# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 07:48:57 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-[3-(2,3-dichlorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(N)CCN(CC1)c2cnc3c([nH]nc3c4cccc(Cl)c4Cl)n2
#
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
 U9Y  U9Y  1-[3-(2,3-dichlorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine  ligand  43  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U9Y
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
 U9Y  C12  C   CR56  0   0.528   -97.1450  22.7922  75.2155
 U9Y  C13  C   CR56  0  -0.032   -97.0792  21.5659  74.5530
 U9Y  C01  C   CR16  0  -0.317   -97.3462  18.4858  74.6336
 U9Y  C02  C   CR16  0  -0.234   -97.5672  17.1502  74.3478
 U9Y  C03  C   CR16  0  -0.231   -98.8597  16.6596  74.2779
 U9Y  C04  C   CR6   0   0.023   -99.9256  17.5212  74.4820
 U9Y  C05  C   CR6   0  -0.073   -99.7104  18.8692  74.7607
 U9Y  C06  C   CR6   0   0.161   -98.4062  19.3659  74.8525
 U9Y  C09  C   CR5   0   0.194   -98.0890  20.7644  75.1547
 U9Y  C15  C   CR6   0   0.498   -95.4727  23.6485  74.0072
 U9Y  C16  C   CR16  0  -0.199   -95.4103  22.3852  73.3005
 U9Y  C19  C   CH2   0  -0.340   -94.7461  25.9479  74.3733
 U9Y  C20  C   CH2   0  -0.422   -95.4363  26.9200  73.4231
 U9Y  C21  C   CT    0   0.068   -94.6977  27.0586  72.0852
 U9Y  C22  C   CH2   0  -0.413   -94.4301  25.6563  71.5225
 U9Y  C23  C   CH2   0  -0.347   -93.7839  24.7236  72.5412
 U9Y  C24  C   CH3   0  -0.660   -93.3819  27.8237  72.2737
 U9Y  N10  N   N     0  -0.245   -98.6971  21.4546  76.0923
 U9Y  N11  N   NR15  0  -0.526   -98.1326  22.6693  76.1218
 U9Y  N14  N   N     0  -0.482   -96.3743  23.8403  74.9638
 U9Y  N17  N   N     0  -0.357   -96.1909  21.3771  73.5673
 U9Y  N18  N   NT    0  -0.484   -94.5968  24.6456  73.7439
 U9Y  CL7  CL  CL    0  -0.092  -101.0712  19.9067  74.9417
 U9Y  CL8  CL  CL    0  -0.093  -101.5287  16.8963  74.3822
 U9Y  H1   H   HCR6  0   0.268   -96.3330  18.8566  74.7043
 U9Y  H2   H   HCR6  0   0.275   -96.7308  16.4839  74.1879
 U9Y  H3   H   HCR6  0   0.289   -99.0453  15.6159  74.0647
 U9Y  H4   H   HCR6  0   0.273   -94.6906  22.2322  72.5087
 U9Y  H5   H   HCH2  0   0.249   -93.7472  26.3060  74.6358
 U9Y  H6   H   HCH2  0   0.274   -95.3045  25.8499  75.2989
 U9Y  H7   H   HCH2  0   0.234   -95.5228  27.8983  73.9062
 U9Y  H8   H   HCH2  0   0.234   -96.4541  26.5667  73.2312
 U9Y  H9   H   HCH2  0   0.234   -95.3789  25.2183  71.1989
 U9Y  H10  H   HCH2  0   0.236   -93.7898  25.7218  70.6373
 U9Y  H11  H   HCH2  0   0.273   -93.6231  23.7437  72.1027
 U9Y  H12  H   HCH2  0   0.255   -92.7947  25.0870  72.8311
 U9Y  H13  H   HCH3  0   0.221   -92.6918  27.3462  72.9711
 U9Y  H14  H   HCH3  0   0.227   -92.8616  27.9228  71.3186
 U9Y  H15  H   HCH3  0   0.227   -93.5806  28.8287  72.6525
