# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 09:38:08 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(CNC(=O)c2cnc(CN[S](=O)(=O)c3ccc(F)c(F)c3)c(C)n2)cn1
#
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
 6ND  6ND  5-({[(3,4-difluorophenyl)sulfonyl]amino}methyl)-6-methyl-N-[(2-methyl-1,3-thiazol-5-yl)methyl]pyrazine-2-carboxamide  ligand  47  30  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6ND
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
 6ND  C10  C  CR6   0   0.202   0.5789   1.8020  -0.1248
 6ND  C11  C  CR6   0   0.235   0.1285   0.7611   0.7085
 6ND  C13  C  CR6   0   0.084  -2.0147   1.4480   0.3331
 6ND  C14  C  CR16  0  -0.075  -1.5650   2.4597  -0.4967
 6ND  C16  C  C     0   0.543  -3.4784   1.2747   0.5999
 6ND  C22  C  CR5   0   0.065  -7.0540  -1.7823  -1.0834
 6ND  C24  C  CR15  0  -0.048  -6.3363  -2.0983   0.9696
 6ND  C25  C  CH3   0  -0.724  -7.6955  -2.0521  -2.3990
 6ND  C26  C  CH3   0  -0.765   1.0656  -0.1867   1.3809
 6ND  C01  C  CR6   0   0.423   4.8834  -1.9766   1.9080
 6ND  C02  C  CR6   0   0.416   4.3165  -2.4645   0.7371
 6ND  C03  C  CR16  0  -0.373   4.0847  -1.6295  -0.3293
 6ND  C04  C  CR6   0  -0.207   4.4349  -0.2890  -0.2036
 6ND  C05  C  CR16  0  -0.226   5.0114   0.2079   0.9530
 6ND  C06  C  CR16  0  -0.398   5.2315  -0.6490   2.0233
 6ND  S07  S  S     0   1.389   4.1054   0.7917  -1.5665
 6ND  N08  N  NC1   0  -0.736   2.4786   1.0420  -1.3966
 6ND  C09  C  CH2   0  -0.378   2.0393   2.0164  -0.3997
 6ND  N12  N  N     0  -0.408  -1.1668   0.6141   0.9229
 6ND  N15  N  N     0  -0.362  -0.2667   2.6289  -0.7134
 6ND  O17  O  O     0  -0.480  -4.3098   1.9986   0.0690
 6ND  N18  N  NH1   0  -0.627  -3.7809   0.2928   1.4525
 6ND  C19  C  CH2   0  -0.379  -5.1429  -0.0024   1.8346
 6ND  C20  C  CR5   0  -0.192  -5.8798  -0.8278   0.8300
 6ND  S21  S  S2    0   0.213  -6.3007  -0.2604  -0.7442
 6ND  N23  N  N     0  -0.381  -6.9932  -2.6279  -0.1048
 6ND  O27  O  OS    0  -0.640   4.8650   2.0132  -1.3490
 6ND  O28  O  OS    0  -0.646   4.2697   0.0572  -2.8090
 6ND  F30  F  F     0  -0.290   5.0863  -2.8168   2.9178
 6ND  H1   H  HCR6  0   0.283  -2.2473   3.1421  -0.9859
 6ND  H2   H  HCR5  0   0.269  -6.2116  -2.6926   1.8653
 6ND  H3   H  HCH3  0   0.264  -6.9774  -1.9685  -3.2151
 6ND  H4   H  HCH3  0   0.264  -8.1083  -3.0586  -2.4034
 6ND  H5   H  HCH3  0   0.264  -8.5022  -1.3466  -2.5996
 6ND  H6   H  HCH3  0   0.261   1.7776   0.3402   2.0189
 6ND  H7   H  HCH3  0   0.273   0.5092  -0.8882   1.9976
 6ND  H8   H  HCH3  0   0.266   1.6448  -0.7535   0.6523
 6ND  H9   H  HCR6  0   0.323   3.6365  -2.0244  -1.2318
 6ND  H10  H  HCR6  0   0.305   5.2918   1.2479   1.0393
 6ND  H11  H  HCR6  0   0.312   5.6752  -0.2851   2.9401
 6ND  H12  H  HNC1  0   0.424   2.0380   1.1616  -2.3048
 6ND  H13  H  HCH2  0   0.291   2.1968   3.0446  -0.7290
 6ND  H14  H  HCH2  0   0.278   2.6139   1.8690   0.5170
 6ND  H15  H  HNH1  0   0.414  -3.0329  -0.2893   1.7985
