# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 19:44:53 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 3-azanyl-5-(azepan-1-yl)-~{N}-carbamimidoyl-6-pyrimidin-5-yl-pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NC(=O)c1nc(c2cncnc2)c(nc1N)N3CCCCCC3
#
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
 94I  94I  3-azanyl-5-(azepan-1-yl)-~{N}-carbamimidoyl-6-pyrimidin-5-yl-pyrazine-2-carboxamide  ligand  47  26  .  2022-07-24  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_94I
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
 94I  C5   C  CR6   0   0.096  -0.1227  -0.1838  -0.2182
 94I  C3   C  CR16  0  -0.015  -0.3119  -2.6023  -0.8386
 94I  C2   C  CR16  0   0.048  -1.7402  -3.9625   0.2548
 94I  C7   C  CR6   0   0.474   1.1854   2.1641   0.1376
 94I  C14  C  CH2   0  -0.335  -2.8154   0.2668  -1.5329
 94I  C13  C  CH2   0  -0.438  -4.1210  -0.2681  -0.9553
 94I  C12  C  CH2   0  -0.452  -5.0619   0.7489  -0.3073
 94I  C9   C  CH2   0  -0.329  -2.7575   2.5090  -0.5704
 94I  C10  C  CH2   0  -0.427  -3.6049   2.6277   0.6891
 94I  C16  C  C     0   0.551   5.1029  -0.9417   0.0911
 94I  N4   N  N     0  -0.484  -0.1308   2.1858  -0.0482
 94I  N6   N  NH1   0  -0.711   3.7933  -0.4703   0.0440
 94I  N8   N  NH2   0  -0.839   5.1295  -2.2941   0.3344
 94I  O1   O  O     0  -0.465   4.0801   1.7923   0.2466
 94I  N7   N  N     0  -0.654   6.0971  -0.1848  -0.1453
 94I  C6   C  CR6   0  -0.056   1.8861   0.9360   0.0181
 94I  N3   N  N     0  -0.393   1.1817  -0.1804  -0.1053
 94I  N9   N  NH2   0  -0.831   1.7744   3.3247   0.4460
 94I  C8   C  CR6   0   0.493  -0.8049   1.0771  -0.3177
 94I  C4   C  CR6   0  -0.106  -0.7573  -1.5077  -0.1033
 94I  N2   N  N     0  -0.389  -0.8004  -3.8215  -0.6689
 94I  N1   N  N     0  -0.383  -2.2265  -3.0038   1.0269
 94I  C1   C  CR16  0  -0.043  -1.7319  -1.7865   0.8474
 94I  N5   N  NT    0  -0.485  -2.1005   1.2114  -0.6811
 94I  C11  C  CH2   0  -0.440  -4.4843   1.4034   0.9511
 94I  H1   H  HCR6  0   0.277   0.4616  -2.4792  -1.5891
 94I  H2   H  HCR6  0   0.268  -2.1444  -4.9585   0.3958
 94I  H3   H  HCH2  0   0.269  -2.1686  -0.5661  -1.8007
 94I  H4   H  HCH2  0   0.257  -3.0294   0.7877  -2.4716
 94I  H5   H  HCH2  0   0.242  -4.6392  -0.7726  -1.7750
 94I  H6   H  HCH2  0   0.222  -5.3702   1.5134  -1.0280
 94I  H7   H  HCH2  0   0.242  -3.3929   2.6235  -1.4499
 94I  H8   H  HCH2  0   0.273  -2.0204   3.3065  -0.6098
 94I  H9   H  HCH2  0   0.228  -2.9622   2.8077   1.5543
 94I  H10  H  HCH2  0   0.228  -4.2289   3.5184   0.5758
 94I  H11  H  HNH1  0   0.412   3.0536  -1.1570  -0.0274
 94I  H12  H  HNH2  0   0.392   4.4252  -2.6634   0.9547
 94I  H13  H  HNH2  0   0.394   6.0402  -2.6829   0.5208
 94I  H14  H  H     0   0.328   6.9622  -0.7011  -0.0279
