# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:49:40 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 3-amino-6-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-N-(pyridin-3-yl)pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)[S](=O)(=O)c2ccc(cc2)c3cnc(N)c(n3)C(=O)Nc4cccnc4
#
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
 GR9  GR9  3-amino-6-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}-N-(pyridin-3-yl)pyrazine-2-carboxamide  ligand  55  32  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GR9
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
 GR9  C1    C  CH2   0  -0.281   5.0802  -0.1529   1.6960
 GR9  N2    N  NT    0  -0.413   4.6238  -1.3971   2.2813
 GR9  C3    C  CH3   0  -0.517   3.9865  -1.1795   3.5596
 GR9  C4    C  CH2   0  -0.280   3.7551  -2.1085   1.3661
 GR9  C5    C  CH2   0  -0.333   4.4777  -2.4111   0.0638
 GR9  N6    N  N     0  -0.560   5.0460  -1.2066  -0.5388
 GR9  S7    S  S     0   1.379   4.2946  -0.4980  -1.8134
 GR9  O8    O  OS    0  -0.653   5.1632   0.5740  -2.2729
 GR9  O9    O  OS    0  -0.653   3.9201  -1.5627  -2.7305
 GR9  C10   C  CR6   0  -0.218   2.7938   0.2345  -1.2252
 GR9  C11   C  CR16  0  -0.210   2.7991   1.5412  -0.7584
 GR9  C12   C  CR16  0  -0.332   1.6372   2.0840  -0.2383
 GR9  C13   C  CR6   0   0.086   0.4594   1.3356  -0.1709
 GR9  C14   C  CR16  0  -0.279   0.4773   0.0273  -0.6612
 GR9  C15   C  CR16  0  -0.216   1.6298  -0.5223  -1.1895
 GR9  C16   C  CR6   0   0.189  -0.7837   1.8948   0.3843
 GR9  C17   C  CR16  0  -0.091  -0.8523   3.1158   1.0676
 GR9  N18   N  N     0  -0.411  -1.9717   3.6005   1.5490
 GR9  C19   C  CR6   0   0.492  -3.1062   2.9024   1.3883
 GR9  C20   C  CR6   0   0.002  -3.0457   1.6476   0.7208
 GR9  N21   N  N     0  -0.434  -1.9017   1.2002   0.2483
 GR9  C22   C  C     0   0.567  -4.2437   0.7828   0.5308
 GR9  O23   O  O     0  -0.472  -5.3543   1.1175   0.9195
 GR9  N24   N  NH1   0  -0.755  -3.9721  -0.3821  -0.0971
 GR9  C25   C  CR6   0   0.296  -4.8316  -1.4235  -0.4254
 GR9  C26   C  CR16  0  -0.211  -6.1907  -1.4821  -0.1231
 GR9  C27   C  CR16  0  -0.312  -6.9018  -2.6036  -0.5216
 GR9  C28   C  CR16  0  -0.084  -6.2546  -3.6218  -1.2007
 GR9  N29   N  N     0  -0.387  -4.9587  -3.5706  -1.4914
 GR9  C30   C  CR16  0  -0.146  -4.2749  -2.5067  -1.1148
 GR9  N31   N  NH2   0  -0.826  -4.2220   3.4412   1.8753
 GR9  C6    C  CH2   0  -0.329   5.8322  -0.4124   0.4027
 GR9  H11C  H  HCH2  0   0.200   4.2467   0.5483   1.5143
 GR9  H12C  H  HCH2  0   0.251   5.7596   0.3424   2.3937
 GR9  H61C  H  HCH2  0   0.278   6.1398   0.5243  -0.0557
 GR9  H62C  H  HCH2  0   0.260   6.7419  -0.9794   0.6169
 GR9  H31C  H  HCH3  0   0.194   3.0885  -0.5452   3.4952
 GR9  H32C  H  HCH3  0   0.236   3.6884  -2.1340   3.9955
 GR9  H33C  H  HCH3  0   0.236   4.6846  -0.6997   4.2474
 GR9  H41C  H  HCH2  0   0.252   3.4549  -3.0557   1.8201