 6ND  H16  H  HCH2  0   0.290  -5.1109  -0.5527   2.7737
 6ND  H17  H  HCH2  0   0.277  -5.6717   0.9313   2.0315
 6ND  F29  F  F     0  -0.294   3.9991  -3.7555   0.6639

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
 6ND  N15  C14  aromatic  1.327  0.020  1.327
 6ND  N15  C10  aromatic  1.321  0.020  1.321
 6ND  C14  C13  aromatic  1.383  0.020  1.383
 6ND  C05  C06  aromatic  1.389  0.020  1.389
 6ND  C05  C04  aromatic  1.385  0.020  1.385
 6ND  C06  C01  aromatic  1.377  0.020  1.377
 6ND  N08  C09  single    1.462  0.020  1.462
 6ND  N08  S07  single    1.655  0.020  1.655
 6ND  O17  C16  double    1.224  0.020  1.224
 6ND  O27  S07  double    1.455  0.020  1.455
 6ND  C09  C10  single    1.501  0.020  1.501
 6ND  C10  C11  aromatic  1.407  0.020  1.407
 6ND  S07  C04  single    1.770  0.020  1.770
 6ND  S07  O28  double    1.453  0.020  1.453
 6ND  C04  C03  aromatic  1.391  0.020  1.391
 6ND  C13  C16  single    1.498  0.020  1.498
 6ND  C13  N12  aromatic  1.328  0.020  1.328
 6ND  C01  F30  single    1.329  0.020  1.329
 6ND  C01  C02  aromatic  1.389  0.020  1.389
 6ND  C16  N18  single    1.335  0.020  1.335
 6ND  C11  N12  aromatic  1.321  0.020  1.321
 6ND  C11  C26  single    1.493  0.020  1.493
 6ND  C03  C02  aromatic  1.374  0.020  1.374
 6ND  C02  F29  single    1.332  0.020  1.332
 6ND  N18  C19  single    1.445  0.020  1.445
 6ND  C19  C20  single    1.494  0.020  1.494
 6ND  C24  C20  aromatic  1.357  0.020  1.357
 6ND  C24  N23  aromatic  1.366  0.020  1.366
 6ND  C20  S21  aromatic  1.725  0.020  1.725
 6ND  N23  C22  aromatic  1.295  0.020  1.295
 6ND  C22  S21  aromatic  1.732  0.020  1.732
 6ND  C22  C25  single    1.488  0.020  1.488
 6ND  C14  H1   single    0.930  0.020  1.080
 6ND  C24  H2   single    0.930  0.020  1.080
 6ND  C25  H3   single    0.970  0.020  1.090
 6ND  C25  H4   single    0.970  0.020  1.090
 6ND  C25  H5   single    0.970  0.020  1.090
 6ND  C26  H6   single    0.970  0.020  1.090
 6ND  C26  H7   single    0.970  0.020  1.090
 6ND  C26  H8   single    0.970  0.020  1.090
 6ND  C03  H9   single    0.930  0.020  1.080
 6ND  C05  H10  single    0.930  0.020  1.080
 6ND  C06  H11  single    0.930  0.020  1.080
 6ND  N08  H12  single    0.890  0.020  1.040
 6ND  C09  H13  single    0.970  0.020  1.090
 6ND  C09  H14  single    0.970  0.020  1.090
 6ND  N18  H15  single    0.860  0.020  1.020
 6ND  C19  H16  single    0.970  0.020  1.090
 6ND  C19  H17  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
 6ND  N15  C10  C09  116.85  3.000
 6ND  C09  C10  C11  121.69  3.000
 6ND  N15  C10  C11  121.46  3.000
 6ND  N12  C11  C26  118.14  3.000
 6ND  C26  C11  C10  122.37  3.000
 6ND  N12  C11  C10  119.48  3.000
 6ND  N12  C13  C16  118.18  3.000
 6ND  N12  C13  C14  121.21  3.000
 6ND  C16  C13  C14  120.60  3.000
 6ND  H1   C14  N15  117.56  3.000
 6ND  H1   C14  C13  121.83  3.000
 6ND  N15  C14  C13  120.61  3.000
 6ND  N18  C16  O17  123.93  3.000
 6ND  N18  C16  C13  114.85  3.000
 6ND  O17  C16  C13  121.22  3.000
