# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 04:01:47 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3,5-bis(azanyl)-6-(1-benzofuran-2-yl)-~{N}-carbamimidoyl-pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)NC(=O)c1nc(c(N)nc1N)c2oc3ccccc3c2
#
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
 9XF  9XF  3,5-bis(azanyl)-6-(1-benzofuran-2-yl)-~{N}-carbamimidoyl-pyrazine-2-carboxamide  ligand  36  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9XF
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
 9XF  C1   C  CR56  0   0.371   3.6228  -0.1251   0.0850
 9XF  N1   N  N     0  -0.422  -0.8784   0.3176   0.0213
 9XF  C2   C  CR16  0  -0.342   4.9855   0.0898   0.1625
 9XF  N2   N  N     0  -0.473  -0.9989   3.0323  -0.0780
 9XF  O2   O  O     0  -0.463  -4.3928   0.4862   0.0641
 9XF  C3   C  CR16  0  -0.278   5.7854  -1.0436   0.1446
 9XF  N3   N  NH2   0  -0.830  -3.2706   3.0064  -0.0672
 9XF  C4   C  CR16  0  -0.259   5.2294  -2.3261   0.0518
 9XF  C5   C  CR16  0  -0.349   3.8605  -2.5157  -0.0254
 9XF  C6   C  CR56  0   0.070   3.0352  -1.3888  -0.0080
 9XF  C7   C  CR15  0  -0.395   1.6244  -1.1559  -0.0660
 9XF  C8   C  CR5   0   0.409   1.4582   0.1905  -0.0043
 9XF  C9   C  CR6   0   0.002   0.2475   0.9916  -0.0125
 9XF  C10  C  CR6   0  -0.045  -2.0618   0.9030   0.0081
 9XF  C11  C  CR6   0   0.483  -2.1254   2.3249  -0.0460
 9XF  C12  C  CR6   0   0.462   0.1792   2.4248  -0.0636
 9XF  C13  C  C     0   0.567  -3.2581   0.0358   0.0703
 9XF  C14  C  C     0   0.553  -3.8144  -2.3742   0.2823
 9XF  N4   N  NH1   0  -0.713  -2.9515  -1.2915   0.1239
 9XF  N6   N  N     0  -0.654  -5.0014  -2.2256   0.7129
 9XF  N5   N  NH2   0  -0.839  -3.1743  -3.5558  -0.0004
 9XF  N7   N  NH2   0  -0.836   1.2555   3.2132  -0.1063
 9XF  O1   O  O     0  -0.500   2.6597   0.8265   0.0872
 9XF  H1   H  HCR6  0   0.272   5.4069   1.0838   0.2341
 9XF  H2   H  HCR6  0   0.261   6.8600  -0.9334   0.2020
 9XF  H3   H  HNH2  0   0.398  -3.2458   4.0114  -0.0852
 9XF  H4   H  HNH2  0   0.417  -4.1527   2.5248  -0.0278
 9XF  H5   H  HCR6  0   0.258   5.8886  -3.1841   0.0408
 9XF  H6   H  HCR6  0   0.258   3.4416  -3.5111  -0.0977
 9XF  H7   H  HCR5  0   0.265   0.8412  -1.8913  -0.1451
 9XF  H8   H  HNH1  0   0.414  -1.9593  -1.4878   0.0918
 9XF  H9   H  H     0   0.329  -5.4805  -3.1194   0.7320
 9XF  H10  H  HNH2  0   0.391  -2.4942  -3.5484  -0.7449
 9XF  H11  H  HNH2  0   0.395  -3.7597  -4.3755  -0.0222
 9XF  H12  H  HNH2  0   0.419   2.1941   2.8606  -0.0709
 9XF  H13  H  HNH2  0   0.403   1.1221   4.2099  -0.1225

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