 GR9  H42C  H  HCH2  0   0.201   2.8281  -1.5474   1.1571
 GR9  H51C  H  HCH2  0   0.263   5.3059  -3.0984   0.2541
 GR9  H52C  H  HCH2  0   0.276   3.8094  -2.9094  -0.6359
 GR9  H11   H  HCR6  0   0.289   3.6931   2.1484  -0.8030
 GR9  H15   H  HCR6  0   0.287   1.6086  -1.5351  -1.5685
 GR9  H12   H  HCR6  0   0.266   1.6668   3.1106   0.0999
 GR9  H14   H  HCR6  0   0.268  -0.4209  -0.5729  -0.6333
 GR9  H17   H  HCR6  0   0.279   0.0333   3.7155   1.2386
 GR9  H311  H  HNH2  0   0.404  -4.1730   4.3269   2.3498
 GR9  H312  H  HNH2  0   0.421  -5.1032   2.9633   1.7973
 GR9  H24   H  HNH1  0   0.426  -3.0014  -0.4969  -0.3612
 GR9  H26   H  HCR6  0   0.295  -6.6889  -0.6860   0.4049
 GR9  H30   H  HCR6  0   0.269  -3.2174  -2.4937  -1.3661
 GR9  H27   H  HCR6  0   0.275  -7.9576  -2.6824  -0.3015
 GR9  H28   H  HCR6  0   0.265  -6.7939  -4.5055  -1.5207

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
 GR9  C1   N2    single    1.449  0.020  1.449
 GR9  C1   C6    single    1.518  0.020  1.518
 GR9  N2   C3    single    1.445  0.020  1.445
 GR9  N2   C4    single    1.449  0.020  1.449
 GR9  C4   C5    single    1.520  0.020  1.520
 GR9  C5   N6    single    1.462  0.020  1.462
 GR9  N6   S7    single    1.641  0.020  1.641
 GR9  N6   C6    single    1.461  0.020  1.461
 GR9  S7   O8    double    1.454  0.020  1.454
 GR9  S7   O9    double    1.454  0.020  1.454
 GR9  S7   C10   single    1.771  0.020  1.771
 GR9  C10  C11   aromatic  1.388  0.020  1.388
 GR9  C10  C15   aromatic  1.389  0.020  1.389
 GR9  C11  C12   aromatic  1.384  0.020  1.384
 GR9  C12  C13   aromatic  1.397  0.020  1.397
 GR9  C13  C14   aromatic  1.397  0.020  1.397
 GR9  C13  C16   single    1.472  0.020  1.472
 GR9  C14  C15   aromatic  1.382  0.020  1.382
 GR9  C16  C17   aromatic  1.401  0.020  1.401
 GR9  C16  N21   aromatic  1.323  0.020  1.323
 GR9  C17  N18   aromatic  1.311  0.020  1.311
 GR9  N18  C19   aromatic  1.342  0.020  1.342
 GR9  C19  C20   aromatic  1.423  0.020  1.423
 GR9  C19  N31   single    1.331  0.020  1.331
 GR9  C20  N21   aromatic  1.316  0.020  1.316
 GR9  C20  C22   single    1.490  0.020  1.490
 GR9  C22  O23   double    1.223  0.020  1.223
 GR9  C22  N24   single    1.351  0.020  1.351
 GR9  N24  C25   single    1.390  0.020  1.390
 GR9  C25  C26   aromatic  1.394  0.020  1.394
 GR9  C25  C30   aromatic  1.399  0.020  1.399
 GR9  C26  C27   aromatic  1.386  0.020  1.386
 GR9  C27  C28   aromatic  1.384  0.020  1.384
 GR9  C28  N29   aromatic  1.329  0.020  1.329
 GR9  N29  C30   aromatic  1.320  0.020  1.320
 GR9  C1   H11C  single    0.970  0.020  1.090
 GR9  C1   H12C  single    0.970  0.020  1.090
 GR9  C6   H61C  single    0.970  0.020  1.090
 GR9  C6   H62C  single    0.970  0.020  1.090
 GR9  C3   H31C  single    0.970  0.020  1.090
 GR9  C3   H32C  single    0.970  0.020  1.090
 GR9  C3   H33C  single    0.970  0.020  1.090
 GR9  C4   H41C  single    0.970  0.020  1.090
