# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 10:21:26 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 3-azanyl-5-(azepan-1-yl)-~{N}-carbamimidoyl-6-(2-methoxypyrimidin-5-yl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cn1)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
 30I  30I  3-azanyl-5-(azepan-1-yl)-~{N}-carbamimidoyl-6-(2-methoxypyrimidin-5-yl)pyrazine-2-carboxamide  ligand  51  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_30I
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
 30I  C10  C  CH2   0  -0.418   2.9707  -3.2335   1.2574
 30I  O2   O  O2    0  -0.448   3.1429   4.0399  -0.1858
 30I  O1   O  O     0  -0.464  -4.7443  -1.1808   0.4835
 30I  N3   N  NH1   0  -0.712  -3.9637   0.9065  -0.0430
 30I  C1   C  C     0   0.552  -5.1383   1.6511  -0.1320
 30I  N2   N  N     0  -0.654  -6.2675   1.0988  -0.3242
 30I  N1   N  NH2   0  -0.838  -4.8721   2.9970  -0.0697
 30I  C3   C  CR6   0  -0.051  -2.4161  -0.8732   0.1868
 30I  N7   N  N     0  -0.399  -1.4809   0.0383  -0.0466
 30I  C12  C  CR6   0   0.110  -0.2091  -0.2686  -0.1164
 30I  C13  C  CR6   0  -0.158   0.7323   0.8607  -0.1563
 30I  C14  C  CR16  0   0.006   1.8002   0.9705   0.7225
 30I  C16  C  CR16  0  -0.011   0.5513   1.9541  -1.0013
 30I  N9   N  N     0  -0.427   1.3517   3.0036  -1.0007
 30I  C15  C  CR6   0   0.592   2.3569   2.9764  -0.1339
 30I  N8   N  N     0  -0.454   2.6147   2.0158   0.7361
 30I  C17  C  CH3   0  -0.417   4.2441   4.1142   0.7126
 30I  C5   C  CR6   0   0.481   0.1714  -1.6474  -0.0376
 30I  N5   N  N     0  -0.473  -0.7361  -2.5453   0.2990
 30I  C4   C  CR6   0   0.478  -2.0161  -2.2060   0.4537
 30I  N4   N  NH2   0  -0.832  -2.8522  -3.1679   0.8590
 30I  N6   N  NT    0  -0.500   1.4475  -2.0686  -0.2915
 30I  C11  C  CH2   0  -0.336   1.8783  -3.3726   0.2002
 30I  C9   C  CH2   0  -0.432   4.3421  -2.8324   0.7273
 30I  C8   C  CH2   0  -0.436   4.3635  -1.6195  -0.1999
 30I  C7   C  CH2   0  -0.482   3.6239  -1.8560  -1.5158
 30I  C6   C  CH2   0  -0.294   2.1273  -1.5705  -1.4876
 30I  H1   H  HCH2  0   0.219   2.6285  -2.5097   2.0039
 30I  H2   H  HCH2  0   0.229   3.0626  -4.1902   1.7796
 30I  H3   H  HNH1  0   0.413  -3.0896   1.3943  -0.1949
 30I  H4   H  H     0   0.329  -7.0027   1.7976  -0.3228
 30I  H5   H  HNH2  0   0.392  -4.1154   3.2909   0.5287
 30I  H6   H  HNH2  0   0.395  -5.6778   3.5965   0.0095
 30I  H7   H  HCR6  0   0.275   2.0049   0.1888   1.4461
 30I  H8   H  HCR6  0   0.278  -0.2721   1.9692  -1.7071
 30I  H9   H  HCH3  0   0.252   4.7491   5.0485   0.4833
 30I  H10  H  HCH3  0   0.236   3.9140   4.1273   1.7515
 30I  H11  H  HCH3  0   0.236   4.9359   3.2837   0.5716
 30I  H12  H  HNH2  0   0.413  -3.8437  -2.9998   0.8658
 30I  H13  H  HNH2  0   0.396  -2.5116  -4.1125   0.9146
 30I  H14  H  HCH2  0   0.235   2.2175  -3.9936  -0.6341
 30I  H15  H  HCH2  0   0.273   1.0228  -3.8837   0.6319
 30I  H16  H  HCH2  0   0.228   5.0074  -2.6510   1.5754
