# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 22:13:37 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: N~3~-benzyl-2-[(6-bromo-1,3-benzodioxol-5-yl)methyl]imidazo[1,2-a]pyrazine-3,8-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccn2c(NCc3ccccc3)c(Cc4cc5OCOc5cc4Br)nc12
#
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
 JR9  JR9  N~3~-benzyl-2-[(6-bromo-1,3-benzodioxol-5-yl)methyl]imidazo[1,2-a]pyrazine-3,8-diamine  ligand  47  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JR9
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
 JR9  N01  N   N     0  -0.447   0.5243   4.6820  -2.1304
 JR9  C02  C   CR16  0  -0.163   1.6156   3.9657  -2.5097
 JR9  C03  C   CR16  0  -0.088   1.9807   2.7762  -1.9789
 JR9  N04  N   N     0  -0.491   1.1785   2.2734  -0.9810
 JR9  C05  C   CR56  0   0.408   0.0648   2.9417  -0.5641
 JR9  C06  C   CR6   0   0.380  -0.2427   4.1908  -1.1892
 JR9  C07  C   CR5   0   0.398   1.2465   1.1191  -0.2366
 JR9  C08  C   CR5   0   0.159   0.1506   1.1722   0.6022
 JR9  N09  N   N     0  -0.458  -0.5707   2.2954   0.3943
 JR9  N10  N   NH2   0  -0.823  -1.3625   4.8313  -0.8047
 JR9  N11  N   NH1   0  -0.681   2.2408   0.1585  -0.3300
 JR9  C12  C   CH2   0  -0.350   3.5528   0.4957   0.2123
 JR9  C13  C   CR6   0   0.092   4.3912  -0.7439   0.3753
 JR9  C14  C   CR16  0  -0.314   5.6498  -0.8364  -0.2077
 JR9  C15  C   CR16  0  -0.240   6.4274  -1.9776  -0.0425
 JR9  C16  C   CR16  0  -0.268   5.9482  -3.0421   0.7062
 JR9  C17  C   CR16  0  -0.241   4.6877  -2.9604   1.2895
 JR9  C18  C   CR16  0  -0.286   3.9162  -1.8209   1.1226
 JR9  C19  C   CH2   0  -0.635  -0.2352   0.1197   1.5900
 JR9  C20  C   CR6   0   0.185  -1.1427  -0.9140   0.9660
 JR9  C21  C   CR6   0  -0.218  -2.5295  -0.8818   1.0277
 JR9  C22  C   CR16  0  -0.307  -3.3443  -1.8434   0.4083
 JR9  C23  C   CR56  0   0.295  -2.7028  -2.8356  -0.2829
 JR9  C24  C   CR56  0   0.325  -1.3205  -2.8880  -0.3671
 JR9  C25  C   CR16  0  -0.387  -0.5279  -1.9527   0.2394
 JR9  O26  O   O     0  -0.483  -3.2368  -3.8854  -0.9471
 JR9  C27  C   CH2   0   0.068  -2.1555  -4.5233  -1.6177
 JR9  O28  O   O     0  -0.483  -0.9557  -3.9725  -1.0879
 JR9  BR   BR  BR    0  -0.053  -3.4315   0.4948   1.9635
 JR9  H1   H   HCR6  0   0.266   2.2215   4.3982  -3.2949
 JR9  H2   H   HCR6  0   0.298   2.8431   2.2062  -2.2863
 JR9  H3   H   HNH2  0   0.397  -1.4905   5.7870  -1.0917
 JR9  H4   H   HNH2  0   0.402  -1.8183   4.5493   0.0465
 JR9  H5   H   HCH2  0   0.233   4.0995   1.2262  -0.3967
 JR9  H6   H   HCR6  0   0.251   6.0286  -0.0107  -0.7986