 94I  H15  H  HNH2  0   0.395   1.2306   4.1698   0.4043
 94I  H16  H  HNH2  0   0.412   2.7781   3.3866   0.4679
 94I  H17  H  HCR6  0   0.285  -2.1154  -1.0014   1.4916
 94I  H18  H  HCH2  0   0.236  -5.2979   1.6997   1.6168
 94I  H19  H  HCH2  0   0.220  -3.9116   0.6530   1.5042
 94I  H20  H  HCH2  0   0.228  -3.9138  -1.0433  -0.2152
 94I  H21  H  HCH2  0   0.240  -5.9750   0.2130  -0.0385
 94I  C15  C  C     0   0.564   3.3539   0.8194   0.1133

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
 94I  N9   C7   single    1.338  0.020  1.338
 94I  O1   C15  double    1.221  0.020  1.221
 94I  N7   C16  double    1.272  0.020  1.272
 94I  C7   N4   aromatic  1.329  0.020  1.329
 94I  C7   C6   aromatic  1.419  0.020  1.419
 94I  C15  C6   single    1.475  0.020  1.475
 94I  C15  N6   single    1.364  0.020  1.364
 94I  N4   C8   aromatic  1.325  0.020  1.325
 94I  C6   N3   aromatic  1.326  0.020  1.326
 94I  C16  N6   single    1.393  0.020  1.393
 94I  C16  N8   single    1.374  0.020  1.374
 94I  C10  C9   single    1.523  0.020  1.523
 94I  C10  C11  single    1.530  0.020  1.530
 94I  C9   N5   single    1.459  0.020  1.459
 94I  C8   N5   single    1.352  0.020  1.352
 94I  C8   C5   aromatic  1.437  0.020  1.437
 94I  C11  C12  single    1.532  0.020  1.532
 94I  N3   C5   aromatic  1.309  0.020  1.309
 94I  N5   C14  single    1.459  0.020  1.459
 94I  C5   C4   single    1.473  0.020  1.473
 94I  C14  C13  single    1.525  0.020  1.525
 94I  C12  C13  single    1.530  0.020  1.530
 94I  C4   C3   aromatic  1.392  0.020  1.392
 94I  C4   C1   aromatic  1.390  0.020  1.390
 94I  C3   N2   aromatic  1.324  0.020  1.324
 94I  C1   N1   aromatic  1.326  0.020  1.326
 94I  N2   C2   aromatic  1.325  0.020  1.325
 94I  N1   C2   aromatic  1.323  0.020  1.323
 94I  C3   H1   single    0.930  0.020  1.080
 94I  C2   H2   single    0.930  0.020  1.080
 94I  C14  H3   single    0.970  0.020  1.090
 94I  C14  H4   single    0.970  0.020  1.090
 94I  C13  H5   single    0.970  0.020  1.090
 94I  C12  H6   single    0.970  0.020  1.090
 94I  C9   H7   single    0.970  0.020  1.090
 94I  C9   H8   single    0.970  0.020  1.090
 94I  C10  H9   single    0.970  0.020  1.090
 94I  C10  H10  single    0.970  0.020  1.090
 94I  N6   H11  single    0.860  0.020  1.020
 94I  N8   H12  single    0.890  0.020  1.040
 94I  N8   H13  single    0.890  0.020  1.040
 94I  N7   H14  single    0.890  0.020  1.040
 94I  N9   H15  single    0.860  0.020  1.020
 94I  N9   H16  single    0.860  0.020  1.020
 94I  C1   H17  single    0.930  0.020  1.080
 94I  C11  H18  single    0.970  0.020  1.090
 94I  C11  H19  single    0.970  0.020  1.090
 94I  C13  H20  single    0.970  0.020  1.090
 94I  C12  H21  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