 30I  H17  H  HCH2  0   0.213   4.7726  -3.6797   0.1832
 30I  H18  H  HCH2  0   0.221   3.9639  -0.7379   0.3100
 30I  H19  H  HCH2  0   0.235   5.4067  -1.3847  -0.4247
 30I  H20  H  HCH2  0   0.253   4.0381  -1.2160  -2.2981
 30I  H21  H  HCH2  0   0.231   3.8077  -2.8808  -1.8504
 30I  H22  H  HCH2  0   0.245   1.6650  -2.0093  -2.3800
 30I  H23  H  HCH2  0   0.252   1.9838  -0.4962  -1.5657
 30I  C2   C  C     0   0.567  -3.8227  -0.4223   0.2262

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
 30I  N4   C4   single    1.337  0.020  1.337
 30I  O1   C2   double    1.221  0.020  1.221
 30I  N2   C1   double    1.272  0.020  1.272
 30I  C4   C3   aromatic  1.417  0.020  1.417
 30I  C4   N5   aromatic  1.333  0.020  1.333
 30I  C2   C3   single    1.478  0.020  1.478
 30I  C2   N3   single    1.363  0.020  1.363
 30I  C1   N3   single    1.394  0.020  1.394
 30I  C1   N1   single    1.373  0.020  1.373
 30I  C3   N7   aromatic  1.327  0.020  1.327
 30I  N5   C5   aromatic  1.320  0.020  1.320
 30I  C11  N6   single    1.459  0.020  1.459
 30I  C11  C10  single    1.527  0.020  1.527
 30I  C5   N6   single    1.368  0.020  1.368
 30I  C5   C12  aromatic  1.433  0.020  1.433
 30I  N7   C12  aromatic  1.310  0.020  1.310
 30I  N6   C6   single    1.463  0.020  1.463
 30I  C12  C13  single    1.471  0.020  1.471
 30I  C10  C9   single    1.524  0.020  1.524
 30I  C9   C8   single    1.527  0.020  1.527
 30I  C7   C6   single    1.524  0.020  1.524
 30I  C7   C8   single    1.528  0.020  1.528
 30I  C13  C16  aromatic  1.394  0.020  1.394
 30I  C13  C14  aromatic  1.387  0.020  1.387
 30I  C16  N9   aromatic  1.320  0.020  1.320
 30I  C14  N8   aromatic  1.325  0.020  1.325
 30I  N9   C15  aromatic  1.328  0.020  1.328
 30I  N8   C15  aromatic  1.321  0.020  1.321
 30I  C15  O2   single    1.323  0.020  1.323
 30I  O2   C17  single    1.423  0.020  1.423
 30I  C10  H1   single    0.970  0.020  1.090
 30I  C10  H2   single    0.970  0.020  1.090
 30I  N3   H3   single    0.860  0.020  1.020
 30I  N2   H4   single    0.890  0.020  1.040
 30I  N1   H5   single    0.890  0.020  1.040
 30I  N1   H6   single    0.890  0.020  1.040
 30I  C14  H7   single    0.930  0.020  1.080
 30I  C16  H8   single    0.930  0.020  1.080
 30I  C17  H9   single    0.970  0.020  1.090
 30I  C17  H10  single    0.970  0.020  1.090
 30I  C17  H11  single    0.970  0.020  1.090
 30I  N4   H12  single    0.860  0.020  1.020
 30I  N4   H13  single    0.860  0.020  1.020
 30I  C11  H14  single    0.970  0.020  1.090
 30I  C11  H15  single    0.970  0.020  1.090
 30I  C9   H16  single    0.970  0.020  1.090
 30I  C9   H17  single    0.970  0.020  1.090
 30I  C8   H18  single    0.970  0.020  1.090
 30I  C8   H19  single    0.970  0.020  1.090
 30I  C7   H20  single    0.970  0.020  1.090
 30I  C7   H21  single    0.970  0.020  1.090
 30I  C6   H22  single    0.970  0.020  1.090
 30I  C6   H23  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
