# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 03:40:30 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 3,5-bis(azanyl)-~{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)nc2N)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
 9XC  9XC  3,5-bis(azanyl)-~{N}-carbamimidoyl-6-(2,4-dimethoxypyrimidin-5-yl)pyrazine-2-carboxamide  ligand  39  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9XC
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
 9XC  N1   N  N     0  -0.480  -3.5877   0.1080   1.2448
 9XC  C2   C  CR6   0  -0.207  -1.5209   0.4062   0.0769
 9XC  C3   C  CR16  0  -0.010  -2.4239   0.7340   1.0634
 9XC  C4   C  CR6   0   0.601  -3.8384  -0.8796   0.4115
 9XC  C5   C  CR6   0   0.565  -1.9211  -0.6656  -0.7502
 9XC  C6   C  CH3   0  -0.417  -5.8869  -1.1896   1.5397
 9XC  N8   N  NH2   0  -0.841   3.1035  -3.3808   0.9256
 9XC  C9   C  CR6   0   0.479   2.1515   2.3658  -0.3747
 9XC  C10  C  CR6   0   0.429  -0.1399   2.4682  -0.4643
 9XC  C12  C  C     0   0.556   3.7849  -2.1890   0.8772
 9XC  O3   O  O     0  -0.467   4.3971   0.5691   0.1170
 9XC  N6   N  NH1   0  -0.714   2.9337  -1.1410   0.5392
 9XC  N7   N  N     0  -0.658   5.0091  -1.9965   1.1656
 9XC  C8   C  CR6   0  -0.059   2.0712   0.9920  -0.0244
 9XC  N3   N  N     0  -0.387   0.8754   0.4249   0.1059
 9XC  N9   N  NH2   0  -0.834   3.3044   3.0260  -0.5051
 9XC  N4   N  N     0  -0.468   1.0334   3.0634  -0.5909
 9XC  N5   N  NH2   0  -0.823  -1.2425   3.2006  -0.6839
 9XC  C1   C  CR6   0   0.092  -0.2285   1.0932  -0.0871
 9XC  O2   O  O2    0  -0.441  -1.1117  -1.0209  -1.7258
 9XC  C7   C  CH3   0  -0.422  -1.5070  -2.0860  -2.5874
 9XC  N2   N  N     0  -0.492  -3.0595  -1.2979  -0.5803
 9XC  O1   O  O2    0  -0.445  -4.9651  -1.5626   0.5212
 9XC  H1   H  HCR6  0   0.280  -2.2040   1.5425   1.7530
 9XC  H2   H  HCH3  0   0.236  -5.4513  -1.2907   2.5338
 9XC  H3   H  HCH3  0   0.236  -6.2375  -0.1658   1.4090
 9XC  H4   H  HCH3  0   0.251  -6.7258  -1.8729   1.4411
 9XC  H5   H  HNH2  0   0.392   2.3392  -3.5091   0.2805
 9XC  H6   H  HNH2  0   0.395   3.6748  -4.2061   1.0107
 9XC  H7   H  HNH1  0   0.412   1.9375  -1.3187   0.5651
 9XC  H8   H  H     0   0.327   5.4636  -2.8832   1.3560
 9XC  H9   H  HNH2  0   0.414   4.1811   2.5461  -0.3946
 9XC  H10  H  HNH2  0   0.395   3.2900   3.9904  -0.7884
 9XC  H11  H  HNH2  0   0.408  -2.1394   2.7592  -0.7904
 9XC  H12  H  HNH2  0   0.401  -1.1405   4.1206  -1.0791
 9XC  H13  H  HCH3  0   0.254  -0.7095  -2.1833  -3.3181
 9XC  H14  H  HCH3  0   0.240  -1.6158  -3.0217  -2.0398
 9XC  H15  H  HCH3  0   0.239  -2.4437  -1.8611  -3.0964
 9XC  C11  C  C     0   0.562   3.2555   0.1455   0.2146

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
 9XC  O3   C11  double    1.222  0.020  1.222
 9XC  N9   C9   single    1.335  0.020  1.335
 9XC  N7   C12  double    1.272  0.020  1.272
 9XC  C11  N6   single    1.365  0.020  1.365
 9XC  C11  C8   single    1.475  0.020  1.475
 9XC  C9   C8   aromatic  1.420  0.020  1.420
 9XC  C9   N4   aromatic  1.335  0.020  1.335
 9XC  C12  N6   single    1.392  0.020  1.392
 9XC  C12  N8   single    1.374  0.020  1.374
 9XC  C8   N3   aromatic  1.330  0.020  1.330
 9XC  N4   C10  aromatic  1.322  0.020  1.322
 9XC  N3   C1   aromatic  1.305  0.020  1.305
 9XC  C10  C1   aromatic  1.429  0.020  1.429
 9XC  C10  N5   single    1.342  0.020  1.342