 JR9  H7   H   HCR6  0   0.255   7.4049  -2.0344  -0.5040
 JR9  H8   H   HCR6  0   0.255   6.5513  -3.9317   0.8348
 JR9  H9   H   HCR6  0   0.255   4.3074  -3.7871   1.8758
 JR9  H10  H   HCR6  0   0.250   2.9347  -1.7637   1.5781
 JR9  H11  H   HCH2  0   0.284   0.6674  -0.3824   1.9411
 JR9  H12  H   HCH2  0   0.277  -0.6924   0.5843   2.4625
 JR9  H13  H   HCR6  0   0.293  -4.4231  -1.8077   0.4729
 JR9  H14  H   HCR6  0   0.275   0.5517  -1.9899   0.1626
 JR9  H15  H   HCH2  0   0.249  -2.1851  -5.5959  -1.4271
 JR9  H16  H   HCH2  0   0.238  -2.2140  -4.3210  -2.6918
 JR9  H17  H   HNH1  0   0.372   2.3032  -0.2741  -1.2431
 JR9  H18  H   HCH2  0   0.258   3.3933   0.9608   1.1882

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
 JR9  C17  C16  aromatic  1.391  0.020  1.391
 JR9  C17  C18  aromatic  1.386  0.020  1.386
 JR9  C16  C15  aromatic  1.387  0.020  1.387
 JR9  C18  C13  aromatic  1.394  0.020  1.394
 JR9  C02  C03  aromatic  1.353  0.020  1.353
 JR9  C02  N01  aromatic  1.359  0.020  1.359
 JR9  C15  C14  aromatic  1.391  0.020  1.391
 JR9  C03  N04  aromatic  1.376  0.020  1.376
 JR9  C13  C14  aromatic  1.390  0.020  1.390
 JR9  C13  C12  single    1.505  0.020  1.505
 JR9  N01  C06  aromatic  1.310  0.020  1.310
 JR9  N11  C12  single    1.459  0.020  1.459
 JR9  N11  C07  single    1.386  0.020  1.386
 JR9  N04  C07  aromatic  1.375  0.020  1.375
 JR9  N04  C05  aromatic  1.364  0.020  1.364
 JR9  C07  C08  aromatic  1.381  0.020  1.381
 JR9  C06  C05  aromatic  1.430  0.020  1.430
 JR9  C06  N10  single    1.346  0.020  1.346
 JR9  C27  O28  single    1.423  0.020  1.423
 JR9  C27  O26  single    1.423  0.020  1.423
 JR9  O28  C24  single    1.352  0.020  1.352
 JR9  C05  N09  aromatic  1.319  0.020  1.319
 JR9  O26  C23  single    1.352  0.020  1.352
 JR9  C24  C23  aromatic  1.386  0.020  1.386
 JR9  C24  C25  aromatic  1.368  0.020  1.368
 JR9  C23  C22  aromatic  1.369  0.020  1.369
 JR9  C25  C20  aromatic  1.409  0.020  1.409
 JR9  C08  N09  aromatic  1.351  0.020  1.351
 JR9  C08  C19  single    1.494  0.020  1.494
 JR9  C22  C21  aromatic  1.404  0.020  1.404
 JR9  C20  C21  aromatic  1.389  0.020  1.389
 JR9  C20  C19  single    1.510  0.020  1.510
 JR9  C21  BR   single    1.893  0.020  1.893
 JR9  C02  H1   single    0.930  0.020  1.080
 JR9  C03  H2   single    0.930  0.020  1.080
 JR9  N10  H3   single    0.890  0.020  1.040
 JR9  N10  H4   single    0.890  0.020  1.040
 JR9  C12  H5   single    0.970  0.020  1.090
 JR9  C14  H6   single    0.930  0.020  1.080
 JR9  C15  H7   single    0.930  0.020  1.080
 JR9  C16  H8   single    0.930  0.020  1.080