 6ND  N23  C22  S21  113.93  3.000
 6ND  S21  C22  C25  121.33  3.000
 6ND  N23  C22  C25  124.75  3.000
 6ND  H2   C24  N23  119.57  3.000
 6ND  H2   C24  C20  124.09  3.000
 6ND  N23  C24  C20  116.34  3.000
 6ND  H5   C25  H4   108.49  3.000
 6ND  H5   C25  H3   107.47  3.000
 6ND  H4   C25  H3   108.54  3.000
 6ND  H5   C25  C22  111.36  3.000
 6ND  H4   C25  C22  109.56  3.000
 6ND  H3   C25  C22  111.33  3.000
 6ND  H8   C26  H7   108.40  3.000
 6ND  H8   C26  H6   107.17  3.000
 6ND  H7   C26  H6   108.28  3.000
 6ND  H8   C26  C11  111.27  3.000
 6ND  H7   C26  C11  110.11  3.000
 6ND  H6   C26  C11  111.48  3.000
 6ND  F30  C01  C06  120.47  3.000
 6ND  F30  C01  C02  118.72  3.000
 6ND  C06  C01  C02  120.81  3.000
 6ND  F29  C02  C03  120.42  3.000
 6ND  F29  C02  C01  118.95  3.000
 6ND  C03  C02  C01  120.63  3.000
 6ND  H9   C03  C04  122.09  3.000
 6ND  H9   C03  C02  119.69  3.000
 6ND  C04  C03  C02  118.23  3.000
 6ND  S07  C04  C05  120.10  3.000
 6ND  S07  C04  C03  118.15  3.000
 6ND  C05  C04  C03  121.74  3.000
 6ND  H10  C05  C06  119.42  3.000
 6ND  H10  C05  C04  121.34  3.000
 6ND  C06  C05  C04  119.24  3.000
 6ND  H11  C06  C05  120.71  3.000
 6ND  H11  C06  C01  119.93  3.000
 6ND  C05  C06  C01  119.36  3.000
 6ND  O28  S07  O27  119.56  3.000
 6ND  O28  S07  N08  105.99  3.000
 6ND  O27  S07  N08  111.78  3.000
 6ND  O28  S07  C04  109.19  3.000
 6ND  O27  S07  C04  107.47  3.000
 6ND  N08  S07  C04  101.32  3.000
 6ND  H12  N08  C09  113.62  3.000
 6ND  H12  N08  S07  110.62  3.000
 6ND  C09  N08  S07  117.80  3.000
 6ND  H14  C09  H13  107.73  3.000
 6ND  H14  C09  N08  108.93  3.000
 6ND  H13  C09  N08  112.27  3.000
 6ND  H14  C09  C10  109.81  3.000
 6ND  H13  C09  C10  109.28  3.000
 6ND  N08  C09  C10  108.79  3.000
 6ND  C13  N12  C11  118.96  3.000
 6ND  C14  N15  C10  118.27  3.000
 6ND  H15  N18  C19  119.35  3.000
 6ND  H15  N18  C16  118.38  3.000
 6ND  C19  N18  C16  122.18  3.000
 6ND  H17  C19  H16  106.92  3.000
 6ND  H17  C19  C20  110.79  3.000
 6ND  H16  C19  C20  108.37  3.000
 6ND  H17  C19  N18  109.25  3.000
 6ND  H16  C19  N18  107.67  3.000
 6ND  C20  C19  N18  113.57  3.000
 6ND  S21  C20  C19  123.50  3.000
 6ND  S21  C20  C24  108.64  3.000
 6ND  C19  C20  C24  127.86  3.000
 6ND  C20  S21  C22   89.76  3.000
 6ND  C24  N23  C22  111.33  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
 6ND  CONST_01  C13  C14  N15  C10     0.00   0.0  0
 6ND  CONST_02  C13  N12  C11  C10     0.00   0.0  0
 6ND  CONST_03  C14  N15  C10  C11     0.00   0.0  0
 6ND  CONST_04  C14  C13  N12  C11     0.00   0.0  0
 6ND  CONST_05  C20  C24  N23  C22     0.00   0.0  0
 6ND  CONST_06  C24  C20  S21  C22     0.00   0.0  0
 6ND  CONST_07  S21  C22  N23  C24     0.00   0.0  0
 6ND  CONST_08  C04  C05  C06  C01     0.00   0.0  0
 6ND  CONST_09  C04  C03  C02  C01     0.00   0.0  0
 6ND  CONST_10  C05  C06  C01  C02     0.00   0.0  0