 9XC  C1   C2   single    1.473  0.020  1.473
 9XC  O2   C7   single    1.426  0.020  1.426
 9XC  O2   C5   single    1.316  0.020  1.316
 9XC  C2   C5   aromatic  1.412  0.020  1.412
 9XC  C2   C3   aromatic  1.377  0.020  1.377
 9XC  C5   N2   aromatic  1.313  0.020  1.313
 9XC  C3   N1   aromatic  1.334  0.020  1.334
 9XC  N2   C4   aromatic  1.329  0.020  1.329
 9XC  N1   C4   aromatic  1.316  0.020  1.316
 9XC  C4   O1   single    1.322  0.020  1.322
 9XC  O1   C6   single    1.423  0.020  1.423
 9XC  C3   H1   single    0.930  0.020  1.080
 9XC  C6   H2   single    0.970  0.020  1.090
 9XC  C6   H3   single    0.970  0.020  1.090
 9XC  C6   H4   single    0.970  0.020  1.090
 9XC  N8   H5   single    0.890  0.020  1.040
 9XC  N8   H6   single    0.890  0.020  1.040
 9XC  N6   H7   single    0.860  0.020  1.020
 9XC  N7   H8   single    0.890  0.020  1.040
 9XC  N9   H9   single    0.860  0.020  1.020
 9XC  N9   H10  single    0.860  0.020  1.020
 9XC  N5   H11  single    0.890  0.020  1.040
 9XC  N5   H12  single    0.890  0.020  1.040
 9XC  C7   H13  single    0.970  0.020  1.090
 9XC  C7   H14  single    0.970  0.020  1.090
 9XC  C7   H15  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
 9XC  C4   N1   C3   115.60  3.000
 9XC  C1   C2   C5   122.52  3.000
 9XC  C5   C2   C3   114.50  3.000
 9XC  C1   C2   C3   122.97  3.000
 9XC  H1   C3   C2   119.98  3.000
 9XC  H1   C3   N1   116.11  3.000
 9XC  C2   C3   N1   123.91  3.000
 9XC  O1   C4   N2   113.51  3.000
 9XC  O1   C4   N1   119.82  3.000
 9XC  N2   C4   N1   126.66  3.000
 9XC  N2   C5   O2   119.93  3.000
 9XC  N2   C5   C2   122.37  3.000
 9XC  O2   C5   C2   117.70  3.000
 9XC  H4   C6   H3   109.36  3.000
 9XC  H4   C6   H2   109.45  3.000
 9XC  H3   C6   H2   108.96  3.000
 9XC  H4   C6   O1   105.69  3.000
 9XC  H3   C6   O1   111.63  3.000
 9XC  H2   C6   O1   111.68  3.000
 9XC  H6   N8   H5   112.32  3.000
 9XC  H6   N8   C12  115.63  3.000
 9XC  H5   N8   C12  117.63  3.000
 9XC  N4   C9   N9   116.68  3.000
 9XC  N4   C9   C8   119.86  3.000
 9XC  N9   C9   C8   123.46  3.000
 9XC  C1   C10  N5   121.17  3.000
 9XC  N5   C10  N4   117.91  3.000
 9XC  C1   C10  N4   120.91  3.000
 9XC  N7   C12  N6   121.97  3.000
 9XC  N6   C12  N8   111.01  3.000
 9XC  N7   C12  N8   126.90  3.000
 9XC  H7   N6   C12  117.61  3.000
 9XC  H7   N6   C11  113.80  3.000
 9XC  C12  N6   C11  128.55  3.000
 9XC  H8   N7   C12  109.96  3.000
 9XC  N3   C8   C11  117.47  3.000
 9XC  N3   C8   C9   119.18  3.000
 9XC  C11  C8   C9   123.35  3.000
 9XC  C1   N3   C8   121.86  3.000
 9XC  H10  N9   H9   120.08  3.000
 9XC  H10  N9   C9   119.31  3.000
 9XC  H9   N9   C9   120.42  3.000
 9XC  C10  N4   C9   119.51  3.000
 9XC  H12  N5   H11  116.75  3.000
 9XC  H12  N5   C10  118.68  3.000
 9XC  H11  N5   C10  120.72  3.000
 9XC  N3   C1   C10  118.66  3.000
 9XC  C10  C1   C2   122.19  3.000
 9XC  N3   C1   C2   119.15  3.000
 9XC  C7   O2   C5   118.61  3.000
 9XC  H15  C7   H14  109.05  3.000
 9XC  H15  C7   H13  109.60  3.000
 9XC  H14  C7   H13  109.54  3.000
 9XC  H15  C7   O2   111.50  3.000
 9XC  H14  C7   O2   111.44  3.000
 9XC  H13  C7   O2   105.65  3.000
 9XC  C5   N2   C4   116.95  3.000
 9XC  C6   O1   C4   118.42  3.000
 9XC  C8   C11  N6   112.95  3.000
 9XC  C8   C11  O3   122.57  3.000
 9XC  N6   C11  O3   124.47  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