 30I  H2   C10  H1   106.20  3.000
 30I  H2   C10  C9   108.70  3.000
 30I  H1   C10  C9   110.15  3.000
 30I  H2   C10  C11  108.12  3.000
 30I  H1   C10  C11  107.99  3.000
 30I  C9   C10  C11  115.28  3.000
 30I  C17  O2   C15  118.47  3.000
 30I  H3   N3   C1   117.43  3.000
 30I  H3   N3   C2   114.20  3.000
 30I  C1   N3   C2   128.36  3.000
 30I  N1   C1   N2   127.20  3.000
 30I  N1   C1   N3   110.93  3.000
 30I  N2   C1   N3   121.74  3.000
 30I  H4   N2   C1   110.13  3.000
 30I  H6   N1   H5   112.34  3.000
 30I  H6   N1   C1   115.58  3.000
 30I  H5   N1   C1   117.26  3.000
 30I  C4   C3   N7   118.72  3.000
 30I  N7   C3   C2   117.78  3.000
 30I  C4   C3   C2   123.42  3.000
 30I  C12  N7   C3   122.19  3.000
 30I  C5   C12  C13  124.79  3.000
 30I  C13  C12  N7   116.29  3.000
 30I  C5   C12  N7   118.71  3.000
 30I  C16  C13  C14  114.96  3.000
 30I  C14  C13  C12  122.43  3.000
 30I  C16  C13  C12  122.39  3.000
 30I  H7   C14  N8   116.47  3.000
 30I  H7   C14  C13  120.71  3.000
 30I  N8   C14  C13  122.82  3.000
 30I  H8   C16  N9   116.72  3.000
 30I  H8   C16  C13  120.27  3.000
 30I  N9   C16  C13  123.01  3.000
 30I  C15  N9   C16  116.31  3.000
 30I  N8   C15  N9   126.33  3.000
 30I  N8   C15  O2   119.61  3.000
 30I  N9   C15  O2   114.05  3.000
 30I  C15  N8   C14  116.54  3.000
 30I  H11  C17  H10  108.94  3.000
 30I  H11  C17  H9   109.45  3.000
 30I  H10  C17  H9   109.36  3.000
 30I  H11  C17  O2   111.69  3.000
 30I  H10  C17  O2   111.58  3.000
 30I  H9   C17  O2   105.74  3.000
 30I  N6   C5   N5   118.64  3.000
 30I  N6   C5   C12  122.28  3.000
 30I  N5   C5   C12  119.09  3.000
 30I  C4   N5   C5   121.09  3.000
 30I  N4   C4   N5   116.89  3.000
 30I  N5   C4   C3   119.25  3.000
 30I  N4   C4   C3   123.86  3.000
 30I  H13  N4   H12  119.37  3.000
 30I  H13  N4   C4   118.73  3.000
 30I  H12  N4   C4   119.88  3.000
 30I  C6   N6   C11  116.27  3.000
 30I  C6   N6   C5   118.72  3.000
 30I  C11  N6   C5   119.23  3.000
 30I  H15  C11  H14  106.28  3.000
 30I  H15  C11  N6   108.79  3.000
 30I  H14  C11  N6   110.00  3.000
 30I  H15  C11  C10  109.35  3.000
 30I  H14  C11  C10  110.98  3.000
 30I  N6   C11  C10  111.30  3.000
 30I  H17  C9   H16  105.95  3.000
 30I  H17  C9   C8   107.90  3.000
 30I  H16  C9   C8   109.32  3.000
 30I  H17  C9   C10  108.84  3.000
 30I  H16  C9   C10  108.75  3.000
 30I  C8   C9   C10  115.65  3.000
 30I  H19  C8   H18  105.76  3.000
 30I  H19  C8   C7   108.56  3.000
 30I  H18  C8   C7   110.44  3.000
 30I  H19  C8   C9   108.00  3.000
 30I  H18  C8   C9   110.61  3.000
 30I  C7   C8   C9   113.15  3.000
 30I  H21  C7   H20  105.45  3.000
 30I  H21  C7   C6   110.26  3.000
 30I  H20  C7   C6   106.02  3.000
 30I  H21  C7   C8   109.10  3.000
 30I  H20  C7   C8   110.03  3.000
 30I  C6   C7   C8   115.50  3.000
 30I  H23  C6   H22  106.34  3.000
 30I  H23  C6   C7   108.28  3.000
 30I  H22  C6   C7   108.90  3.000
