# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:55:28 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  54  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   3.3402  -0.2431   1.3102
 H6J  C17  C  C1    0  -0.401   4.2783   1.4616  -1.4377
 H6J  C20  C  CH2   0  -0.301   2.1935   1.9940   1.3348
 H6J  C21  C  CH2   0  -0.343   1.4207   1.5780   2.5962
 H6J  C24  C  CR6   0   0.142  -2.1088   2.7749  -0.4203
 H6J  C26  C  CR16  0  -0.155  -3.5005   4.0775  -1.8670
 H6J  C28  C  CR16  0  -0.089  -1.7405   5.0202  -0.5773
 H6J  C02  C  C     0   0.559  -3.1192  -5.5901  -0.1760
 H6J  C04  C  CH2   0  -0.622  -3.3483  -4.1506  -0.5421
 H6J  C05  C  CH2   0  -0.245  -2.3831  -3.2130   0.1586
 H6J  C07  C  CR6   0   0.544  -1.9848  -0.7843   0.2188
 H6J  C08  C  CR16  0  -0.527  -0.9524  -0.8940   1.1505
 H6J  C09  C  CR6   0   0.576  -0.3397   0.2980   1.5488
 H6J  C11  C  CH2   0  -0.356   1.3928  -0.8676   2.8243
 H6J  C12  C  CH2   0  -0.412   2.3974  -1.3440   1.7791
 H6J  C18  C  C2    0  -0.444   5.2079   0.7243  -2.0241
 H6J  C23  C  CR6   0   0.368  -1.7082   1.4635   0.1665
 H6J  C25  C  CR16  0  -0.299  -3.1657   2.8472  -1.3256
 H6J  C27  C  CR16  0  -0.315  -2.7723   5.1946  -1.4898
 H6J  N10  N  NT    0  -0.483   0.6799   0.3418   2.4468
 H6J  N14  N  N     0  -0.579   2.6335   0.8201   0.5969
 H6J  N22  N  N     0  -0.484  -0.7468   1.4793   1.0670
 H6J  N29  N  N     0  -0.394  -1.4147   3.8480  -0.0537
 H6J  N30  N  N     0  -0.513  -2.3523   0.4037  -0.2881
 H6J  O01  O  O     0  -0.442  -2.2917  -5.9806   0.6089
 H6J  O03  O  OH1   0  -0.593  -3.9483  -6.3976  -0.8259
 H6J  O16  O  OS    0  -0.653   1.7012   1.7754  -1.5234
 H6J  O19  O  OS    0  -0.659   2.6276  -0.5596  -1.4910
 H6J  S15  S  S     0   1.363   2.6842   0.8218  -1.0359
 H6J  H1   H  HCH2  0   0.259   3.8656   0.2094   2.1555
 H6J  H2   H  HCH2  0   0.269   4.1194  -0.6697   0.6769
 H6J  H3   H  H     0   0.318   4.4295   2.4951  -1.1478
 H6J  H4   H  HCH2  0   0.287   1.5382   2.5803   0.6977
 H6J  H5   H  HCH2  0   0.247   3.0439   2.6165   1.6323
 H6J  H6   H  HCH2  0   0.254   2.1092   1.4340   3.4283
 H6J  H7   H  HCH2  0   0.272   0.7574   2.3970   2.8734
 H6J  H8   H  HCR6  0   0.272  -4.3170   4.1598  -2.5721
 H6J  H9   H  HCR6  0   0.259  -1.1502   5.8718  -0.2563
 H6J  H10  H  HCH2  0   0.293  -3.2608  -4.0494  -1.6280
 H6J  H11  H  HCH2  0   0.295  -4.3822  -3.8921  -0.2940
 H6J  H12  H  HCH2  0   0.242  -2.4818  -3.3203   1.2428
 H6J  H13  H  HCH2  0   0.240  -1.3532  -3.4821  -0.0970
 H6J  H14  H  HCR6  0   0.275  -0.6384  -1.8564   1.5225
 H6J  H15  H  HCH2  0   0.263   0.6810  -1.6607   3.0547
 H6J  H16  H  HCH2  0   0.261   1.9133  -0.6548   3.7598
 H6J  H17  H  HCH2  0   0.240   1.8822  -1.7592   0.9114
 H6J  H18  H  HCH2  0   0.241   2.9882  -2.1526   2.2171