 94I  C4   C5   C8   126.13  3.000
 94I  C4   C5   N3   115.15  3.000
 94I  C8   C5   N3   118.46  3.000
 94I  H1   C3   N2   117.14  3.000
 94I  H1   C3   C4   120.29  3.000
 94I  N2   C3   C4   122.57  3.000
 94I  H2   C2   N1   116.91  3.000
 94I  H2   C2   N2   116.92  3.000
 94I  N1   C2   N2   126.16  3.000
 94I  N9   C7   C6   123.57  3.000
 94I  C6   C7   N4   119.42  3.000
 94I  N9   C7   N4   117.01  3.000
 94I  H4   C14  H3   105.63  3.000
 94I  H4   C14  N5   106.76  3.000
 94I  H3   C14  N5   110.36  3.000
 94I  H4   C14  C13  108.93  3.000
 94I  H3   C14  C13  109.50  3.000
 94I  N5   C14  C13  115.19  3.000
 94I  H20  C13  H5   105.70  3.000
 94I  H20  C13  C12  107.56  3.000
 94I  H5   C13  C12  109.45  3.000
 94I  H20  C13  C14  110.09  3.000
 94I  H5   C13  C14  106.48  3.000
 94I  C12  C13  C14  117.00  3.000
 94I  H21  C12  H6   105.62  3.000
 94I  H21  C12  C11  108.83  3.000
 94I  H6   C12  C11  110.40  3.000
 94I  H21  C12  C13  106.99  3.000
 94I  H6   C12  C13  111.02  3.000
 94I  C11  C12  C13  113.59  3.000
 94I  H8   C9   H7   106.79  3.000
 94I  H8   C9   N5   110.15  3.000
 94I  H7   C9   N5   107.13  3.000
 94I  H8   C9   C10  110.50  3.000
 94I  H7   C9   C10  109.54  3.000
 94I  N5   C9   C10  112.51  3.000
 94I  H10  C10  H9   106.46  3.000
 94I  H10  C10  C11  109.97  3.000
 94I  H9   C10  C11  109.53  3.000
 94I  H10  C10  C9   107.18  3.000
 94I  H9   C10  C9   109.91  3.000
 94I  C11  C10  C9   113.52  3.000
 94I  N7   C16  N8   127.12  3.000
 94I  N8   C16  N6   110.93  3.000
 94I  N7   C16  N6   121.83  3.000
 94I  C8   N4   C7   121.22  3.000
 94I  H11  N6   C15  114.19  3.000
 94I  H11  N6   C16  117.39  3.000
 94I  C15  N6   C16  128.40  3.000
 94I  H13  N8   H12  112.10  3.000
 94I  H13  N8   C16  115.47  3.000
 94I  H12  N8   C16  117.11  3.000
 94I  H14  N7   C16  110.02  3.000
 94I  N3   C6   C15  117.91  3.000
 94I  N3   C6   C7   118.31  3.000
 94I  C15  C6   C7   123.65  3.000
 94I  C6   N3   C5   122.65  3.000
 94I  H16  N9   H15  119.26  3.000
 94I  H16  N9   C7   119.86  3.000
 94I  H15  N9   C7   118.78  3.000
 94I  N5   C8   N4   117.32  3.000
 94I  N5   C8   C5   124.09  3.000
 94I  N4   C8   C5   118.59  3.000
 94I  C1   C4   C3   115.34  3.000
 94I  C1   C4   C5   122.41  3.000
 94I  C3   C4   C5   121.86  3.000
 94I  C2   N2   C3   116.67  3.000
 94I  C1   N1   C2   116.68  3.000
 94I  H17  C1   N1   116.87  3.000
 94I  H17  C1   C4   120.56  3.000
 94I  N1   C1   C4   122.56  3.000
 94I  C8   N5   C9   119.97  3.000
 94I  C8   N5   C14  124.20  3.000
 94I  C9   N5   C14  113.55  3.000
 94I  H19  C11  H18  105.53  3.000
 94I  H19  C11  C10  109.54  3.000
 94I  H18  C11  C10  108.39  3.000
 94I  H19  C11  C12  108.64  3.000
 94I  H18  C11  C12  109.62  3.000