 GR9  C4   H42C  single    0.970  0.020  1.090
 GR9  C5   H51C  single    0.970  0.020  1.090
 GR9  C5   H52C  single    0.970  0.020  1.090
 GR9  C11  H11   single    0.930  0.020  1.080
 GR9  C15  H15   single    0.930  0.020  1.080
 GR9  C12  H12   single    0.930  0.020  1.080
 GR9  C14  H14   single    0.930  0.020  1.080
 GR9  C17  H17   single    0.930  0.020  1.080
 GR9  N31  H311  single    0.860  0.020  1.020
 GR9  N31  H312  single    0.860  0.020  1.020
 GR9  N24  H24   single    0.860  0.020  1.020
 GR9  C26  H26   single    0.930  0.020  1.080
 GR9  C30  H30   single    0.930  0.020  1.080
 GR9  C27  H27   single    0.930  0.020  1.080
 GR9  C28  H28   single    0.930  0.020  1.080

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
 GR9  H12C  C1   H11C  106.65  3.000
 GR9  H12C  C1   C6    108.26  3.000
 GR9  H11C  C1   C6    110.01  3.000
 GR9  H12C  C1   N2    109.11  3.000
 GR9  H11C  C1   N2    111.97  3.000
 GR9  C6    C1   N2    110.69  3.000
 GR9  C4    N2   C3    111.62  3.000
 GR9  C4    N2   C1    110.82  3.000
 GR9  C3    N2   C1    111.53  3.000
 GR9  H33C  C3   H32C  107.93  3.000
 GR9  H33C  C3   H31C  107.77  3.000
 GR9  H32C  C3   H31C  107.73  3.000
 GR9  H33C  C3   N2    109.98  3.000
 GR9  H32C  C3   N2    110.01  3.000
 GR9  H31C  C3   N2    113.24  3.000
 GR9  H42C  C4   H41C  106.78  3.000
 GR9  H42C  C4   C5    109.78  3.000
 GR9  H41C  C4   C5    108.31  3.000
 GR9  H42C  C4   N2    111.95  3.000
 GR9  H41C  C4   N2    109.15  3.000
 GR9  C5    C4   N2    110.73  3.000
 GR9  H52C  C5   H51C  106.82  3.000
 GR9  H52C  C5   N6    110.55  3.000
 GR9  H51C  C5   N6    107.18  3.000
 GR9  H52C  C5   C4    110.49  3.000
 GR9  H51C  C5   C4    109.65  3.000
 GR9  N6    C5   C4    111.96  3.000
 GR9  C6    N6   S7    120.82  3.000
 GR9  C6    N6   C5    113.04  3.000
 GR9  S7    N6   C5    119.87  3.000
 GR9  C10   S7   O9    107.10  3.000
 GR9  C10   S7   O8    107.83  3.000
 GR9  O9    S7   O8    119.62  3.000
 GR9  C10   S7   N6    107.99  3.000
 GR9  O9    S7   N6    106.96  3.000
 GR9  O8    S7   N6    106.88  3.000
 GR9  C15   C10  C11   120.51  3.000
 GR9  C15   C10  S7    119.57  3.000
 GR9  C11   C10  S7    119.87  3.000
 GR9  H11   C11  C12   119.29  3.000
 GR9  H11   C11  C10   121.20  3.000
 GR9  C12   C11  C10   119.51  3.000
 GR9  H12   C12  C13   121.11  3.000
 GR9  H12   C12  C11   117.84  3.000
 GR9  C13   C12  C11   121.05  3.000
 GR9  C16   C13  C14   119.93  3.000
 GR9  C16   C13  C12   121.78  3.000
 GR9  C14   C13  C12   118.28  3.000
 GR9  H14   C14  C15   118.83  3.000
 GR9  H14   C14  C13   120.02  3.000
 GR9  C15   C14  C13   121.15  3.000
 GR9  H15   C15  C14   119.34  3.000
 GR9  H15   C15  C10   121.18  3.000
 GR9  C14   C15  C10   119.48  3.000
 GR9  N21   C16  C17   117.79  3.000
 GR9  N21   C16  C13   118.39  3.000
 GR9  C17   C16  C13   123.82  3.000
 GR9  H17   C17  N18   115.81  3.000
 GR9  H17   C17  C16   121.30  3.000