 H6J  H19  H  H     0   0.278   6.1793   1.1452  -2.2446
 H6J  H20  H  H     0   0.280   5.0416  -0.3059  -2.3079
 H6J  H21  H  HCR6  0   0.268  -3.7089   1.9539  -1.5971
 H6J  H22  H  HCR6  0   0.271  -2.9921   6.1759  -1.8872
 H6J  H23  H  HNH1  0   0.389  -3.3615  -1.6778  -0.9384
 H6J  H24  H  HOH1  0   0.482  -3.7842  -7.3180  -0.5711
 H6J  N06  N  NH1   0  -0.676  -2.6634  -1.8549  -0.2344

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  1.324  0.020  1.324
 H6J  C26  C25  aromatic  1.385  0.020  1.385
 H6J  N29  C24  aromatic  1.330  0.020  1.330
 H6J  C25  C24  aromatic  1.393  0.020  1.393
 H6J  C24  C23  single    1.492  0.020  1.492
 H6J  C18  C17  double    1.323  0.020  1.323
 H6J  C23  N30  aromatic  1.321  0.020  1.321
 H6J  C23  N22  aromatic  1.317  0.020  1.317
 H6J  N30  C07  aromatic  1.343  0.020  1.343
 H6J  C17  S15  single    1.764  0.020  1.764
 H6J  N22  C09  aromatic  1.339  0.020  1.339
 H6J  O16  S15  double    1.454  0.020  1.454
 H6J  S15  N14  single    1.634  0.020  1.634
 H6J  S15  O19  double    1.455  0.020  1.455
 H6J  C20  N14  single    1.455  0.020  1.455
 H6J  C20  C21  single    1.537  0.020  1.537
 H6J  C07  N06  single    1.346  0.020  1.346
 H6J  C07  C08  aromatic  1.395  0.020  1.395
 H6J  C09  C08  aromatic  1.398  0.020  1.398
 H6J  C09  N10  single    1.359  0.020  1.359
 H6J  N06  C05  single    1.441  0.020  1.441
 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    1.523  0.020  1.523
 H6J  C04  C02  single    1.503  0.020  1.503
 H6J  C11  C12  single    1.526  0.020  1.526
 H6J  C02  O01  double    1.206  0.020  1.206
 H6J  C02  O03  single    1.327  0.020  1.327
 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
 H6J  O03  H24  single    0.850  0.020  0.980

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   105.51  3.000
 H6J  H2   C13  N14  110.26  3.000
 H6J  H1   C13  N14  107.97  3.000
 H6J  H2   C13  C12  109.76  3.000
 H6J  H1   C13  C12  111.01  3.000
 H6J  N14  C13  C12  112.11  3.000
 H6J  H3   C17  S15  114.26  3.000
 H6J  H3   C17  C18  123.48  3.000
 H6J  S15  C17  C18  122.25  3.000
 H6J  H5   C20  H4   108.73  3.000
 H6J  H5   C20  N14  111.20  3.000
 H6J  H4   C20  N14  108.70  3.000
 H6J  H5   C20  C21  108.75  3.000
 H6J  H4   C20  C21  108.92  3.000
 H6J  N14  C20  C21  110.49  3.000
 H6J  H7   C21  H6   106.84  3.000
 H6J  H7   C21  N10  110.87  3.000
 H6J  H6   C21  N10  106.80  3.000
 H6J  H7   C21  C20  108.14  3.000
 H6J  H6   C21  C20  110.17  3.000
 H6J  N10  C21  C20  113.79  3.000
 H6J  N29  C24  C25  122.22  3.000
 H6J  C25  C24  C23  120.33  3.000
 H6J  N29  C24  C23  117.45  3.000
 H6J  H8   C26  C27  120.84  3.000
 H6J  H8   C26  C25  120.31  3.000
 H6J  C27  C26  C25  118.85  3.000
 H6J  H9   C28  N29  116.35  3.000
 H6J  H9   C28  C27  120.02  3.000
 H6J  N29  C28  C27  123.63  3.000