 U9Y  H16  H   HNR5  0   0.418   -98.4567  23.3555  76.7855
 U9Y  N25  N   NH2   0  -0.786   -95.5871  27.7491  71.1523
 U9Y  H17  H   HNH2  0   0.337   -95.7703  28.6846  71.5006
 U9Y  H18  H   HNH2  0   0.337   -95.1015  27.8847  70.2715

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
 U9Y  N25  C21  single    1.462  0.020  1.462
 U9Y  C22  C21  single    1.534  0.020  1.534
 U9Y  C22  C23  single    1.525  0.020  1.525
 U9Y  C24  C21  single    1.534  0.020  1.534
 U9Y  C21  C20  single    1.534  0.020  1.534
 U9Y  C23  N18  single    1.454  0.020  1.454
 U9Y  C16  N17  aromatic  1.303  0.020  1.303
 U9Y  C16  C15  aromatic  1.449  0.020  1.449
 U9Y  C20  C19  single    1.524  0.020  1.524
 U9Y  CL8  C04  single    1.723  0.020  1.723
 U9Y  N18  C15  single    1.353  0.020  1.353
 U9Y  N18  C19  single    1.454  0.020  1.454
 U9Y  N17  C13  aromatic  1.340  0.020  1.340
 U9Y  C15  N14  aromatic  1.328  0.020  1.328
 U9Y  CL7  C05  single    1.721  0.020  1.721
 U9Y  C04  C03  aromatic  1.386  0.020  1.386
 U9Y  C04  C05  aromatic  1.393  0.020  1.393
 U9Y  C03  C02  aromatic  1.384  0.020  1.384
 U9Y  C05  C06  aromatic  1.399  0.020  1.399
 U9Y  C13  C09  aromatic  1.423  0.020  1.423
 U9Y  C13  C12  aromatic  1.395  0.020  1.395
 U9Y  C02  C01  aromatic  1.384  0.020  1.384
 U9Y  N14  C12  aromatic  1.325  0.020  1.325
 U9Y  C06  C01  aromatic  1.395  0.020  1.395
 U9Y  C06  C09  single    1.465  0.020  1.465
 U9Y  C09  N10  aromatic  1.313  0.020  1.313
 U9Y  C12  N11  aromatic  1.346  0.020  1.346
 U9Y  N11  N10  aromatic  1.340  0.020  1.340
 U9Y  C01  H1   single    0.930  0.020  1.080
 U9Y  C02  H2   single    0.930  0.020  1.080
 U9Y  C03  H3   single    0.930  0.020  1.080
 U9Y  C16  H4   single    0.930  0.020  1.080
 U9Y  C19  H5   single    0.970  0.020  1.090
 U9Y  C19  H6   single    0.970  0.020  1.090
 U9Y  C20  H7   single    0.970  0.020  1.090
 U9Y  C20  H8   single    0.970  0.020  1.090
 U9Y  C22  H9   single    0.970  0.020  1.090
 U9Y  C22  H10  single    0.970  0.020  1.090
 U9Y  C23  H11  single    0.970  0.020  1.090
 U9Y  C23  H12  single    0.970  0.020  1.090
 U9Y  C24  H13  single    0.970  0.020  1.090
 U9Y  C24  H14  single    0.970  0.020  1.090
 U9Y  C24  H15  single    0.970  0.020  1.090
 U9Y  N11  H16  single    0.860  0.020  1.020
 U9Y  N25  H17  single    0.890  0.020  1.040
 U9Y  N25  H18  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
 U9Y  N14  C12  N11  128.82  3.000
 U9Y  N11  C12  C13  105.90  3.000
 U9Y  N14  C12  C13  125.27  3.000
 U9Y  N17  C13  C09  134.59  3.000
 U9Y  C09  C13  C12  105.12  3.000
 U9Y  N17  C13  C12  120.28  3.000
 U9Y  H1   C01  C06  119.04  3.000
 U9Y  H1   C01  C02  119.63  3.000
 U9Y  C06  C01  C02  121.33  3.000
 U9Y  H2   C02  C03  119.76  3.000