 30I  H23  C6   N6   109.51  3.000
 30I  H22  C6   N6   109.46  3.000
 30I  C7   C6   N6   114.06  3.000
 30I  C3   C2   N3   112.99  3.000
 30I  N3   C2   O1   124.68  3.000
 30I  C3   C2   O1   122.32  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
 30I  CONST_01  C5   N5   C4   C3     0.00   0.0  0
 30I  CONST_02  C5   C12  N7   C3     0.00   0.0  0
 30I  CONST_03  C13  C12  N7   C3   180.00   0.0  0
 30I  CONST_04  N5   C4   C3   N7     0.00   0.0  0
 30I  CONST_05  N5   C5   C12  N7     0.00   0.0  0
 30I  CONST_08  C4   N5   C5   C12    0.00   0.0  0
 30I  CONST_09  C4   C3   N7   C12    0.00   0.0  0
 30I  CONST_10  N9   C16  C13  C12  180.00   0.0  0
 30I  CONST_11  N8   C14  C13  C12  180.00   0.0  0
 30I  CONST_13  C15  N9   C16  C13    0.00   0.0  0
 30I  CONST_14  C15  N8   C14  C13    0.00   0.0  0
 30I  CONST_16  N9   C16  C13  C14    0.00   0.0  0
 30I  CONST_17  N9   C15  N8   C14    0.00   0.0  0
 30I  CONST_19  N8   C14  C13  C16    0.00   0.0  0
 30I  CONST_20  N8   C15  N9   C16    0.00   0.0  0
 30I  CONST_21  N6   C5   C12  N7   180.00   0.0  0
 30I  CONST_23  N6   C5   N5   C4   180.00   0.0  0
 30I  CONST_24  C16  N9   C15  O2   180.00   0.0  0
 30I  CONST_25  C14  N8   C15  O2   180.00   0.0  0
 30I  CONST_26  N5   C4   C3   C2   180.00   0.0  0
 30I  CONST_27  C12  N7   C3   C2   180.00   0.0  0
 30I  CONST_28  N4   C4   C3   N7   180.00   0.0  0
 30I  CONST_29  N4   C4   N5   C5   180.00   0.0  0
 30I  CONST_30  H8   C16  C13  C12    0.00   0.0  0
 30I  CONST_31  H7   C14  C13  C12    0.00   0.0  0
 30I  CONST_32  H12  N4   C4   C3     0.00   0.0  0
 30I  CONST_33  H13  N4   C4   C3   180.00   0.0  0
 30I  CONST_34  C3   C2   N3   C1   180.00   0.0  0
 30I  CONST_35  H3   N3   C2   C3     0.00   0.0  0
 30I  CONST_36  C1   N3   C2   O1     0.00   0.0  0
 30I  CONST_39  H4   N2   C1   N3   180.00   0.0  0
 30I  CONST_41  H6   N1   C1   N3   180.00   0.0  0
 30I  Var_01    C4   C3   C2   O1    -0.63  30.0  2
 30I  Var_02    H9   C17  O2   C15  179.12  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
 30I  plan-1  O2   0.020
 30I  plan-1  C12  0.020
 30I  plan-1  C13  0.020
 30I  plan-1  C14  0.020
 30I  plan-1  C16  0.020
 30I  plan-1  N9   0.020
 30I  plan-1  C15  0.020
 30I  plan-1  N8   0.020
 30I  plan-1  H7   0.020
 30I  plan-1  H8   0.020
 30I  plan-2  C3   0.020
 30I  plan-2  N7   0.020
 30I  plan-2  C12  0.020
 30I  plan-2  C13  0.020
 30I  plan-2  C5   0.020
 30I  plan-2  N5   0.020
 30I  plan-2  C4   0.020
 30I  plan-2  N4   0.020
 30I  plan-2  N6   0.020
 30I  plan-2  C2   0.020
 30I  plan-3  O1   0.020
 30I  plan-3  N3   0.020
 30I  plan-3  C1   0.020
 30I  plan-3  N2   0.020
 30I  plan-3  N1   0.020
 30I  plan-3  C3   0.020
 30I  plan-3  H3   0.020
 30I  plan-3  H4   0.020
 30I  plan-3  H5   0.020
 30I  plan-3  H6   0.020
 30I  plan-3  C2   0.020
 30I  plan-4  C4   0.020
 30I  plan-4  N4   0.020
 30I  plan-4  H12  0.020
 30I  plan-4  H13  0.020