 JR9  C17  H9   single    0.930  0.020  1.080
 JR9  C18  H10  single    0.930  0.020  1.080
 JR9  C19  H11  single    0.970  0.020  1.090
 JR9  C19  H12  single    0.970  0.020  1.090
 JR9  C22  H13  single    0.930  0.020  1.080
 JR9  C25  H14  single    0.930  0.020  1.080
 JR9  C27  H15  single    0.970  0.020  1.090
 JR9  C27  H16  single    0.970  0.020  1.090
 JR9  N11  H17  single    0.890  0.020  1.040
 JR9  C12  H18  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
 JR9  C06  N01  C02  118.23  3.000
 JR9  H1   C02  C03  119.01  3.000
 JR9  H1   C02  N01  116.20  3.000
 JR9  C03  C02  N01  124.79  3.000
 JR9  H2   C03  N04  118.68  3.000
 JR9  H2   C03  C02  124.66  3.000
 JR9  N04  C03  C02  116.65  3.000
 JR9  C07  N04  C05  106.63  3.000
 JR9  C05  N04  C03  121.25  3.000
 JR9  C07  N04  C03  132.11  3.000
 JR9  N09  C05  C06  129.93  3.000
 JR9  N09  C05  N04  112.04  3.000
 JR9  C06  C05  N04  118.03  3.000
 JR9  N10  C06  C05  118.01  3.000
 JR9  N10  C06  N01  120.93  3.000
 JR9  C05  C06  N01  121.05  3.000
 JR9  N11  C07  C08  129.56  3.000
 JR9  C08  C07  N04  104.91  3.000
 JR9  N11  C07  N04  125.52  3.000
 JR9  C19  C08  N09  123.34  3.000
 JR9  C19  C08  C07  125.40  3.000
 JR9  N09  C08  C07  111.23  3.000
 JR9  C08  N09  C05  105.19  3.000
 JR9  H4   N10  H3   116.75  3.000
 JR9  H4   N10  C06  119.03  3.000
 JR9  H3   N10  C06  118.45  3.000
 JR9  H17  N11  C12  112.24  3.000
 JR9  H17  N11  C07  113.66  3.000
 JR9  C12  N11  C07  117.38  3.000
 JR9  H18  C12  H5   106.56  3.000
 JR9  H18  C12  C13  109.58  3.000
 JR9  H5   C12  C13  109.32  3.000
 JR9  H18  C12  N11  107.39  3.000
 JR9  H5   C12  N11  113.31  3.000
 JR9  C13  C12  N11  110.53  3.000
 JR9  C18  C13  C14  118.80  3.000
 JR9  C14  C13  C12  120.91  3.000
 JR9  C18  C13  C12  120.29  3.000
 JR9  H6   C14  C15  119.63  3.000
 JR9  H6   C14  C13  119.63  3.000
 JR9  C15  C14  C13  120.73  3.000
 JR9  H7   C15  C16  120.13  3.000
 JR9  H7   C15  C14  119.83  3.000
 JR9  C16  C15  C14  120.05  3.000
 JR9  H8   C16  C17  120.21  3.000
 JR9  H8   C16  C15  120.17  3.000
 JR9  C17  C16  C15  119.62  3.000
 JR9  H9   C17  C18  119.83  3.000
 JR9  H9   C17  C16  120.04  3.000
 JR9  C18  C17  C16  120.13  3.000
 JR9  H10  C18  C17  119.80  3.000
 JR9  H10  C18  C13  119.54  3.000
 JR9  C17  C18  C13  120.66  3.000
 JR9  H12  C19  H11  106.61  3.000
 JR9  H12  C19  C20  111.76  3.000
 JR9  H11  C19  C20  108.37  3.000
 JR9  H12  C19  C08  109.73  3.000
 JR9  H11  C19  C08  108.87  3.000
 JR9  C20  C19  C08  111.35  3.000
 JR9  C25  C20  C21  118.41  3.000