 GR9  N18   C17  C16   122.89  3.000
 GR9  C19   N18  C17   119.05  3.000
 GR9  N31   C19  C20   124.35  3.000
 GR9  N31   C19  N18   117.02  3.000
 GR9  C20   C19  N18   118.63  3.000
 GR9  C22   C20  N21   117.12  3.000
 GR9  C22   C20  C19   122.53  3.000
 GR9  N21   C20  C19   120.35  3.000
 GR9  C20   N21  C16   121.27  3.000
 GR9  N24   C22  O23   124.48  3.000
 GR9  N24   C22  C20   113.47  3.000
 GR9  O23   C22  C20   122.05  3.000
 GR9  H24   N24  C25   116.51  3.000
 GR9  H24   N24  C22   114.31  3.000
 GR9  C25   N24  C22   129.17  3.000
 GR9  C30   C25  C26   117.54  3.000
 GR9  C30   C25  N24   116.77  3.000
 GR9  C26   C25  N24   125.70  3.000
 GR9  H26   C26  C27   120.09  3.000
 GR9  H26   C26  C25   121.75  3.000
 GR9  C27   C26  C25   118.16  3.000
 GR9  H27   C27  C28   120.17  3.000
 GR9  H27   C27  C26   120.08  3.000
 GR9  C28   C27  C26   119.74  3.000
 GR9  H28   C28  N29   116.88  3.000
 GR9  H28   C28  C27   120.80  3.000
 GR9  N29   C28  C27   122.33  3.000
 GR9  C30   N29  C28   118.29  3.000
 GR9  H30   C30  N29   116.60  3.000
 GR9  H30   C30  C25   119.45  3.000
 GR9  N29   C30  C25   123.95  3.000
 GR9  H312  N31  H311  119.85  3.000
 GR9  H312  N31  C19   120.91  3.000
 GR9  H311  N31  C19   119.21  3.000
 GR9  H62C  C6   H61C  107.10  3.000
 GR9  H62C  C6   N6    106.99  3.000
 GR9  H61C  C6   N6    110.41  3.000
 GR9  H62C  C6   C1    109.50  3.000
 GR9  H61C  C6   C1    110.61  3.000
 GR9  N6    C6   C1    112.04  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
 GR9  CONST_01  C13   C12  C11  C10    0.00   0.0  0
 GR9  CONST_02  C13   C14  C15  C10    0.00   0.0  0
 GR9  CONST_03  C14   C15  C10  C11    0.00   0.0  0
 GR9  CONST_04  C14   C13  C12  C11    0.00   0.0  0
 GR9  CONST_05  C16   C13  C12  C11  180.00   0.0  0
 GR9  CONST_06  C15   C10  C11  C12    0.00   0.0  0
 GR9  CONST_07  C15   C14  C13  C12    0.00   0.0  0
 GR9  CONST_08  C17   C16  C13  C12    0.00   0.0  0
 GR9  CONST_09  N21   C16  C13  C12  180.00   0.0  0
 GR9  CONST_10  N18   C17  C16  C13  180.00   0.0  0
 GR9  CONST_11  C20   N21  C16  C13  180.00   0.0  0
 GR9  CONST_12  C17   C16  C13  C14  180.00   0.0  0
 GR9  CONST_13  N21   C16  C13  C14    0.00   0.0  0
 GR9  CONST_14  C16   C13  C14  C15  180.00   0.0  0
 GR9  CONST_15  C19   N18  C17  C16    0.00   0.0  0
 GR9  CONST_16  C19   C20  N21  C16    0.00   0.0  0
 GR9  CONST_17  C20   N21  C16  C17    0.00   0.0  0
 GR9  CONST_18  C20   C19  N18  C17    0.00   0.0  0
 GR9  CONST_19  N21   C16  C17  N18    0.00   0.0  0
 GR9  CONST_20  N21   C20  C19  N18    0.00   0.0  0
 GR9  CONST_21  C28   C27  C26  C25    0.00   0.0  0
 GR9  CONST_22  C28   N29  C30  C25    0.00   0.0  0
 GR9  CONST_23  N29   C30  C25  C26    0.00   0.0  0
 GR9  CONST_24  N29   C28  C27  C26    0.00   0.0  0
 GR9  CONST_25  C30   C25  C26  C27    0.00   0.0  0
 GR9  CONST_26  C30   N29  C28  C27    0.00   0.0  0
 GR9  CONST_27  C12   C11  C10  S7   180.00   0.0  0