 9XF  C4   C3   aromatic  1.401  0.020  1.401
 9XF  C4   C5   aromatic  1.384  0.020  1.384
 9XF  C3   C2   aromatic  1.387  0.020  1.387
 9XF  C5   C6   aromatic  1.397  0.020  1.397
 9XF  C2   C1   aromatic  1.382  0.020  1.382
 9XF  C6   C1   aromatic  1.397  0.020  1.397
 9XF  C6   C7   aromatic  1.431  0.020  1.431
 9XF  C1   O1   aromatic  1.354  0.020  1.354
 9XF  C7   C8   aromatic  1.358  0.020  1.358
 9XF  O1   C8   aromatic  1.362  0.020  1.362
 9XF  C8   C9   single    1.452  0.020  1.452
 9XF  C9   N1   aromatic  1.313  0.020  1.313
 9XF  C9   C12  aromatic  1.436  0.020  1.436
 9XF  N6   C14  double    1.271  0.020  1.271
 9XF  N1   C10  aromatic  1.320  0.020  1.320
 9XF  N7   C12  single    1.335  0.020  1.335
 9XF  C12  N2   aromatic  1.326  0.020  1.326
 9XF  N4   C14  single    1.394  0.020  1.394
 9XF  N4   C13  single    1.363  0.020  1.363
 9XF  C14  N5   single    1.373  0.020  1.373
 9XF  C10  C13  single    1.479  0.020  1.479
 9XF  C10  C11  aromatic  1.424  0.020  1.424
 9XF  C13  O2   double    1.221  0.020  1.221
 9XF  N2   C11  aromatic  1.331  0.020  1.331
 9XF  C11  N3   single    1.333  0.020  1.333
 9XF  C2   H1   single    0.930  0.020  1.080
 9XF  C3   H2   single    0.930  0.020  1.080
 9XF  N3   H3   single    0.860  0.020  1.020
 9XF  N3   H4   single    0.860  0.020  1.020
 9XF  C4   H5   single    0.930  0.020  1.080
 9XF  C5   H6   single    0.930  0.020  1.080
 9XF  C7   H7   single    0.930  0.020  1.080
 9XF  N4   H8   single    0.860  0.020  1.020
 9XF  N6   H9   single    0.890  0.020  1.040
 9XF  N5   H10  single    0.890  0.020  1.040
 9XF  N5   H11  single    0.890  0.020  1.040
 9XF  N7   H12  single    0.860  0.020  1.020
 9XF  N7   H13  single    0.860  0.020  1.020

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
 9XF  O1   C1   C6   109.68  3.000
 9XF  O1   C1   C2   126.31  3.000
 9XF  C6   C1   C2   124.01  3.000
 9XF  C10  N1   C9   122.74  3.000
 9XF  H1   C2   C3   121.79  3.000
 9XF  H1   C2   C1   122.05  3.000
 9XF  C3   C2   C1   116.16  3.000
 9XF  C12  N2   C11  120.56  3.000
 9XF  H2   C3   C4   119.41  3.000
 9XF  H2   C3   C2   119.26  3.000
 9XF  C4   C3   C2   121.33  3.000
 9XF  H4   N3   H3   120.07  3.000
 9XF  H4   N3   C11  120.53  3.000
 9XF  H3   N3   C11  119.35  3.000
 9XF  H5   C4   C5   119.56  3.000
 9XF  H5   C4   C3   119.00  3.000
 9XF  C5   C4   C3   121.44  3.000
 9XF  H6   C5   C6   120.94  3.000
 9XF  H6   C5   C4   120.83  3.000
 9XF  C6   C5   C4   118.23  3.000
 9XF  C7   C6   C5   135.49  3.000
 9XF  C7   C6   C1   105.68  3.000
 9XF  C5   C6   C1   118.83  3.000
