# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:23:31 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCNc1cc(nc(n1)c2ccccn2)N3CCCN(CC3)[S](=O)(=O)C=C
#
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
 H6J  H6J  N-{6-[4-(ethenylsulfonyl)-1,4-diazepan-1-yl]-2-(pyridin-2-yl)pyrimidin-4-yl}-beta-alanine  ligand  53  30  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H6J
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
 H6J  C13  C  CH2    0  -0.322   3.3310  -0.2517   1.3231
 H6J  C17  C  C1     0  -0.401   4.2820   1.4882  -1.4067
 H6J  C20  C  CH2    0  -0.301   2.1859   1.9865   1.3577
 H6J  C21  C  CH2    0  -0.343   1.4094   1.5610   2.6135
 H6J  C24  C  CR6    0   0.142  -2.0907   2.7833  -0.4246
 H6J  C26  C  CR16   0  -0.155  -3.4576   4.0951  -1.8870
 H6J  C28  C  CR16   0  -0.089  -1.7082   5.0267  -0.5754
 H6J  C02  C  C      0   0.422  -3.2304  -5.6305  -0.2075
 H6J  C04  C  CH2    0  -0.630  -3.4186  -4.1381  -0.5334
 H6J  C05  C  CH2    0  -0.245  -2.4147  -3.2139   0.1284
 H6J  C07  C  CR6    0   0.538  -1.9977  -0.7794   0.2109
 H6J  C08  C  CR16   0  -0.526  -0.9663  -0.8958   1.1451
 H6J  C09  C  CR6    0   0.573  -0.3509   0.2912   1.5505
 H6J  C11  C  CH2    0  -0.355   1.3760  -0.8852   2.8243
 H6J  C12  C  CH2    0  -0.412   2.3832  -1.3545   1.7784
 H6J  C18  C  C2     0  -0.444   5.2205   0.7632  -1.9943
 H6J  C23  C  CR6    0   0.366  -1.7043   1.4685   0.1646
 H6J  C25  C  CR16   0  -0.300  -3.1364   2.8628  -1.3424
 H6J  C27  C  CR16   0  -0.316  -2.7276   5.2077  -1.5003
 H6J  N10  N  NT     0  -0.483   0.6661   0.3278   2.4539
 H6J  N14  N  N      0  -0.579   2.6301   0.8179   0.6134
 H6J  N22  N  N      0  -0.486  -0.7492   1.4773   1.0720
 H6J  N29  N  N      0  -0.394  -1.3953   3.8523  -0.0489
 H6J  N30  N  N      0  -0.514  -2.3523   0.4144  -0.2960
 H6J  O01  O  O      0  -0.606  -2.3701  -5.9324   0.6418
 H6J  O03  O  OC    -1  -0.625  -3.9671  -6.4177  -0.8344
 H6J  O16  O  OS     0  -0.653   1.7030   1.7807  -1.5055
 H6J  O19  O  OS     0  -0.660   2.6480  -0.5460  -1.4848
 H6J  S15  S  S      0   1.363   2.6911   0.8325  -1.0187
 H6J  H1   H  HCH2   0   0.258   3.8526   0.1936   2.1744
 H6J  H2   H  HCH2   0   0.269   4.1129  -0.6751   0.6913
 H6J  H3   H  H      0   0.318   4.4240   2.5200  -1.1071
 H6J  H4   H  HCH2   0   0.287   1.5322   2.5767   0.7228
 H6J  H5   H  HCH2   0   0.246   3.0350   2.6071   1.6626
 H6J  H6   H  HCH2   0   0.253   2.0963   1.4088   3.4456
 H6J  H7   H  HCH2   0   0.271   0.7484   2.3797   2.8972
 H6J  H8   H  HCR6   0   0.272  -4.2650   4.1823  -2.6019
 H6J  H9   H  HCR6   0   0.258  -1.1165   5.8746  -0.2473
 H6J  H10  H  HCH2   0   0.234  -3.3789  -4.0099  -1.6203
 H6J  H11  H  HCH2   0   0.239  -4.4327  -3.8467  -0.2379
 H6J  H12  H  HCH2   0   0.223  -2.4695  -3.3218   1.2149
 H6J  H13  H  HCH2   0   0.219  -1.3968  -3.4947  -0.1637
 H6J  H14  H  HCR6   0   0.273  -0.6566  -1.8625   1.5094
 H6J  H15  H  HCH2   0   0.262   0.6630  -1.6797   3.0458
 H6J  H16  H  HCH2   0   0.260   1.8943  -0.6811   3.7631
 H6J  H17  H  HCH2   0   0.240   1.8697  -1.7595   0.9049