 GR9  CONST_28  C14   C15  C10  S7   180.00   0.0  0
 GR9  CONST_29  C22   C20  N21  C16  180.00   0.0  0
 GR9  CONST_30  N31   C19  N18  C17  180.00   0.0  0
 GR9  CONST_31  C22   C20  C19  N18  180.00   0.0  0
 GR9  CONST_32  N31   C19  C20  N21  180.00   0.0  0
 GR9  CONST_33  C27   C26  C25  N24  180.00   0.0  0
 GR9  CONST_34  N29   C30  C25  N24  180.00   0.0  0
 GR9  CONST_35  H12   C12  C11  C10  180.00   0.0  0
 GR9  CONST_36  H14   C14  C15  C10  180.00   0.0  0
 GR9  CONST_37  H15   C15  C10  C11  180.00   0.0  0
 GR9  CONST_38  H11   C11  C12  C13  180.00   0.0  0
 GR9  CONST_39  H17   C17  C16  C13    0.00   0.0  0
 GR9  CONST_40  H27   C27  C26  C25  180.00   0.0  0
 GR9  CONST_41  H30   C30  C25  C26  180.00   0.0  0
 GR9  CONST_42  H28   C28  C27  C26  180.00   0.0  0
 GR9  CONST_43  H26   C26  C27  C28  180.00   0.0  0
 GR9  CONST_44  C25   N24  C22  C20  180.00   0.0  0
 GR9  CONST_45  C26   C25  N24  C22    0.00   0.0  0
 GR9  CONST_46  C30   C25  N24  C22  180.00   0.0  0
 GR9  CONST_47  H311  N31  C19  N18    0.00   0.0  0
 GR9  CONST_48  H312  N31  C19  N18  180.00   0.0  0
 GR9  CONST_49  H24   N24  C25  C26  180.00   0.0  0
 GR9  CONST_50  C25   N24  C22  O23    0.00   0.0  0
 GR9  Var_01    C5    C4   N2   C1    58.96  30.0  1
 GR9  Var_02    C5    N6   C6   C1   -49.88  30.0  1
 GR9  Var_03    N6    C6   C1   N2    54.09  30.0  1
 GR9  Var_04    N6    C5   C4   N2   -54.00  30.0  1
 GR9  Var_05    C6    C1   N2   C4   -58.98  30.0  1
 GR9  Var_06    C6    N6   C5   C4    49.80  30.0  1
 GR9  Var_07    C10   S7   N6   C5    70.20  30.0  3
 GR9  Var_08    C11   C10  S7   N6    89.29  30.0  2
 GR9  Var_09    O23   C22  C20  C19    1.33  30.0  2
 GR9  Var_10    H31C  C3   N2   C1    61.62  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
 GR9  plan-1  S7    0.020
 GR9  plan-1  C10   0.020
 GR9  plan-1  C11   0.020
 GR9  plan-1  C12   0.020
 GR9  plan-1  C13   0.020
 GR9  plan-1  C14   0.020
 GR9  plan-1  C15   0.020
 GR9  plan-1  C16   0.020
 GR9  plan-1  H11   0.020
 GR9  plan-1  H15   0.020
 GR9  plan-1  H12   0.020
 GR9  plan-1  H14   0.020
 GR9  plan-2  C13   0.020
 GR9  plan-2  C16   0.020
 GR9  plan-2  C17   0.020
 GR9  plan-2  N18   0.020
 GR9  plan-2  C19   0.020
 GR9  plan-2  C20   0.020
 GR9  plan-2  N21   0.020
 GR9  plan-2  C22   0.020
 GR9  plan-2  N31   0.020
 GR9  plan-2  H17   0.020
 GR9  plan-3  N24   0.020
 GR9  plan-3  C25   0.020
 GR9  plan-3  C26   0.020
 GR9  plan-3  C27   0.020
 GR9  plan-3  C28   0.020
 GR9  plan-3  N29   0.020
 GR9  plan-3  C30   0.020
 GR9  plan-3  H26   0.020
 GR9  plan-3  H30   0.020
 GR9  plan-3  H27   0.020
 GR9  plan-3  H28   0.020
 GR9  plan-4  C19   0.020
 GR9  plan-4  N31   0.020
 GR9  plan-4  H311  0.020
 GR9  plan-4  H312  0.020
 GR9  plan-5  C20   0.020
 GR9  plan-5  C22   0.020
 GR9  plan-5  O23   0.020
 GR9  plan-5  N24   0.020
 GR9  plan-5  C25   0.020
 GR9  plan-5  H24   0.020