 H6J  O03  C02  O01  123.40  3.000
 H6J  O03  C02  C04  111.61  3.000
 H6J  O01  C02  C04  124.99  3.000
 H6J  H11  C04  H10  106.18  3.000
 H6J  H11  C04  C05  110.51  3.000
 H6J  H10  C04  C05  110.51  3.000
 H6J  H11  C04  C02  108.37  3.000
 H6J  H10  C04  C02  108.55  3.000
 H6J  C05  C04  C02  112.49  3.000
 H6J  H13  C05  H12  106.98  3.000
 H6J  H13  C05  N06  110.55  3.000
 H6J  H12  C05  N06  110.19  3.000
 H6J  H13  C05  C04  109.80  3.000
 H6J  H12  C05  C04  109.86  3.000
 H6J  N06  C05  C04  109.43  3.000
 H6J  N30  C07  N06  116.01  3.000
 H6J  N06  C07  C08  122.37  3.000
 H6J  N30  C07  C08  121.62  3.000
 H6J  H14  C08  C09  122.34  3.000
 H6J  H14  C08  C07  121.07  3.000
 H6J  C09  C08  C07  116.59  3.000
 H6J  N22  C09  N10  115.92  3.000
 H6J  N10  C09  C08  122.98  3.000
 H6J  N22  C09  C08  121.09  3.000
 H6J  H16  C11  H15  105.79  3.000
 H6J  H16  C11  N10  107.11  3.000
 H6J  H15  C11  N10  109.87  3.000
 H6J  H16  C11  C12  109.51  3.000
 H6J  H15  C11  C12  110.33  3.000
 H6J  N10  C11  C12  113.87  3.000
 H6J  H18  C12  H17  107.01  3.000
 H6J  H18  C12  C11  108.20  3.000
 H6J  H17  C12  C11  110.65  3.000
 H6J  H18  C12  C13  108.87  3.000
 H6J  H17  C12  C13  108.80  3.000
 H6J  C11  C12  C13  113.12  3.000
 H6J  H20  C18  H19  117.09  3.000
 H6J  H20  C18  C17  122.61  3.000
 H6J  H19  C18  C17  120.29  3.000
 H6J  N30  C23  N22  126.93  3.000
 H6J  N22  C23  C24  117.03  3.000
 H6J  N30  C23  C24  116.04  3.000
 H6J  H21  C25  C26  120.98  3.000
 H6J  H21  C25  C24  120.12  3.000
 H6J  C26  C25  C24  118.90  3.000
 H6J  H22  C27  C28  120.44  3.000
 H6J  H22  C27  C26  121.65  3.000
 H6J  C28  C27  C26  117.91  3.000
 H6J  C11  N10  C09  120.83  3.000
 H6J  C11  N10  C21  115.61  3.000
 H6J  C09  N10  C21  118.63  3.000
 H6J  S15  N14  C20  121.04  3.000
 H6J  C20  N14  C13  119.04  3.000
 H6J  S15  N14  C13  118.25  3.000
 H6J  C23  N22  C09  117.20  3.000
 H6J  C28  N29  C24  118.48  3.000
 H6J  C23  N30  C07  116.51  3.000
 H6J  H24  O03  C02  110.08  3.000
 H6J  O19  S15  O16  119.43  3.000
 H6J  O19  S15  N14  108.08  3.000
 H6J  O16  S15  N14  108.35  3.000
 H6J  O19  S15  C17  107.95  3.000
 H6J  N14  S15  C17  104.84  3.000
 H6J  O16  S15  C17  107.26  3.000
 H6J  H23  N06  C07  116.42  3.000
 H6J  H23  N06  C05  119.42  3.000
 H6J  C07  N06  C05  124.02  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  CONST_33  H24  O03  C02  C04   180.00   0.0  0
 H6J  Var_01    C07  N06  C05  C04   179.67  30.0  1
 H6J  Var_02    N14  S15  C17  C18   113.61  30.0  3
 H6J  Var_03    N06  C05  C04  C02  -179.79  30.0  1
 H6J  Var_04    O01  C02  C04  C05     1.80  30.0  3
 H6J  Var_05    H19  C18  C17  S15  -179.20   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-4  H24  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