 H6J  H18  H  HCH2   0   0.241   2.9696  -2.1693   2.2105
 H6J  H19  H  H      0   0.278   6.1897   1.1936  -2.2057
 H6J  H20  H  H      0   0.280   5.0640  -0.2658  -2.2874
 H6J  H21  H  HCR6   0   0.267  -3.6814   1.9726  -1.6208
 H6J  H22  H  HCR6   0   0.271  -2.9370   6.1905  -1.8997
 H6J  H23  H  HNH1   0   0.382  -3.3472  -1.6618  -0.9775
 H6J  N06  N  NH1    0  -0.668  -2.6862  -1.8416  -0.2392

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
 H6J  C27  C28  aromatic  1.388  0.020  1.388
 H6J  C27  C26  aromatic  1.386  0.020  1.386
 H6J  C28  N29  aromatic  1.325  0.020  1.325
 H6J  C26  C25  aromatic  1.385  0.020  1.385
 H6J  N29  C24  aromatic  1.329  0.020  1.329
 H6J  C25  C24  aromatic  1.394  0.020  1.394
 H6J  C24  C23  single    1.492  0.020  1.492
 H6J  C18  C17  double    1.323  0.020  1.323
 H6J  C23  N30  aromatic  1.320  0.020  1.320
 H6J  C23  N22  aromatic  1.317  0.020  1.317
 H6J  N30  C07  aromatic  1.345  0.020  1.345
 H6J  C17  S15  single    1.764  0.020  1.764
 H6J  N22  C09  aromatic  1.340  0.020  1.340
 H6J  O16  S15  double    1.453  0.020  1.453
 H6J  S15  N14  single    1.633  0.020  1.633
 H6J  S15  O19  double    1.456  0.020  1.456
 H6J  C20  N14  single    1.455  0.020  1.455
 H6J  C20  C21  single    1.537  0.020  1.537
 H6J  C07  N06  single    1.343  0.020  1.343
 H6J  C07  C08  aromatic  1.396  0.020  1.396
 H6J  C09  C08  aromatic  1.397  0.020  1.397
 H6J  C09  N10  single    1.361  0.020  1.361
 H6J  N06  C05  single    1.446  0.020  1.446
 H6J  N14  C13  single    1.462  0.020  1.462
 H6J  C21  N10  single    1.449  0.020  1.449
 H6J  N10  C11  single    1.454  0.020  1.454
 H6J  C05  C04  single    1.517  0.020  1.517
 H6J  C13  C12  single    1.524  0.020  1.524
 H6J  C04  C02  single    1.539  0.020  1.539
 H6J  C11  C12  single    1.526  0.020  1.526
 H6J  C02  O01  deloc     1.246  0.020  1.246
 H6J  C02  O03  deloc     1.247  0.020  1.247
 H6J  C13  H1   single    0.970  0.020  1.090
 H6J  C13  H2   single    0.970  0.020  1.090
 H6J  C17  H3   single    0.930  0.020  1.080
 H6J  C20  H4   single    0.970  0.020  1.090
 H6J  C20  H5   single    0.970  0.020  1.090
 H6J  C21  H6   single    0.970  0.020  1.090
 H6J  C21  H7   single    0.970  0.020  1.090
 H6J  C26  H8   single    0.930  0.020  1.080
 H6J  C28  H9   single    0.930  0.020  1.080
 H6J  C04  H10  single    0.970  0.020  1.090
 H6J  C04  H11  single    0.970  0.020  1.090
 H6J  C05  H12  single    0.970  0.020  1.090
 H6J  C05  H13  single    0.970  0.020  1.090
 H6J  C08  H14  single    0.930  0.020  1.080
 H6J  C11  H15  single    0.970  0.020  1.090
 H6J  C11  H16  single    0.970  0.020  1.090
 H6J  C12  H17  single    0.970  0.020  1.090
 H6J  C12  H18  single    0.970  0.020  1.090
 H6J  C18  H19  single    0.930  0.020  1.080
 H6J  C18  H20  single    0.930  0.020  1.080
 H6J  C25  H21  single    0.930  0.020  1.080
 H6J  C27  H22  single    0.930  0.020  1.080
 H6J  N06  H23  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
 H6J  H2   C13  H1   105.49  3.000
 H6J  H2   C13  N14  110.26  3.000
