791   2.5764   2.8925
 32I  N7   N  N     0  -0.482  -1.4871   2.7726   0.7569
 32I  C14  C  CR6   0   0.589  -2.2873   2.8476  -0.3012
 32I  N6   N  N     0  -0.475  -2.3711   1.9771  -1.2853
 32I  O2   O  O2    0  -0.432  -3.0471   3.9275  -0.3089
 32I  C16  C  CH3   0  -0.396  -3.9444   4.1138  -1.3944
 32I  C9   C  CR6   0   0.498   1.9760  -2.4369  -0.7047
 32I  N2   N  NH2   0  -0.821   2.7798  -3.4311  -1.0951
 32I  N9   N  N     0  -0.464   0.6931  -2.7405  -0.5125
 32I  C7   C  CR6   0   0.482  -0.1764  -1.8054  -0.1751
 32I  C6   C  CH2   0  -0.292  -1.8892  -3.5167  -0.2641
 32I  C1   C  CH2   0  -0.441  -3.3660  -3.6064  -0.6405
 32I  C5   C  CH2   0  -0.328  -2.1860  -1.5425   1.1913
 32I  C4   C  CH2   0  -0.445  -3.5505  -0.9947   0.7812
 32I  C3   C  CH2   0  -0.423  -4.7029  -1.9971   0.8835
 32I  C2   C  CH2   0  -0.449  -4.3486  -3.4402   0.5181
 32I  H1   H  HNH1  0   0.403   3.1125   1.1129  -0.1011
 32I  H2   H  H     0   0.311   7.0301   1.5198  -0.0640
 32I  H3   H  HNH2  0   0.374   4.0917   3.0963  -0.5404
 32I  H4   H  HNH2  0   0.375   5.6761   3.3421  -0.0868
 32I  H5   H  HCR6  0   0.259  -1.6211   0.1990  -1.9959
 32I  H6   H  HCH3  0   0.242   0.7766   2.2386   3.6528
 32I  H7   H  HCH3  0   0.231   0.3976   3.5461   2.5118
 32I  H8   H  HCH3  0   0.239  -0.9115   2.6788   3.3329
 32I  H9   H  HCH3  0   0.225  -3.4183   4.1750  -2.3471
 32I  H10  H  HCH3  0   0.228  -4.6798   3.3114  -1.4516
 32I  H11  H  HCH3  0   0.242  -4.4514   5.0547  -1.2001
 32I  H12  H  HNH2  0   0.378   2.4051  -4.3618  -1.1377
 32I  H13  H  HNH2  0   0.401   3.7731  -3.2910  -1.1435
 32I  H14  H  HCH2  0   0.255  -1.2881  -3.8448  -1.1085
 32I  H15  H  HCH2  0   0.217  -1.6849  -4.2199   0.5538
 32I  H16  H  HCH2  0   0.223  -3.5893  -2.9052  -1.4498
 32I  H17  H  HCH2  0   0.241  -3.5000  -4.6045  -1.0647
 32I  H18  H  HCH2  0   0.247  -2.2959  -2.2804   1.9955
 32I  H19  H  HCH2  0   0.258  -1.5698  -0.7549   1.6165
 32I  H20  H  HCH2  0   0.233  -3.7848  -0.1247   1.3995
 32I  H21  H  HCH2  0   0.235  -3.4733  -0.6171  -0.2395
 32I  H22  H  HCH2  0   0.227  -5.1055  -1.9892   1.8994
 32I  H23  H  HCH2  0   0.226  -5.5161  -1.6471   0.2433
 32I  H24  H  HCH2  0   0.241  -5.2752  -3.9667   0.2805
 32I  H25  H  HCH2  0   0.213  -3.9430  -3.9596   1.3924
 32I  C11  C  C     0   0.565   3.8295  -0.6875  -0.5739

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
 32I  N2   C9   single    1.337  0.020  1.337
 32I  O1   C11  double    1.220  0.020  1.220
 32I  N5   C12  double    1.275  0.020  1.275
 32I  C9   N9   aromatic  1.332  0.020  1.332
 32I  C9   C18  aromatic  1.416  0.020  1.416
 32I  C11  C18  single    1.474  0.020  1.474
 32I  C11  N3   single    1.368  0.020  1.368
 32I  N9   C7   aromatic  1.321  0.020  1.321
 32I  C18  N8   aromatic  1.331  0.020  1.331
 32I  C12  N3   single    1.385  0.020  1.385