 U9Y  H2   C02  C01  120.12  3.000
 U9Y  C03  C02  C01  120.12  3.000
 U9Y  H3   C03  C04  119.81  3.000
 U9Y  H3   C03  C02  120.82  3.000
 U9Y  C04  C03  C02  119.37  3.000
 U9Y  CL8  C04  C05  120.40  3.000
 U9Y  C05  C04  C03  120.81  3.000
 U9Y  CL8  C04  C03  118.79  3.000
 U9Y  CL7  C05  C06  121.09  3.000
 U9Y  C06  C05  C04  120.05  3.000
 U9Y  CL7  C05  C04  118.83  3.000
 U9Y  C09  C06  C05  123.66  3.000
 U9Y  C09  C06  C01  118.03  3.000
 U9Y  C05  C06  C01  118.31  3.000
 U9Y  N10  C09  C06  123.26  3.000
 U9Y  N10  C09  C13  109.54  3.000
 U9Y  C06  C09  C13  127.16  3.000
 U9Y  N18  C15  N14  118.23  3.000
 U9Y  N14  C15  C16  120.42  3.000
 U9Y  N18  C15  C16  121.31  3.000
 U9Y  H4   C16  N17  116.07  3.000
 U9Y  H4   C16  C15  120.63  3.000
 U9Y  N17  C16  C15  123.30  3.000
 U9Y  H6   C19  H5   107.15  3.000
 U9Y  H6   C19  N18  109.94  3.000
 U9Y  H5   C19  N18  107.67  3.000
 U9Y  H6   C19  C20  110.86  3.000
 U9Y  H5   C19  C20  110.76  3.000
 U9Y  N18  C19  C20  110.36  3.000
 U9Y  H8   C20  H7   107.01  3.000
 U9Y  H8   C20  C21  108.90  3.000
 U9Y  H7   C20  C21  110.00  3.000
 U9Y  H8   C20  C19  108.94  3.000
 U9Y  H7   C20  C19  109.31  3.000
 U9Y  C21  C20  C19  112.52  3.000
 U9Y  N25  C21  C24  111.38  3.000
 U9Y  C24  C21  C22  110.57  3.000
 U9Y  N25  C21  C22  107.67  3.000
 U9Y  C24  C21  C20  110.54  3.000
 U9Y  C22  C21  C20  108.73  3.000
 U9Y  N25  C21  C20  107.83  3.000
 U9Y  H10  C22  H9   106.99  3.000
 U9Y  H10  C22  C23  109.21  3.000
 U9Y  H9   C22  C23  108.67  3.000
 U9Y  H10  C22  C21  110.12  3.000
 U9Y  H9   C22  C21  108.85  3.000
 U9Y  C23  C22  C21  112.82  3.000
 U9Y  H12  C23  H11  105.85  3.000
 U9Y  H12  C23  N18  107.73  3.000
 U9Y  H11  C23  N18  111.63  3.000
 U9Y  H12  C23  C22  110.94  3.000
 U9Y  H11  C23  C22  110.18  3.000
 U9Y  N18  C23  C22  110.40  3.000
 U9Y  H15  C24  H14  107.85  3.000
 U9Y  H15  C24  H13  107.22  3.000
 U9Y  H14  C24  H13  107.30  3.000
 U9Y  H15  C24  C21  110.22  3.000
 U9Y  H14  C24  C21  110.28  3.000
 U9Y  H13  C24  C21  113.75  3.000
 U9Y  N11  N10  C09  107.28  3.000
 U9Y  H16  N11  N10  119.74  3.000
 U9Y  H16  N11  C12  128.10  3.000
 U9Y  N10  N11  C12  112.15  3.000
 U9Y  C15  N14  C12  114.67  3.000
 U9Y  C16  N17  C13  116.03  3.000
 U9Y  C23  N18  C19  111.55  3.000
 U9Y  C19  N18  C15  120.62  3.000
 U9Y  C23  N18  C15  124.23  3.000
 U9Y  H18  N25  H17  105.14  3.000
 U9Y  H18  N25  C21  109.01  3.000
 U9Y  H17  N25  C21  109.03  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
 U9Y  CONST_01  C16  N17  C13  C12    0.00   0.0  0
 U9Y  CONST_02  C06  C09  C13  C12  180.00   0.0  0
 U9Y  CONST_03  N10  C09  C13  C12    0.00   0.0  0
 U9Y  CONST_04  C16  C15  N14  C12    0.00   0.0  0
 U9Y  CONST_05  C09  N10  N11  C12    0.00   0.0  0
 U9Y  CONST_06  C15  C16  N17  C13    0.00   0.0  0