 H6J  H1   C13  N14  107.98  3.000
 H6J  H2   C13  C12  109.76  3.000
 H6J  H1   C13  C12  111.03  3.000
 H6J  N14  C13  C12  112.10  3.000
 H6J  H3   C17  S15  114.28  3.000
 H6J  H3   C17  C18  123.46  3.000
 H6J  S15  C17  C18  122.25  3.000
 H6J  H5   C20  H4   108.76  3.000
 H6J  H5   C20  N14  111.16  3.000
 H6J  H4   C20  N14  108.74  3.000
 H6J  H5   C20  C21  108.74  3.000
 H6J  H4   C20  C21  108.91  3.000
 H6J  N14  C20  C21  110.48  3.000
 H6J  H7   C21  H6   106.77  3.000
 H6J  H7   C21  N10  110.91  3.000
 H6J  H6   C21  N10  106.78  3.000
 H6J  H7   C21  C20  108.13  3.000
 H6J  H6   C21  C20  110.13  3.000
 H6J  N10  C21  C20  113.89  3.000
 H6J  N29  C24  C25  122.19  3.000
 H6J  C25  C24  C23  120.32  3.000
 H6J  N29  C24  C23  117.49  3.000
 H6J  H8   C26  C27  120.85  3.000
 H6J  H8   C26  C25  120.30  3.000
 H6J  C27  C26  C25  118.85  3.000
 H6J  H9   C28  N29  116.35  3.000
 H6J  H9   C28  C27  120.01  3.000
 H6J  N29  C28  C27  123.64  3.000
 H6J  O03  C02  O01  126.70  3.000
 H6J  O03  C02  C04  115.68  3.000
 H6J  O01  C02  C04  117.62  3.000
 H6J  H11  C04  H10  105.67  3.000
 H6J  H11  C04  C05  109.45  3.000
 H6J  H10  C04  C05  109.74  3.000
 H6J  H11  C04  C02  108.29  3.000
 H6J  H10  C04  C02  108.61  3.000
 H6J  C05  C04  C02  114.68  3.000
 H6J  H13  C05  H12  106.64  3.000
 H6J  H13  C05  N06  110.48  3.000
 H6J  H12  C05  N06  109.69  3.000
 H6J  H13  C05  C04  110.03  3.000
 H6J  H12  C05  C04  109.90  3.000
 H6J  N06  C05  C04  110.06  3.000
 H6J  N30  C07  N06  116.14  3.000
 H6J  N06  C07  C08  122.47  3.000
 H6J  N30  C07  C08  121.40  3.000
 H6J  H14  C08  C09  122.48  3.000
 H6J  H14  C08  C07  120.84  3.000
 H6J  C09  C08  C07  116.66  3.000
 H6J  N22  C09  N10  115.81  3.000
 H6J  N10  C09  C08  123.01  3.000
 H6J  N22  C09  C08  121.17  3.000
 H6J  H16  C11  H15  105.79  3.000
 H6J  H16  C11  N10  107.16  3.000
 H6J  H15  C11  N10  109.90  3.000
 H6J  H16  C11  C12  109.49  3.000
 H6J  H15  C11  C12  110.29  3.000
 H6J  N10  C11  C12  113.85  3.000
 H6J  H18  C12  H17  107.00  3.000
 H6J  H18  C12  C11  108.21  3.000
 H6J  H17  C12  C11  110.62  3.000
 H6J  H18  C12  C13  108.90  3.000
 H6J  H17  C12  C13  108.79  3.000
 H6J  C11  C12  C13  113.13  3.000
 H6J  H20  C18  H19  117.10  3.000
 H6J  H20  C18  C17  122.61  3.000
 H6J  H19  C18  C17  120.29  3.000
 H6J  N30  C23  N22  126.97  3.000
 H6J  N22  C23  C24  117.00  3.000
 H6J  N30  C23  C24  116.02  3.000
 H6J  H21  C25  C26  120.99  3.000
 H6J  H21  C25  C24  120.09  3.000
 H6J  C26  C25  C24  118.93  3.000
 H6J  H22  C27  C28  120.45  3.000
 H6J  H22  C27  C26  121.65  3.000
 H6J  C28  C27  C26  117.91  3.000
 H6J  C11  N10  C09  120.78  3.000
 H6J  C11  N10  C21  115.58  3.000
 H6J  C09  N10  C21  118.65  3.000
 H6J  S15  N14  C20  121.02  3.000
 H6J  C20  N14  C13  119.04  3.000
 H6J  S15  N14  C13  118.27  3.000
 H6J  C23  N22  C09  117.11  3.000
 H6J  C28  N29  C24  118.49  3.000
 H6J  C23  N30  C07  116.61  3.000
 H6J  O19  S15  O16  119.36  3.000
 H6J  O19  S15  N14  108.08  3.000
 H6J  O16  S15  N14  108.37  3.000
 H6J  O19  S15  C17  107.95  3.000