 32I  C12  N4   single    1.370  0.020  1.370
 32I  C4   C5   single    1.526  0.020  1.526
 32I  C4   C3   single    1.531  0.020  1.531
 32I  C5   N1   single    1.460  0.020  1.460
 32I  C7   N1   single    1.358  0.020  1.358
 32I  C7   C8   aromatic  1.436  0.020  1.436
 32I  N8   C8   aromatic  1.306  0.020  1.306
 32I  C3   C2   single    1.530  0.020  1.530
 32I  N1   C6   single    1.454  0.020  1.454
 32I  C8   C10  single    1.475  0.020  1.475
 32I  C2   C1   single    1.528  0.020  1.528
 32I  C6   C1   single    1.527  0.020  1.527
 32I  C10  C15  aromatic  1.409  0.020  1.409
 32I  C10  C13  aromatic  1.376  0.020  1.376
 32I  O3   C15  single    1.318  0.020  1.318
 32I  O3   C17  single    1.426  0.020  1.426
 32I  C15  N7   aromatic  1.313  0.020  1.313
 32I  C13  N6   aromatic  1.333  0.020  1.333
 32I  N6   C14  aromatic  1.317  0.020  1.317
 32I  N7   C14  aromatic  1.329  0.020  1.329
 32I  C14  O2   single    1.320  0.020  1.320
 32I  O2   C16  single    1.421  0.020  1.421
 32I  N3   H1   single    0.860  0.020  1.020
 32I  N5   H2   single    0.890  0.020  1.040
 32I  N4   H3   single    0.890  0.020  1.040
 32I  N4   H4   single    0.890  0.020  1.040
 32I  C13  H5   single    0.930  0.020  1.080
 32I  C17  H6   single    0.970  0.020  1.090
 32I  C17  H7   single    0.970  0.020  1.090
 32I  C17  H8   single    0.970  0.020  1.090
 32I  C16  H9   single    0.970  0.020  1.090
 32I  C16  H10  single    0.970  0.020  1.090
 32I  C16  H11  single    0.970  0.020  1.090
 32I  N2   H12  single    0.860  0.020  1.020
 32I  N2   H13  single    0.860  0.020  1.020
 32I  C6   H14  single    0.970  0.020  1.090
 32I  C6   H15  single    0.970  0.020  1.090
 32I  C1   H16  single    0.970  0.020  1.090
 32I  C1   H17  single    0.970  0.020  1.090
 32I  C5   H18  single    0.970  0.020  1.090
 32I  C5   H19  single    0.970  0.020  1.090
 32I  C4   H20  single    0.970  0.020  1.090
 32I  C4   H21  single    0.970  0.020  1.090
 32I  C3   H22  single    0.970  0.020  1.090
 32I  C3   H23  single    0.970  0.020  1.090
 32I  C2   H24  single    0.970  0.020  1.090
 32I  C2   H25  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
 32I  C5   N1   C6   115.94  3.000
 32I  C6   N1   C7   118.96  3.000
 32I  C5   N1   C7   120.24  3.000
 32I  H1   N3   C12  117.83  3.000
 32I  H1   N3   C11  112.95  3.000
 32I  C12  N3   C11  129.07  3.000
 32I  N4   C12  N5   126.81  3.000
 32I  N4   C12  N3   111.19  3.000
 32I  N5   C12  N3   121.89  3.000
 32I  H2   N5   C12  110.19  3.000
 32I  H4   N4   H3   111.86  3.000
 32I  H4   N4   C12  116.97  3.000
 32I  H3   N4   C12  118.65  3.000
 32I  C9   C18  N8   118.71  3.000
 32I  N8   C18  C11  117.22  3.000
 32I  C9   C18  C11  123.97  3.000
 32I  C8   N8   C18  122.14  3.000
 32I  C7   C8   C10  123.98  3.000
 32I  C10  C8   N8   116.99  3.000
 32I  C7   C8   N8   118.58  3.000
