# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 05:55:38 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 3,5-bis(azanyl)-~{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)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
 9X9  9X9  3,5-bis(azanyl)-~{N}-carbamimidoyl-6-(2-methoxypyrimidin-5-yl)pyrazine-2-carboxamide  ligand  35  22  .  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_9X9
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
 9X9  C4   C  CR6   0   0.480  -2.0439  -2.3347   0.0402
 9X9  C3   C  CR6   0  -0.053  -1.9256  -0.9200   0.0428
 9X9  C2   C  CR6   0   0.093   0.3746  -1.0951   0.0047
 9X9  C1   C  CR6   0   0.429   0.2469  -2.5180   0.0744
 9X9  C11  C  CH3   0  -0.417   5.2977   2.7952   0.5422
 9X9  C9   C  CR6   0   0.597   3.9426   0.9964  -0.1652
 9X9  N9   N  N     0  -0.425   3.8444  -0.0651  -0.9549
 9X9  C10  C  CR16  0  -0.048   2.7130  -0.7423  -0.8898
 9X9  N8   N  N     0  -0.454   3.0160   1.4404   0.6671
 9X9  C8   C  CR16  0  -0.001   1.8897   0.7479   0.7224
 9X9  C5   C  CR6   0  -0.100   1.6634  -0.3913  -0.0415
 9X9  N2   N  N     0  -0.407  -0.7152  -0.3734   0.0159
 9X9  N3   N  NH2   0  -0.828   1.3215  -3.3224   0.1322
 9X9  N1   N  N     0  -0.466  -0.9433  -3.0903   0.0729
 9X9  N4   N  NH2   0  -0.833  -3.2130  -2.9769   0.0112
 9X9  C6   C  C     0   0.564  -3.0864  -0.0079   0.0497
 9X9  N5   N  NH1   0  -0.713  -2.7294   1.3093   0.0362
 9X9  C7   C  C     0   0.555  -3.5518   2.4321   0.0509
 9X9  N7   N  N     0  -0.656  -4.7839   2.3623   0.3606
 9X9  N6   N  NH2   0  -0.842  -2.8334   3.5696  -0.2278
 9X9  H1   H  HCH3  0   0.236   4.5688   3.5734   0.3161
 9X9  H2   H  HCH3  0   0.236   5.2469   2.5606   1.6056
 9X9  H3   H  HCH3  0   0.252   6.2943   3.1525   0.2988
 9X9  H4   H  HCR6  0   0.285   2.6300  -1.5968  -1.5535
 9X9  H5   H  HCR6  0   0.275   1.1301   1.1099   1.4068
 9X9  H6   H  HNH2  0   0.410   2.2210  -2.9622   0.4010
 9X9  H7   H  HNH2  0   0.403   1.1666  -4.2999   0.3171
 9X9  H8   H  HNH2  0   0.415  -4.0773  -2.4629   0.0257
 9X9  H9   H  HNH2  0   0.397  -3.2242  -3.9817   0.0433
 9X9  H10  H  HNH1  0   0.412  -1.7297   1.4634   0.0024
 9X9  H11  H  H     0   0.327  -5.2104   3.2789   0.2794
 9X9  H12  H  HNH2  0   0.393  -2.0664   3.4880  -0.8773
 9X9  H13  H  HNH2  0   0.394  -3.3782   4.4036  -0.3791
 9X9  O2   O  O2    0  -0.447   5.0959   1.6370  -0.2607
 9X9  O1   O  O     0  -0.465  -4.2383  -0.4130   0.0593

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
 9X9  C11  O2   single    1.424  0.020  1.424
 9X9  O2   C9   single    1.323  0.020  1.323
 9X9  C9   N9   aromatic  1.327  0.020  1.327
 9X9  C9   N8   aromatic  1.322  0.020  1.322
 9X9  N9   C10  aromatic  1.320  0.020  1.320
 9X9  N8   C8   aromatic  1.323  0.020  1.323
 9X9  C10  C5   aromatic  1.394  0.020  1.394
 9X9  C8   C5   aromatic  1.390  0.020  1.390
 9X9  C5   C2   single    1.469  0.020  1.469
 9X9  C2   N2   aromatic  1.307  0.020  1.307
 9X9  C2   C1   aromatic  1.430  0.020  1.430
 9X9  N3   C1   single    1.344  0.020  1.344