 H6J  N14  S15  C17  104.88  3.000
 H6J  O16  S15  C17  107.28  3.000
 H6J  H23  N06  C07  116.15  3.000
 H6J  H23  N06  C05  118.62  3.000
 H6J  C07  N06  C05  124.66  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
 H6J  CONST_01  C27  C28  N29  C24     0.00   0.0  0
 H6J  CONST_02  C27  C26  C25  C24     0.00   0.0  0
 H6J  CONST_03  C07  N30  C23  C24   180.00   0.0  0
 H6J  CONST_04  C09  N22  C23  C24   180.00   0.0  0
 H6J  CONST_05  N29  C28  C27  C26     0.00   0.0  0
 H6J  CONST_06  N29  C24  C25  C26     0.00   0.0  0
 H6J  CONST_07  C23  C24  C25  C26   180.00   0.0  0
 H6J  CONST_08  C25  C26  C27  C28     0.00   0.0  0
 H6J  CONST_09  C25  C24  N29  C28     0.00   0.0  0
 H6J  CONST_10  C23  C24  N29  C28   180.00   0.0  0
 H6J  CONST_11  N22  C23  N30  C07     0.00   0.0  0
 H6J  CONST_12  N22  C09  C08  C07     0.00   0.0  0
 H6J  CONST_13  C23  N30  C07  C08     0.00   0.0  0
 H6J  CONST_14  C23  N22  C09  C08     0.00   0.0  0
 H6J  CONST_15  N30  C23  N22  C09     0.00   0.0  0
 H6J  CONST_16  N30  C07  C08  C09     0.00   0.0  0
 H6J  CONST_17  N30  C23  C24  C25     0.00   0.0  0
 H6J  CONST_18  N22  C23  C24  C25   180.00   0.0  0
 H6J  CONST_19  N29  C24  C23  N22     0.00   0.0  0
 H6J  CONST_20  N30  C23  C24  N29   180.00   0.0  0
 H6J  CONST_21  N10  C09  C08  C07   180.00   0.0  0
 H6J  CONST_22  N10  C09  N22  C23   180.00   0.0  0
 H6J  CONST_23  N06  C07  C08  C09   180.00   0.0  0
 H6J  CONST_24  N06  C07  N30  C23   180.00   0.0  0
 H6J  CONST_25  H9   C28  N29  C24   180.00   0.0  0
 H6J  CONST_26  H8   C26  C25  C24   180.00   0.0  0
 H6J  CONST_27  H21  C25  C24  C23     0.00   0.0  0
 H6J  CONST_28  H22  C27  C26  C25   180.00   0.0  0
 H6J  CONST_29  H14  C08  C09  N10     0.00   0.0  0
 H6J  CONST_30  N30  C07  N06  C05   180.00   0.0  0
 H6J  CONST_31  C08  C07  N06  C05     0.00   0.0  0
 H6J  CONST_32  H23  N06  C07  C08   180.00   0.0  0
 H6J  Var_01    C07  N06  C05  C04   178.12  30.0  1
 H6J  Var_02    N14  S15  C17  C18   113.67  30.0  3
 H6J  Var_03    N06  C05  C04  C02  -179.74  30.0  2
 H6J  Var_04    O01  C02  C04  C05     6.14  30.0  3
 H6J  Var_05    H19  C18  C17  S15  -179.18   0.0  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
 H6J  plan-1  C24  0.020
 H6J  plan-1  C07  0.020
 H6J  plan-1  C08  0.020
 H6J  plan-1  C09  0.020
 H6J  plan-1  C23  0.020
 H6J  plan-1  N10  0.020
 H6J  plan-1  N22  0.020
 H6J  plan-1  N30  0.020
 H6J  plan-1  H14  0.020
 H6J  plan-1  N06  0.020
 H6J  plan-2  C24  0.020
 H6J  plan-2  C26  0.020
 H6J  plan-2  C28  0.020
 H6J  plan-2  C23  0.020
 H6J  plan-2  C25  0.020
 H6J  plan-2  C27  0.020
 H6J  plan-2  N29  0.020
 H6J  plan-2  H8   0.020
 H6J  plan-2  H9   0.020
 H6J  plan-2  H21  0.020
 H6J  plan-2  H22  0.020
 H6J  plan-3  C05  0.020
 H6J  plan-3  C07  0.020
 H6J  plan-3  H23  0.020
 H6J  plan-3  N06  0.020
 H6J  plan-4  C02  0.020
 H6J  plan-4  C04  0.020
 H6J  plan-4  O01  0.020
 H6J  plan-4  O03  0.020
 H6J  plan-5  C17  0.020
 H6J  plan-5  C18  0.020
 H6J  plan-5  S15  0.020
 H6J  plan-5  H3   0.020
 H6J  plan-5  H19  0.020
 H6J  plan-5  H20  0.020