 32I  C15  C10  C13  114.44  3.000
 32I  C13  C10  C8   121.42  3.000
 32I  C15  C10  C8   123.98  3.000
 32I  H5   C13  N6   116.11  3.000
 32I  H5   C13  C10  119.83  3.000
 32I  N6   C13  C10  124.06  3.000
 32I  N7   C15  O3   119.93  3.000
 32I  N7   C15  C10  122.41  3.000
 32I  O3   C15  C10  117.65  3.000
 32I  C17  O3   C15  118.46  3.000
 32I  H8   C17  H7   108.88  3.000
 32I  H8   C17  H6   109.30  3.000
 32I  H7   C17  H6   109.50  3.000
 32I  H8   C17  O3   111.66  3.000
 32I  H7   C17  O3   111.55  3.000
 32I  H6   C17  O3   105.88  3.000
 32I  C14  N7   C15  116.98  3.000
 32I  O2   C14  N6   119.99  3.000
 32I  O2   C14  N7   113.41  3.000
 32I  N6   C14  N7   126.60  3.000
 32I  C14  N6   C13  115.51  3.000
 32I  C16  O2   C14  118.37  3.000
 32I  H11  C16  H10  109.40  3.000
 32I  H11  C16  H9   109.45  3.000
 32I  H10  C16  H9   108.72  3.000
 32I  H11  C16  O2   105.77  3.000
 32I  H10  C16  O2   111.70  3.000
 32I  H9   C16  O2   111.74  3.000
 32I  N9   C9   N2   116.85  3.000
 32I  N9   C9   C18  119.53  3.000
 32I  N2   C9   C18  123.62  3.000
 32I  H13  N2   H12  119.76  3.000
 32I  H13  N2   C9   120.33  3.000
 32I  H12  N2   C9   118.51  3.000
 32I  C7   N9   C9   120.63  3.000
 32I  N9   C7   C8   119.48  3.000
 32I  C8   C7   N1   122.08  3.000
 32I  N9   C7   N1   118.43  3.000
 32I  H15  C6   H14  106.40  3.000
 32I  H15  C6   C1   109.03  3.000
 32I  H14  C6   C1   109.00  3.000
 32I  H15  C6   N1   110.31  3.000
 32I  H14  C6   N1   107.85  3.000
 32I  C1   C6   N1   113.97  3.000
 32I  H17  C1   H16  105.86  3.000
 32I  H17  C1   C2   108.35  3.000
 32I  H16  C1   C2   111.09  3.000
 32I  H17  C1   C6   105.55  3.000
 32I  H16  C1   C6   110.01  3.000
 32I  C2   C1   C6   115.38  3.000
 32I  H19  C5   H18  104.92  3.000
 32I  H19  C5   C4   110.60  3.000
 32I  H18  C5   C4   110.41  3.000
 32I  H19  C5   N1   108.86  3.000
 32I  H18  C5   N1   107.77  3.000
 32I  C4   C5   N1   113.85  3.000
 32I  H21  C4   H20  105.60  3.000
 32I  H21  C4   C3   110.03  3.000
 32I  H20  C4   C3   108.79  3.000
 32I  H21  C4   C5   108.20  3.000
 32I  H20  C4   C5   108.99  3.000
 32I  C3   C4   C5   114.84  3.000
 32I  H23  C3   H22  105.56  3.000
 32I  H23  C3   C2   109.54  3.000
 32I  H22  C3   C2   108.30  3.000
 32I  H23  C3   C4   108.15  3.000
 32I  H22  C3   C4   109.56  3.000
 32I  C2   C3   C4   115.29  3.000
 32I  H25  C2   H24  105.03  3.000
 32I  H25  C2   C3   110.03  3.000
 32I  H24  C2   C3   108.07  3.000
 32I  H25  C2   C1   108.40  3.000
 32I  H24  C2   C1   109.16  3.000
 32I  C3   C2   C1   115.63  3.000
 32I  C18  C11  N3   112.17  3.000
 32I  N3   C11  O1   124.66  3.000
 32I  C18  C11  O1   123.17  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
 32I  CONST_01  C7   N9   C9   C18    0.00   0.0  0
 32I  CONST_02  C7   C8   N8   C18    0.00   0.0  0