 9X9  N2   C3   aromatic  1.328  0.020  1.328
 9X9  N7   C7   double    1.272  0.020  1.272
 9X9  C1   N1   aromatic  1.321  0.020  1.321
 9X9  N5   C7   single    1.392  0.020  1.392
 9X9  N5   C6   single    1.365  0.020  1.365
 9X9  C7   N6   single    1.374  0.020  1.374
 9X9  C3   C6   single    1.476  0.020  1.476
 9X9  C3   C4   aromatic  1.420  0.020  1.420
 9X9  N1   C4   aromatic  1.335  0.020  1.335
 9X9  C6   O1   double    1.221  0.020  1.221
 9X9  C4   N4   single    1.334  0.020  1.334
 9X9  C11  H1   single    0.970  0.020  1.090
 9X9  C11  H2   single    0.970  0.020  1.090
 9X9  C11  H3   single    0.970  0.020  1.090
 9X9  C10  H4   single    0.930  0.020  1.080
 9X9  C8   H5   single    0.930  0.020  1.080
 9X9  N3   H6   single    0.890  0.020  1.040
 9X9  N3   H7   single    0.890  0.020  1.040
 9X9  N4   H8   single    0.860  0.020  1.020
 9X9  N4   H9   single    0.860  0.020  1.020
 9X9  N5   H10  single    0.860  0.020  1.020
 9X9  N7   H11  single    0.890  0.020  1.040
 9X9  N6   H12  single    0.890  0.020  1.040
 9X9  N6   H13  single    0.890  0.020  1.040

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
 9X9  N4   C4   N1   116.77  3.000
 9X9  N4   C4   C3   123.56  3.000
 9X9  N1   C4   C3   119.67  3.000
 9X9  C6   C3   N2   117.54  3.000
 9X9  C6   C3   C4   123.38  3.000
 9X9  N2   C3   C4   119.07  3.000
 9X9  N2   C2   C5   117.85  3.000
 9X9  N2   C2   C1   118.32  3.000
 9X9  C5   C2   C1   123.81  3.000
 9X9  N1   C1   N3   117.48  3.000
 9X9  N1   C1   C2   120.76  3.000
 9X9  N3   C1   C2   121.76  3.000
 9X9  H3   C11  H2   109.40  3.000
 9X9  H3   C11  H1   109.40  3.000
 9X9  H2   C11  H1   108.95  3.000
 9X9  H3   C11  O2   105.74  3.000
 9X9  H2   C11  O2   111.63  3.000
 9X9  H1   C11  O2   111.65  3.000
 9X9  N8   C9   N9   126.26  3.000
 9X9  N8   C9   O2   119.59  3.000
 9X9  N9   C9   O2   114.14  3.000
 9X9  C10  N9   C9   116.39  3.000
 9X9  H4   C10  C5   120.85  3.000
 9X9  H4   C10  N9   116.06  3.000
 9X9  C5   C10  N9   123.09  3.000
 9X9  C8   N8   C9   116.55  3.000
 9X9  H5   C8   C5   120.41  3.000
 9X9  H5   C8   N8   116.60  3.000
 9X9  C5   C8   N8   122.99  3.000
 9X9  C8   C5   C10  114.71  3.000
 9X9  C8   C5   C2   121.20  3.000
 9X9  C10  C5   C2   123.97  3.000
 9X9  C2   N2   C3   122.19  3.000
 9X9  H7   N3   H6   115.87  3.000
 9X9  H7   N3   C1   117.78  3.000
 9X9  H6   N3   C1   120.83  3.000
 9X9  C1   N1   C4   119.84  3.000
 9X9  H9   N4   H8   120.05  3.000
 9X9  H9   N4   C4   119.35  3.000
 9X9  H8   N4   C4   120.44  3.000
 9X9  N5   C6   O1   124.54  3.000
 9X9  O1   C6   C3   122.47  3.000
 9X9  N5   C6   C3   112.99  3.000
 9X9  H10  N5   C7   117.47  3.000
 9X9  H10  N5   C6   113.93  3.000
 9X9  C7   N5   C6   128.60  3.000
 9X9  N6   C7   N7   126.95  3.000
 9X9  N6   C7   N5   110.91  3.000
 9X9  N7   C7   N5   122.04  3.000
 9X9  H11  N7   C7   109.76  3.000
 9X9  H13  N6   H12  112.43  3.000
 9X9  H13  N6   C7   115.67  3.000
 9X9  H12  N6   C7   117.48  3.000
 9X9  C9   O2   C11  118.48  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