 JR9  C21  C20  C19  124.46  3.000
 JR9  C25  C20  C19  117.09  3.000
 JR9  BR   C21  C22  116.07  3.000
 JR9  BR   C21  C20  120.97  3.000
 JR9  C22  C21  C20  122.95  3.000
 JR9  H13  C22  C23  121.44  3.000
 JR9  H13  C22  C21  122.00  3.000
 JR9  C23  C22  C21  116.56  3.000
 JR9  O26  C23  C24  109.55  3.000
 JR9  C24  C23  C22  121.70  3.000
 JR9  O26  C23  C22  128.74  3.000
 JR9  O28  C24  C25  128.93  3.000
 JR9  C25  C24  C23  121.68  3.000
 JR9  O28  C24  C23  109.38  3.000
 JR9  H14  C25  C24  121.51  3.000
 JR9  H14  C25  C20  119.80  3.000
 JR9  C24  C25  C20  118.69  3.000
 JR9  C27  O26  C23  106.23  3.000
 JR9  H16  C27  H15  110.62  3.000
 JR9  H16  C27  O28  109.82  3.000
 JR9  H15  C27  O28  109.81  3.000
 JR9  H16  C27  O26  109.81  3.000
 JR9  H15  C27  O26  109.76  3.000
 JR9  O28  C27  O26  106.96  3.000
 JR9  C27  O28  C24  106.35  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
 JR9  CONST_01  N04  C03  C02  N01    0.00   0.0  0
 JR9  CONST_02  N04  C05  C06  N01    0.00   0.0  0
 JR9  CONST_03  N09  C05  C06  N01  180.00   0.0  0
 JR9  CONST_04  C07  N04  C03  C02  180.00   0.0  0
 JR9  CONST_05  C05  N04  C03  C02    0.00   0.0  0
 JR9  CONST_06  C05  C06  N01  C02    0.00   0.0  0
 JR9  CONST_07  C06  N01  C02  C03    0.00   0.0  0
 JR9  CONST_08  C08  C07  N04  C03  180.00   0.0  0
 JR9  CONST_09  C06  C05  N04  C03    0.00   0.0  0
 JR9  CONST_10  N09  C05  N04  C03  180.00   0.0  0
 JR9  CONST_11  N09  C08  C07  N04    0.00   0.0  0
 JR9  CONST_12  C08  N09  C05  N04    0.00   0.0  0
 JR9  CONST_13  C08  C07  N04  C05    0.00   0.0  0
 JR9  CONST_14  C07  C08  N09  C05    0.00   0.0  0
 JR9  CONST_15  C07  N04  C05  C06  180.00   0.0  0
 JR9  CONST_16  C08  N09  C05  C06  180.00   0.0  0
 JR9  CONST_17  N09  C05  N04  C07    0.00   0.0  0
 JR9  CONST_18  C16  C17  C18  C13    0.00   0.0  0
 JR9  CONST_19  C16  C15  C14  C13    0.00   0.0  0
 JR9  CONST_20  C17  C16  C15  C14    0.00   0.0  0
 JR9  CONST_21  C17  C18  C13  C14    0.00   0.0  0
 JR9  CONST_22  C18  C17  C16  C15    0.00   0.0  0
 JR9  CONST_23  C18  C13  C14  C15    0.00   0.0  0
 JR9  CONST_24  C23  C24  C25  C20    0.00   0.0  0
 JR9  CONST_25  C23  C22  C21  C20    0.00   0.0  0
 JR9  CONST_26  C24  C23  C22  C21    0.00   0.0  0
 JR9  CONST_27  C24  C25  C20  C21    0.00   0.0  0
 JR9  CONST_28  C25  C24  C23  C22    0.00   0.0  0
 JR9  CONST_29  C25  C20  C21  C22    0.00   0.0  0
 JR9  CONST_30  N10  C06  N01  C02  180.00   0.0  0
 JR9  CONST_31  N11  C07  N04  C03    0.00   0.0  0
 JR9  CONST_32  C19  C08  C07  N04  180.00   0.0  0
 JR9  CONST_33  N10  C06  C05  N04  180.00   0.0  0