 9XF  H7   C7   C8   126.24  3.000
 9XF  H7   C7   C6   127.49  3.000
 9XF  C8   C7   C6   106.27  3.000
 9XF  O1   C8   C9   118.57  3.000
 9XF  C9   C8   C7   130.46  3.000
 9XF  O1   C8   C7   110.97  3.000
 9XF  C12  C9   C8   126.21  3.000
 9XF  C12  C9   N1   118.21  3.000
 9XF  C8   C9   N1   115.59  3.000
 9XF  C13  C10  C11  123.42  3.000
 9XF  C11  C10  N1   118.88  3.000
 9XF  C13  C10  N1   117.69  3.000
 9XF  C10  C11  N3   123.33  3.000
 9XF  N3   C11  N2   117.08  3.000
 9XF  C10  C11  N2   119.59  3.000
 9XF  N7   C12  C9   123.53  3.000
 9XF  N7   C12  N2   116.46  3.000
 9XF  C9   C12  N2   120.01  3.000
 9XF  N4   C13  C10  112.99  3.000
 9XF  C10  C13  O2   122.37  3.000
 9XF  N4   C13  O2   124.64  3.000
 9XF  N5   C14  N6   127.26  3.000
 9XF  N5   C14  N4   110.88  3.000
 9XF  N6   C14  N4   121.72  3.000
 9XF  H8   N4   C14  117.39  3.000
 9XF  H8   N4   C13  114.09  3.000
 9XF  C14  N4   C13  128.43  3.000
 9XF  H9   N6   C14  110.14  3.000
 9XF  H11  N5   H10  112.45  3.000
 9XF  H11  N5   C14  115.70  3.000
 9XF  H10  N5   C14  117.39  3.000
 9XF  H13  N7   H12  118.23  3.000
 9XF  H13  N7   C12  118.61  3.000
 9XF  H12  N7   C12  123.07  3.000
 9XF  C8   O1   C1   107.40  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
 9XF  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 9XF  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 9XF  CONST_03  C8   C7   C6   C1     0.00   0.0  0
 9XF  CONST_04  C7   C8   O1   C1     0.00   0.0  0
 9XF  CONST_05  C9   C8   O1   C1   180.00   0.0  0
 9XF  CONST_06  C7   C8   C9   N1     0.00   0.0  0
 9XF  CONST_07  O1   C8   C9   N1   180.00   0.0  0
 9XF  CONST_08  N2   C12  C9   N1     0.00   0.0  0
 9XF  CONST_09  N2   C11  C10  N1     0.00   0.0  0
 9XF  CONST_10  C5   C4   C3   C2     0.00   0.0  0
 9XF  CONST_11  C5   C6   C1   C2     0.00   0.0  0
 9XF  CONST_12  C7   C6   C1   C2   180.00   0.0  0
 9XF  CONST_13  C8   O1   C1   C2   180.00   0.0  0
 9XF  CONST_14  C8   C9   C12  N2   180.00   0.0  0
 9XF  CONST_15  C6   C5   C4   C3     0.00   0.0  0
 9XF  CONST_16  C6   C1   C2   C3     0.00   0.0  0
 9XF  CONST_17  O1   C1   C2   C3   180.00   0.0  0
 9XF  CONST_18  C7   C6   C5   C4   180.00   0.0  0
 9XF  CONST_19  O1   C1   C6   C5   180.00   0.0  0
 9XF  CONST_20  C8   C7   C6   C5   180.00   0.0  0
 9XF  CONST_21  C8   O1   C1   C6     0.00   0.0  0
 9XF  CONST_22  O1   C8   C7   C6     0.00   0.0  0
 9XF  CONST_23  C9   C8   C7   C6   180.00   0.0  0
 9XF  CONST_24  O1   C1   C6   C7     0.00   0.0  0
 9XF  CONST_25  C12  C9   C8   C7   180.00   0.0  0
 9XF  CONST_26  C10  N1   C9   C8   180.00   0.0  0