 94I  C10  C11  C12  114.71  3.000
 94I  C6   C15  O1   122.39  3.000
 94I  C6   C15  N6   113.07  3.000
 94I  O1   C15  N6   124.55  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
 94I  CONST_01  C7   N4   C8   C5     0.00   0.0  0
 94I  CONST_02  C7   C6   N3   C5     0.00   0.0  0
 94I  CONST_03  N2   C3   C4   C5   180.00   0.0  0
 94I  CONST_04  N1   C1   C4   C5   180.00   0.0  0
 94I  CONST_07  N1   C1   C4   C3     0.00   0.0  0
 94I  CONST_08  N1   C2   N2   C3     0.00   0.0  0
 94I  CONST_09  C4   C3   N2   C2     0.00   0.0  0
 94I  CONST_10  C4   C1   N1   C2     0.00   0.0  0
 94I  CONST_11  N3   C6   C7   N4     0.00   0.0  0
 94I  CONST_12  N3   C5   C8   N4     0.00   0.0  0
 94I  CONST_14  C8   N4   C7   C6     0.00   0.0  0
 94I  CONST_15  C8   C5   N3   C6     0.00   0.0  0
 94I  CONST_16  C4   C5   N3   C6   180.00   0.0  0
 94I  CONST_19  C1   C4   C3   N2     0.00   0.0  0
 94I  CONST_20  C1   N1   C2   N2     0.00   0.0  0
 94I  CONST_21  N5   C8   N4   C7   180.00   0.0  0
 94I  CONST_22  N5   C8   C5   N3   180.00   0.0  0
 94I  CONST_24  C15  C6   N3   C5   180.00   0.0  0
 94I  CONST_25  C15  C6   C7   N4   180.00   0.0  0
 94I  CONST_26  N9   C7   C6   N3   180.00   0.0  0
 94I  CONST_27  C8   N4   C7   N9   180.00   0.0  0
 94I  CONST_28  H1   C3   C4   C5     0.00   0.0  0
 94I  CONST_29  H17  C1   C4   C5     0.00   0.0  0
 94I  CONST_30  H2   C2   N2   C3   180.00   0.0  0
 94I  CONST_31  H15  N9   C7   N4     0.00   0.0  0
 94I  CONST_32  H16  N9   C7   N4   180.00   0.0  0
 94I  CONST_33  C6   C15  N6   C16  180.00   0.0  0
 94I  CONST_34  H11  N6   C15  C6     0.00   0.0  0
 94I  CONST_35  O1   C15  N6   C16    0.00   0.0  0
 94I  CONST_38  H14  N7   C16  N6   180.00   0.0  0
 94I  CONST_40  H13  N8   C16  N6   180.00   0.0  0
 94I  Var_01    O1   C15  C6   C7    -3.23  30.0  2

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
 94I  plan-1  C5   0.020
 94I  plan-1  C7   0.020
 94I  plan-1  N4   0.020
 94I  plan-1  C6   0.020
 94I  plan-1  N3   0.020
 94I  plan-1  N9   0.020
 94I  plan-1  C8   0.020
 94I  plan-1  C4   0.020
 94I  plan-1  N5   0.020
 94I  plan-1  C15  0.020
 94I  plan-2  C5   0.020
 94I  plan-2  C3   0.020
 94I  plan-2  C2   0.020
 94I  plan-2  C4   0.020
 94I  plan-2  N2   0.020
 94I  plan-2  N1   0.020
 94I  plan-2  C1   0.020
 94I  plan-2  H1   0.020
 94I  plan-2  H2   0.020
 94I  plan-2  H17  0.020
 94I  plan-3  C16  0.020
 94I  plan-3  N6   0.020
 94I  plan-3  N8   0.020
 94I  plan-3  O1   0.020
 94I  plan-3  N7   0.020
 94I  plan-3  C6   0.020
 94I  plan-3  H11  0.020
 94I  plan-3  H12  0.020
 94I  plan-3  H13  0.020
 94I  plan-3  H14  0.020
 94I  plan-3  C15  0.020
 94I  plan-4  C7   0.020
 94I  plan-4  N9   0.020
 94I  plan-4  H15  0.020
 94I  plan-4  H16  0.020