 6ND  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 6ND  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 6ND  CONST_13  C06  C01  C02  C03     0.00   0.0  0
 6ND  CONST_14  N15  C14  C13  N12     0.00   0.0  0
 6ND  CONST_15  N15  C10  C11  N12     0.00   0.0  0
 6ND  CONST_16  N23  C22  S21  C20     0.00   0.0  0
 6ND  CONST_17  N23  C24  C20  S21     0.00   0.0  0
 6ND  CONST_18  C16  C13  N12  C11   180.00   0.0  0
 6ND  CONST_19  C26  C11  N12  C13   180.00   0.0  0
 6ND  CONST_20  C09  C10  N15  C14   180.00   0.0  0
 6ND  CONST_21  N15  C14  C13  C16   180.00   0.0  0
 6ND  CONST_22  C19  C20  S21  C22   180.00   0.0  0
 6ND  CONST_23  C25  C22  N23  C24   180.00   0.0  0
 6ND  CONST_24  C20  S21  C22  C25   180.00   0.0  0
 6ND  CONST_25  N15  C10  C11  C26   180.00   0.0  0
 6ND  CONST_26  S07  C04  C03  C02   180.00   0.0  0
 6ND  CONST_27  F30  C01  C02  C03   180.00   0.0  0
 6ND  CONST_28  F29  C02  C03  C04   180.00   0.0  0
 6ND  CONST_29  F30  C01  C06  C05   180.00   0.0  0
 6ND  CONST_30  S07  C04  C05  C06   180.00   0.0  0
 6ND  CONST_31  F29  C02  C01  C06   180.00   0.0  0
 6ND  CONST_32  N12  C11  C10  C09   180.00   0.0  0
 6ND  CONST_33  N23  C24  C20  C19   180.00   0.0  0
 6ND  CONST_34  H1   C14  N15  C10   180.00   0.0  0
 6ND  CONST_35  H2   C24  N23  C22   180.00   0.0  0
 6ND  CONST_36  H10  C05  C06  C01   180.00   0.0  0
 6ND  CONST_37  H9   C03  C02  C01   180.00   0.0  0
 6ND  CONST_38  H11  C06  C01  C02   180.00   0.0  0
 6ND  CONST_39  C19  N18  C16  C13   180.00   0.0  0
 6ND  CONST_40  H15  N18  C16  C13     0.00   0.0  0
 6ND  CONST_41  C19  N18  C16  O17     0.00   0.0  0
 6ND  Var_01    N08  C09  C10  C11    78.39  30.0  2
 6ND  Var_02    O17  C16  C13  C14     1.75  30.0  2
 6ND  Var_03    N18  C19  C20  C24   113.63  30.0  2
 6ND  Var_04    N08  S07  C04  C03    77.64  30.0  2
 6ND  Var_05    H6   C26  C11  C10    58.07  30.0  2
 6ND  Var_06    H3   C25  C22  S21    60.12  30.0  2
 6ND  Var_07    S07  N08  C09  C10  -163.58  30.0  1
 6ND  Var_08    C20  C19  N18  C16    80.77  30.0  3
 6ND  Var_09    C09  N08  S07  C04    79.79  30.0  1

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
 6ND  plan-1  C22  0.020
 6ND  plan-1  C24  0.020
 6ND  plan-1  C25  0.020
 6ND  plan-1  C19  0.020
 6ND  plan-1  C20  0.020
 6ND  plan-1  S21  0.020
 6ND  plan-1  N23  0.020
 6ND  plan-1  H2   0.020
 6ND  plan-2  C01  0.020
 6ND  plan-2  C02  0.020
 6ND  plan-2  C03  0.020
 6ND  plan-2  C04  0.020
 6ND  plan-2  C05  0.020
 6ND  plan-2  C06  0.020
 6ND  plan-2  S07  0.020
 6ND  plan-2  F30  0.020
 6ND  plan-2  H9   0.020
 6ND  plan-2  H10  0.020
 6ND  plan-2  H11  0.020
 6ND  plan-2  F29  0.020
 6ND  plan-3  C10  0.020
 6ND  plan-3  C11  0.020
 6ND  plan-3  C13  0.020
 6ND  plan-3  C14  0.020
 6ND  plan-3  C16  0.020
 6ND  plan-3  C26  0.020
 6ND  plan-3  C09  0.020
 6ND  plan-3  N12  0.020
 6ND  plan-3  N15  0.020
 6ND  plan-3  H1   0.020
 6ND  plan-4  C13  0.020
 6ND  plan-4  C16  0.020
 6ND  plan-4  O17  0.020
 6ND  plan-4  N18  0.020
 6ND  plan-4  C19  0.020
 6ND  plan-4  H15  0.020