 JR9  CONST_34  N11  C07  N04  C05  180.00   0.0  0
 JR9  CONST_35  C19  C08  N09  C05  180.00   0.0  0
 JR9  CONST_36  N10  C06  C05  N09    0.00   0.0  0
 JR9  CONST_37  N11  C07  C08  N09  180.00   0.0  0
 JR9  CONST_38  C17  C18  C13  C12  180.00   0.0  0
 JR9  CONST_39  C15  C14  C13  C12  180.00   0.0  0
 JR9  CONST_40  C24  C25  C20  C19  180.00   0.0  0
 JR9  CONST_41  C22  C21  C20  C19  180.00   0.0  0
 JR9  CONST_42  BR   C21  C22  C23  180.00   0.0  0
 JR9  CONST_43  BR   C21  C20  C25  180.00   0.0  0
 JR9  CONST_44  H2   C03  C02  N01  180.00   0.0  0
 JR9  CONST_45  H1   C02  C03  N04  180.00   0.0  0
 JR9  CONST_46  H9   C17  C18  C13  180.00   0.0  0
 JR9  CONST_47  H7   C15  C14  C13  180.00   0.0  0
 JR9  CONST_48  H8   C16  C15  C14  180.00   0.0  0
 JR9  CONST_49  H10  C18  C13  C14  180.00   0.0  0
 JR9  CONST_50  H6   C14  C15  C16  180.00   0.0  0
 JR9  CONST_51  H13  C22  C21  C20  180.00   0.0  0
 JR9  CONST_52  H14  C25  C20  C21  180.00   0.0  0
 JR9  CONST_55  H3   N10  C06  N01    0.00   0.0  0
 JR9  CONST_56  H4   N10  C06  N01  180.00   0.0  0
 JR9  Var_01    O28  C27  O26  C23   12.06  30.0  1
 JR9  Var_02    O26  C27  O28  C24  -12.05  30.0  1
 JR9  Var_03    C20  C19  C08  C07  -89.14  30.0  2
 JR9  Var_04    C25  C20  C19  C08   83.07  30.0  2
 JR9  Var_05    C13  C12  N11  C07  164.65  30.0  3
 JR9  Var_06    C18  C13  C12  N11  -55.11  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
 JR9  plan-1  C12  0.020
 JR9  plan-1  C13  0.020
 JR9  plan-1  C14  0.020
 JR9  plan-1  C15  0.020
 JR9  plan-1  C16  0.020
 JR9  plan-1  C17  0.020
 JR9  plan-1  C18  0.020
 JR9  plan-1  H6   0.020
 JR9  plan-1  H7   0.020
 JR9  plan-1  H8   0.020
 JR9  plan-1  H9   0.020
 JR9  plan-1  H10  0.020
 JR9  plan-2  N01  0.020
 JR9  plan-2  C02  0.020
 JR9  plan-2  C03  0.020
 JR9  plan-2  N04  0.020
 JR9  plan-2  C05  0.020
 JR9  plan-2  C06  0.020
 JR9  plan-2  C07  0.020
 JR9  plan-2  C08  0.020
 JR9  plan-2  N09  0.020
 JR9  plan-2  N10  0.020
 JR9  plan-2  N11  0.020
 JR9  plan-2  C19  0.020
 JR9  plan-2  H1   0.020
 JR9  plan-2  H2   0.020
 JR9  plan-3  C19  0.020
 JR9  plan-3  C20  0.020
 JR9  plan-3  C21  0.020
 JR9  plan-3  C22  0.020
 JR9  plan-3  C23  0.020
 JR9  plan-3  C24  0.020
 JR9  plan-3  C25  0.020
 JR9  plan-3  O26  0.020
 JR9  plan-3  O28  0.020
 JR9  plan-3  BR   0.020
 JR9  plan-3  H13  0.020
 JR9  plan-3  H14  0.020
 JR9  plan-4  C06  0.020
 JR9  plan-4  N10  0.020
 JR9  plan-4  H3   0.020
 JR9  plan-4  H4   0.020
 JR9  plan-5  C07  0.020
 JR9  plan-5  N11  0.020
 JR9  plan-5  C12  0.020
 JR9  plan-5  H17  0.020