 9XC  CONST_01  C1   C2   C3   N1    180.00   0.0  0
 9XC  CONST_02  C5   C2   C3   N1      0.00   0.0  0
 9XC  CONST_03  C5   N2   C4   N1      0.00   0.0  0
 9XC  CONST_04  C8   N3   C1   C2    180.00   0.0  0
 9XC  CONST_05  N4   C10  C1   C2    180.00   0.0  0
 9XC  CONST_06  C4   N2   C5   C2      0.00   0.0  0
 9XC  CONST_07  C4   N1   C3   C2      0.00   0.0  0
 9XC  CONST_10  N2   C5   C2   C3      0.00   0.0  0
 9XC  CONST_11  N2   C4   N1   C3      0.00   0.0  0
 9XC  CONST_14  C1   N3   C8   C9      0.00   0.0  0
 9XC  CONST_15  C1   C10  N4   C9      0.00   0.0  0
 9XC  CONST_16  C8   C9   N4   C10     0.00   0.0  0
 9XC  CONST_17  C8   N3   C1   C10     0.00   0.0  0
 9XC  CONST_18  N4   C9   C8   N3      0.00   0.0  0
 9XC  CONST_19  N4   C10  C1   N3      0.00   0.0  0
 9XC  CONST_20  N2   C5   C2   C1    180.00   0.0  0
 9XC  CONST_21  N5   C10  C1   C2      0.00   0.0  0
 9XC  CONST_22  O2   C5   C2   C3    180.00   0.0  0
 9XC  CONST_23  O1   C4   N1   C3    180.00   0.0  0
 9XC  CONST_24  O2   C5   N2   C4    180.00   0.0  0
 9XC  CONST_25  O1   C4   N2   C5    180.00   0.0  0
 9XC  CONST_26  N5   C10  N4   C9    180.00   0.0  0
 9XC  CONST_27  N9   C9   N4   C10   180.00   0.0  0
 9XC  CONST_28  N4   C9   C8   C11   180.00   0.0  0
 9XC  CONST_29  C1   N3   C8   C11   180.00   0.0  0
 9XC  CONST_30  N9   C9   C8   N3    180.00   0.0  0
 9XC  CONST_31  N5   C10  C1   N3    180.00   0.0  0
 9XC  CONST_32  O2   C5   C2   C1      0.00   0.0  0
 9XC  CONST_33  H1   C3   N1   C4    180.00   0.0  0
 9XC  CONST_34  H9   N9   C9   C8      0.00   0.0  0
 9XC  CONST_35  H10  N9   C9   C8    180.00   0.0  0
 9XC  CONST_36  H11  N5   C10  N4    180.00   0.0  0
 9XC  CONST_37  H12  N5   C10  N4      0.00   0.0  0
 9XC  CONST_38  C8   C11  N6   C12   180.00   0.0  0
 9XC  CONST_39  H7   N6   C11  C8      0.00   0.0  0
 9XC  CONST_40  O3   C11  N6   C12     0.00   0.0  0
 9XC  CONST_41  C11  N6   C12  N8    180.00   0.0  0
 9XC  CONST_42  N7   C12  N6   C11     0.00   0.0  0
 9XC  CONST_43  H8   N7   C12  N8      0.00   0.0  0
 9XC  CONST_45  H6   N8   C12  N6    180.00   0.0  0
 9XC  Var_01    N2   C4   O1   C6   -179.15  30.0  2
 9XC  Var_02    O3   C11  C8   C9     -0.56  30.0  2
 9XC  Var_03    N2   C5   O2   C7      0.63  30.0  2
 9XC  Var_04    H2   C6   O1   C4    -61.28  30.0  3
 9XC  Var_05    H13  C7   O2   C5    178.58  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
 9XC  plan-1  N1   0.020
 9XC  plan-1  C2   0.020
 9XC  plan-1  C3   0.020
 9XC  plan-1  C4   0.020
 9XC  plan-1  C5   0.020
 9XC  plan-1  C1   0.020
 9XC  plan-1  O2   0.020
 9XC  plan-1  N2   0.020
 9XC  plan-1  O1   0.020
 9XC  plan-1  H1   0.020
 9XC  plan-2  C2   0.020
 9XC  plan-2  C9   0.020
 9XC  plan-2  C10  0.020
 9XC  plan-2  C8   0.020
 9XC  plan-2  N3   0.020
 9XC  plan-2  N9   0.020
 9XC  plan-2  N4   0.020
 9XC  plan-2  N5   0.020
 9XC  plan-2  C1   0.020
 9XC  plan-2  C11  0.020
 9XC  plan-3  N8   0.020
 9XC  plan-3  C12  0.020
 9XC  plan-3  O3   0.020
 9XC  plan-3  N6   0.020
 9XC  plan-3  N7   0.020
 9XC  plan-3  C8   0.020
 9XC  plan-3  H5   0.020
 9XC  plan-3  H6   0.020
 9XC  plan-3  H7   0.020
 9XC  plan-3  H8   0.020
 9XC  plan-3  C11  0.020
 9XC  plan-4  C9   0.020
 9XC  plan-4  N9   0.020
 9XC  plan-4  H9   0.020
 9XC  plan-4  H10  0.020
 9XC  plan-5  C10  0.020
 9XC  plan-5  N5   0.020
 9XC  plan-5  H11  0.020
 9XC  plan-5  H12  0.020