 9X9  CONST_01  C2   N2   C3   C4      0.00   0.0  0
 9X9  CONST_02  C2   C1   N1   C4      0.00   0.0  0
 9X9  CONST_03  C5   C2   N2   C3    180.00   0.0  0
 9X9  CONST_04  C1   C2   N2   C3      0.00   0.0  0
 9X9  CONST_05  C1   N1   C4   C3      0.00   0.0  0
 9X9  CONST_06  N9   C10  C5   C2    180.00   0.0  0
 9X9  CONST_07  N8   C8   C5   C2    180.00   0.0  0
 9X9  CONST_10  C5   C10  N9   C9      0.00   0.0  0
 9X9  CONST_11  C5   C8   N8   C9      0.00   0.0  0
 9X9  CONST_12  C8   N8   C9   N9      0.00   0.0  0
 9X9  CONST_13  C8   C5   C10  N9      0.00   0.0  0
 9X9  CONST_14  N8   C9   N9   C10     0.00   0.0  0
 9X9  CONST_15  N8   C8   C5   C10     0.00   0.0  0
 9X9  CONST_18  N1   C1   C2   C5    180.00   0.0  0
 9X9  CONST_19  N1   C1   C2   N2      0.00   0.0  0
 9X9  CONST_20  N1   C4   C3   N2      0.00   0.0  0
 9X9  CONST_21  N3   C1   N1   C4    180.00   0.0  0
 9X9  CONST_22  C6   C3   N2   C2    180.00   0.0  0
 9X9  CONST_23  C10  N9   C9   O2    180.00   0.0  0
 9X9  CONST_24  C8   N8   C9   O2    180.00   0.0  0
 9X9  CONST_25  N4   C4   N1   C1    180.00   0.0  0
 9X9  CONST_26  N3   C1   C2   C5      0.00   0.0  0
 9X9  CONST_27  N3   C1   C2   N2    180.00   0.0  0
 9X9  CONST_28  N4   C4   C3   N2    180.00   0.0  0
 9X9  CONST_29  C6   C3   C4   N1    180.00   0.0  0
 9X9  CONST_30  H4   C10  C5   C2      0.00   0.0  0
 9X9  CONST_31  H5   C8   C5   C2      0.00   0.0  0
 9X9  CONST_32  H8   N4   C4   C3      0.00   0.0  0
 9X9  CONST_33  H9   N4   C4   C3    180.00   0.0  0
 9X9  CONST_35  H7   N3   C1   C2    180.00   0.0  0
 9X9  CONST_36  C7   N5   C6   C3    180.00   0.0  0
 9X9  CONST_37  H10  N5   C6   C3      0.00   0.0  0
 9X9  CONST_38  C7   N5   C6   O1      0.00   0.0  0
 9X9  CONST_40  N6   C7   N5   C6    180.00   0.0  0
 9X9  CONST_41  H11  N7   C7   N5    180.00   0.0  0
 9X9  CONST_43  H13  N6   C7   N5    180.00   0.0  0
 9X9  Var_01    N5   C6   C3   C4   -179.32  30.0  2
 9X9  Var_02    N9   C9   O2   C11   179.69  30.0  2
 9X9  Var_03    H1   C11  O2   C9    -60.83  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
 9X9  plan-1  C4   0.020
 9X9  plan-1  C3   0.020
 9X9  plan-1  C2   0.020
 9X9  plan-1  C1   0.020
 9X9  plan-1  C5   0.020
 9X9  plan-1  N2   0.020
 9X9  plan-1  N3   0.020
 9X9  plan-1  N1   0.020
 9X9  plan-1  N4   0.020
 9X9  plan-1  C6   0.020
 9X9  plan-2  C2   0.020
 9X9  plan-2  C9   0.020
 9X9  plan-2  N9   0.020
 9X9  plan-2  C10  0.020
 9X9  plan-2  N8   0.020
 9X9  plan-2  C8   0.020
 9X9  plan-2  C5   0.020
 9X9  plan-2  H4   0.020
 9X9  plan-2  H5   0.020
 9X9  plan-2  O2   0.020
 9X9  plan-3  C3   0.020
 9X9  plan-3  C6   0.020
 9X9  plan-3  N5   0.020
 9X9  plan-3  C7   0.020
 9X9  plan-3  N7   0.020
 9X9  plan-3  N6   0.020
 9X9  plan-3  H10  0.020
 9X9  plan-3  H11  0.020
 9X9  plan-3  H12  0.020
 9X9  plan-3  H13  0.020
 9X9  plan-3  O1   0.020
 9X9  plan-4  C1   0.020
 9X9  plan-4  N3   0.020
 9X9  plan-4  H6   0.020
 9X9  plan-4  H7   0.020
 9X9  plan-5  C4   0.020
 9X9  plan-5  N4   0.020
 9X9  plan-5  H8   0.020
 9X9  plan-5  H9   0.020