 32I  CONST_03  C10  C8   N8   C18  180.00   0.0  0
 32I  CONST_04  N9   C9   C18  N8     0.00   0.0  0
 32I  CONST_05  N9   C7   C8   N8     0.00   0.0  0
 32I  CONST_08  C9   N9   C7   C8     0.00   0.0  0
 32I  CONST_09  C9   C18  N8   C8     0.00   0.0  0
 32I  CONST_10  N7   C15  C10  C8   180.00   0.0  0
 32I  CONST_11  N6   C13  C10  C8   180.00   0.0  0
 32I  CONST_13  C14  N7   C15  C10    0.00   0.0  0
 32I  CONST_14  C14  N6   C13  C10    0.00   0.0  0
 32I  CONST_16  N7   C15  C10  C13    0.00   0.0  0
 32I  CONST_17  N7   C14  N6   C13    0.00   0.0  0
 32I  CONST_19  N6   C13  C10  C15    0.00   0.0  0
 32I  CONST_20  N6   C14  N7   C15    0.00   0.0  0
 32I  CONST_21  C9   N9   C7   N1   180.00   0.0  0
 32I  CONST_22  N8   C8   C7   N1   180.00   0.0  0
 32I  CONST_24  N9   C9   C18  C11  180.00   0.0  0
 32I  CONST_25  C8   N8   C18  C11  180.00   0.0  0
 32I  CONST_26  N2   C9   C18  N8   180.00   0.0  0
 32I  CONST_27  O3   C15  C10  C8     0.00   0.0  0
 32I  CONST_28  O3   C15  C10  C13  180.00   0.0  0
 32I  CONST_29  O2   C14  N6   C13  180.00   0.0  0
 32I  CONST_30  O2   C14  N7   C15  180.00   0.0  0
 32I  CONST_31  C14  N7   C15  O3   180.00   0.0  0
 32I  CONST_32  C7   N9   C9   N2   180.00   0.0  0
 32I  CONST_33  H5   C13  C10  C8     0.00   0.0  0
 32I  CONST_34  H12  N2   C9   C18  180.00   0.0  0
 32I  CONST_35  H13  N2   C9   C18    0.00   0.0  0
 32I  CONST_36  C18  C11  N3   C12  180.00   0.0  0
 32I  CONST_37  H1   N3   C11  C18    0.00   0.0  0
 32I  CONST_38  C12  N3   C11  O1     0.00   0.0  0
 32I  CONST_39  N5   C12  N3   C11    0.00   0.0  0
 32I  CONST_40  N4   C12  N3   C11  180.00   0.0  0
 32I  CONST_41  H2   N5   C12  N3   180.00   0.0  0
 32I  CONST_43  H4   N4   C12  N3   180.00   0.0  0
 32I  Var_01    C9   C18  C11  O1     0.98  30.0  2
 32I  Var_02    N7   C15  O3   C17    0.42  30.0  2
 32I  Var_03    H6   C17  O3   C15  177.85  30.0  3
 32I  Var_04    H9   C16  O2   C14  -60.48  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
 32I  plan-1  C8   0.020
 32I  plan-1  C10  0.020
 32I  plan-1  C13  0.020
 32I  plan-1  C15  0.020
 32I  plan-1  O3   0.020
 32I  plan-1  N7   0.020
 32I  plan-1  C14  0.020
 32I  plan-1  N6   0.020
 32I  plan-1  O2   0.020
 32I  plan-1  H5   0.020
 32I  plan-2  N1   0.020
 32I  plan-2  C18  0.020
 32I  plan-2  N8   0.020
 32I  plan-2  C8   0.020
 32I  plan-2  C10  0.020
 32I  plan-2  C9   0.020
 32I  plan-2  N2   0.020
 32I  plan-2  N9   0.020
 32I  plan-2  C7   0.020
 32I  plan-2  C11  0.020
 32I  plan-3  O1   0.020
 32I  plan-3  N3   0.020
 32I  plan-3  C12  0.020
 32I  plan-3  N5   0.020
 32I  plan-3  N4   0.020
 32I  plan-3  C18  0.020
 32I  plan-3  H1   0.020
 32I  plan-3  H2   0.020
 32I  plan-3  H3   0.020
 32I  plan-3  H4   0.020
 32I  plan-3  C11  0.020
 32I  plan-4  C9   0.020
 32I  plan-4  N2   0.020
 32I  plan-4  H12  0.020
 32I  plan-4  H13  0.020