 U9Y  CONST_09  N11  N10  C09  C13    0.00   0.0  0
 U9Y  CONST_10  C15  N14  C12  C13    0.00   0.0  0
 U9Y  CONST_11  N10  N11  C12  C13    0.00   0.0  0
 U9Y  CONST_12  C04  C03  C02  C01    0.00   0.0  0
 U9Y  CONST_13  C04  C05  C06  C01    0.00   0.0  0
 U9Y  CONST_15  C05  C04  C03  C02    0.00   0.0  0
 U9Y  CONST_16  C05  C06  C01  C02    0.00   0.0  0
 U9Y  CONST_17  C09  C06  C01  C02  180.00   0.0  0
 U9Y  CONST_18  C06  C05  C04  C03    0.00   0.0  0
 U9Y  CONST_19  C06  C01  C02  C03    0.00   0.0  0
 U9Y  CONST_20  C09  C06  C05  C04  180.00   0.0  0
 U9Y  CONST_22  N17  C13  C09  C06    0.00   0.0  0
 U9Y  CONST_23  N11  N10  C09  C06  180.00   0.0  0
 U9Y  CONST_24  C16  N17  C13  C09  180.00   0.0  0
 U9Y  CONST_25  N14  C12  C13  C09  180.00   0.0  0
 U9Y  CONST_26  N11  C12  C13  C09    0.00   0.0  0
 U9Y  CONST_27  N11  C12  N14  C15  180.00   0.0  0
 U9Y  CONST_28  N17  C13  C09  N10  180.00   0.0  0
 U9Y  CONST_29  N14  C12  N11  N10  180.00   0.0  0
 U9Y  CONST_30  N17  C13  C12  N11  180.00   0.0  0
 U9Y  CONST_31  N17  C16  C15  N14    0.00   0.0  0
 U9Y  CONST_32  N17  C13  C12  N14    0.00   0.0  0
 U9Y  CONST_33  N18  C15  N14  C12  180.00   0.0  0
 U9Y  CONST_34  N18  C15  C16  N17  180.00   0.0  0
 U9Y  CONST_35  CL7  C05  C06  C01  180.00   0.0  0
 U9Y  CONST_36  CL8  C04  C03  C02  180.00   0.0  0
 U9Y  CONST_37  CL7  C05  C04  C03  180.00   0.0  0
 U9Y  CONST_38  CL8  C04  C05  C06  180.00   0.0  0
 U9Y  CONST_39  CL7  C05  C06  C09    0.00   0.0  0
 U9Y  CONST_40  H4   C16  N17  C13  180.00   0.0  0
 U9Y  CONST_41  H16  N11  C12  C13  180.00   0.0  0
 U9Y  CONST_42  H3   C03  C02  C01  180.00   0.0  0
 U9Y  CONST_43  H1   C01  C02  C03  180.00   0.0  0
 U9Y  CONST_44  H2   C02  C03  C04  180.00   0.0  0
 U9Y  Var_01    C22  C23  N18  C15   98.18  30.0  1
 U9Y  Var_02    C20  C19  N18  C15  -98.62  30.0  1
 U9Y  Var_03    C23  N18  C15  C16   17.63  30.0  1
 U9Y  Var_04    N18  C23  C22  C21   55.68  30.0  1
 U9Y  Var_05    N18  C19  C20  C21  -56.41  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 U9Y  chir_01  C21  C22  C24  C20  positiv

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
 U9Y  plan-1  C01  0.020
 U9Y  plan-1  C02  0.020
 U9Y  plan-1  C03  0.020
 U9Y  plan-1  C04  0.020
 U9Y  plan-1  C05  0.020
 U9Y  plan-1  C06  0.020
 U9Y  plan-1  C09  0.020
 U9Y  plan-1  CL7  0.020
 U9Y  plan-1  CL8  0.020
 U9Y  plan-1  H1   0.020
 U9Y  plan-1  H2   0.020
 U9Y  plan-1  H3   0.020
 U9Y  plan-2  C12  0.020
 U9Y  plan-2  C13  0.020
 U9Y  plan-2  C06  0.020
 U9Y  plan-2  C09  0.020
 U9Y  plan-2  C15  0.020
 U9Y  plan-2  C16  0.020
 U9Y  plan-2  N10  0.020
 U9Y  plan-2  N11  0.020
 U9Y  plan-2  N14  0.020
 U9Y  plan-2  N17  0.020
 U9Y  plan-2  N18  0.020
 U9Y  plan-2  H4   0.020
 U9Y  plan-2  H16  0.020