 9XF  CONST_27  C11  C10  N1   C9     0.00   0.0  0
 9XF  CONST_28  C11  N2   C12  C9     0.00   0.0  0
 9XF  CONST_29  C12  C9   N1   C10    0.00   0.0  0
 9XF  CONST_30  C12  N2   C11  C10    0.00   0.0  0
 9XF  CONST_31  O1   C8   C9   C12    0.00   0.0  0
 9XF  CONST_32  N7   C12  C9   N1   180.00   0.0  0
 9XF  CONST_33  N3   C11  C10  N1   180.00   0.0  0
 9XF  CONST_34  C13  C10  C11  N2   180.00   0.0  0
 9XF  CONST_35  C12  N2   C11  N3   180.00   0.0  0
 9XF  CONST_36  N7   C12  C9   C8     0.00   0.0  0
 9XF  CONST_37  C13  C10  N1   C9   180.00   0.0  0
 9XF  CONST_38  N7   C12  N2   C11  180.00   0.0  0
 9XF  CONST_39  H2   C3   C2   C1   180.00   0.0  0
 9XF  CONST_40  H6   C5   C6   C1   180.00   0.0  0
 9XF  CONST_41  H7   C7   C6   C1   180.00   0.0  0
 9XF  CONST_42  H5   C4   C3   C2   180.00   0.0  0
 9XF  CONST_43  H1   C2   C3   C4   180.00   0.0  0
 9XF  CONST_44  H12  N7   C12  N2   180.00   0.0  0
 9XF  CONST_45  H13  N7   C12  N2     0.00   0.0  0
 9XF  CONST_46  H3   N3   C11  N2     0.00   0.0  0
 9XF  CONST_47  H4   N3   C11  N2   180.00   0.0  0
 9XF  CONST_48  C14  N4   C13  C10  180.00   0.0  0
 9XF  CONST_49  H8   N4   C13  C10    0.00   0.0  0
 9XF  CONST_50  C14  N4   C13  O2     0.00   0.0  0
 9XF  CONST_52  N5   C14  N4   C13  180.00   0.0  0
 9XF  CONST_53  H9   N6   C14  N4   180.00   0.0  0
 9XF  CONST_55  H11  N5   C14  N4   180.00   0.0  0
 9XF  Var_01    N4   C13  C10  N1    -0.48  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
 9XF  plan-1  N1   0.020
 9XF  plan-1  N2   0.020
 9XF  plan-1  N3   0.020
 9XF  plan-1  C8   0.020
 9XF  plan-1  C9   0.020
 9XF  plan-1  C10  0.020
 9XF  plan-1  C11  0.020
 9XF  plan-1  C12  0.020
 9XF  plan-1  C13  0.020
 9XF  plan-1  N7   0.020
 9XF  plan-2  C1   0.020
 9XF  plan-2  C2   0.020
 9XF  plan-2  C3   0.020
 9XF  plan-2  C4   0.020
 9XF  plan-2  C5   0.020
 9XF  plan-2  C6   0.020
 9XF  plan-2  C7   0.020
 9XF  plan-2  C8   0.020
 9XF  plan-2  C9   0.020
 9XF  plan-2  O1   0.020
 9XF  plan-2  H1   0.020
 9XF  plan-2  H2   0.020
 9XF  plan-2  H5   0.020
 9XF  plan-2  H6   0.020
 9XF  plan-2  H7   0.020
 9XF  plan-3  O2   0.020
 9XF  plan-3  C10  0.020
 9XF  plan-3  C13  0.020
 9XF  plan-3  C14  0.020
 9XF  plan-3  N4   0.020
 9XF  plan-3  N6   0.020
 9XF  plan-3  N5   0.020
 9XF  plan-3  H8   0.020
 9XF  plan-3  H9   0.020
 9XF  plan-3  H10  0.020
 9XF  plan-3  H11  0.020
 9XF  plan-4  N3   0.020
 9XF  plan-4  C11  0.020
 9XF  plan-4  H3   0.020
 9XF  plan-4  H4   0.020
 9XF  plan-5  C12  0.020
 9XF  plan-5  N7   0.020
 9XF  plan-5  H12  0.020
 9XF  plan-5  H13  0.020

