# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:19:59 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[6-(4-acryloyl-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)C(=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
 H6G  H6G  N-[6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl]-beta-alanine  ligand  53  29  .  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_H6G
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
 H6G  C13  C  CH2   0  -0.270   4.0689  -0.6304   1.2219
 H6G  C15  C  C     0   0.529   4.7121  -2.6815   0.1189
 H6G  C17  C  C2    0  -0.450   5.1457  -4.8973  -0.8400
 H6G  C20  C  CH2   0  -0.311   1.7465  -1.4629  -0.9869
 H6G  C22  C  CR6   0   0.363  -0.8941   2.3204   0.0175
 H6G  C24  C  CR16  0  -0.283  -2.1091   4.4136   0.6530
 H6G  C26  C  CR16  0  -0.293  -0.8952   6.4598   0.8204
 H6G  C02  C  C     0   0.578  -5.1776  -3.4434  -0.4047
 H6G  C04  C  CH2   0  -0.600  -4.8888  -2.0004  -0.1143
 H6G  C05  C  CH2   0  -0.228  -3.4529  -1.6240  -0.4285
 H6G  C07  C  CR6   0   0.559  -2.0413   0.3830  -0.1758
 H6G  C08  C  CR16  0  -0.520  -0.8620  -0.2946  -0.4806
 H6G  C09  C  CR6   0   0.573   0.3127   0.4682  -0.5147
 H6G  C11  C  CH2   0  -0.318   2.7271   0.7301  -0.5175
 H6G  C12  C  CH2   0  -0.477   3.1601   0.5663   0.9425
 H6G  C16  C  C1    0  -0.312   4.3493  -3.8382  -0.7532
 H6G  C19  C  CH2   0  -0.333   2.3081  -2.1310   0.2714
 H6G  C23  C  CR6   0   0.141  -0.9171   3.7846   0.3013
 H6G  C25  C  CR16  0  -0.133  -2.0942   5.7729   0.9173
 H6G  C27  C  CR16  0  -0.071   0.2374   5.7431   0.4596
 H6G  N10  N  NT    0  -0.488   1.5344  -0.0444  -0.8304
 H6G  N14  N  NT    0  -0.475   3.7121  -1.8352   0.4850
 H6G  N21  N  N     0  -0.478   0.2775   1.7813  -0.2491
 H6G  N28  N  N     0  -0.392   0.2333   4.4439   0.2069
 H6G  N29  N  N     0  -0.513  -2.0600   1.7010   0.0666
 H6G  O01  O  O     0  -0.454  -4.3847  -4.2371  -0.8452
 H6G  O03  O  OH1   0  -0.582  -6.4337  -3.7649  -0.1133
 H6G  O18  O  O     0  -0.453   5.8682  -2.5096   0.4677
 H6G  H1   H  HCH2  0   0.255   5.0891  -0.3732   0.9451
 H6G  H2   H  HCH2  0   0.229   4.0780  -0.8299   2.2984
 H6G  H3   H  H     0   0.237   4.8967  -5.7301  -1.4823
 H6G  H4   H  H     0   0.257   6.0629  -4.9699  -0.2712
 H6G  H5   H  HCH2  0   0.251   2.4453  -1.6160  -1.8142
 H6G  H6   H  HCH2  0   0.252   0.8233  -1.9535  -1.2837
 H6G  H7   H  HCR6  0   0.257  -3.0233   3.8423   0.7168
 H6G  H8   H  HCR6  0   0.250  -0.8322   7.5208   1.0162
 H6G  H9   H  HCH2  0   0.280  -5.5885  -1.3904  -0.6938
 H6G  H10  H  HCH2  0   0.290  -5.1125  -1.8081   0.9387
 H6G  H11  H  HCH2  0   0.237  -2.7793  -2.2563   0.1548
 H6G  H12  H  HCH2  0   0.233  -3.2372  -1.8103  -1.4860
 H6G  H13  H  HCR6  0   0.249  -0.8750  -1.3556  -0.6674
 H6G  H14  H  HCH2  0   0.281   2.5221   1.7761  -0.7220
 H6G  H15  H  HCH2  0   0.236   3.5236   0.4139  -1.1962
 H6G  H16  H  HCH2  0   0.235   2.2688   0.5410   1.5733
 H6G  H17  H  HCH2  0   0.250   3.7106   1.4554   1.2560
 H6G  H18  H  H     0   0.247   3.4434  -3.8117  -1.3448
 H6G  H19  H  HCH2  0   0.264   1.7416  -1.8104   1.1489
 H6G  H20  H  HCH2  0   0.266   2.1570  -3.2076   0.2153
 H6G  H21  H  HCR6  0   0.249  -3.0048   6.2856   1.1958
 H6G  H22  H  HCR6  0   0.241   1.1934   6.2481   0.3718
 H6G  H23  H  HNH1  0   0.363  -4.0303   0.3665   0.0120
 H6G  H24  H  HOH1  0   0.452  -6.5699  -4.7045  -0.2949
 H6G  N06  N  NH1   0  -0.672  -3.2350  -0.2419  -0.0877

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
 H6G  C26  C27  aromatic  1.388  0.020  1.388
 H6G  C26  C25  aromatic  1.385  0.020  1.385
 H6G  C27  N28  aromatic  1.324  0.020  1.324
 H6G  C25  C24  aromatic  1.385  0.020  1.385
 H6G  N28  C23  aromatic  1.329  0.020  1.329
 H6G  C24  C23  aromatic  1.393  0.020  1.393
 H6G  C23  C22  single    1.492  0.020  1.492
 H6G  C17  C16  double    1.328  0.020  1.328
 H6G  C22  N29  aromatic  1.321  0.020  1.321
 H6G  C22  N21  aromatic  1.317  0.020  1.317
 H6G  C16  C15  single    1.493  0.020  1.493
 H6G  N29  C07  aromatic  1.340  0.020  1.340
 H6G  N21  C09  aromatic  1.340  0.020  1.340
 H6G  C19  C20  single    1.531  0.020  1.531
 H6G  C19  N14  single    1.451  0.020  1.451
 H6G  C07  N06  single    1.350  0.020  1.350
 H6G  C07  C08  aromatic  1.394  0.020  1.394
 H6G  C15  N14  single    1.360  0.020  1.360
 H6G  C15  O18  double    1.220  0.020  1.220
 H6G  C09  C08  aromatic  1.401  0.020  1.401
 H6G  C09  N10  single    1.362  0.020  1.362
 H6G  C20  N10  single    1.443  0.020  1.443
 H6G  N06  C05  single    1.440  0.020  1.440
 H6G  N14  C13  single    1.457  0.020  1.457
 H6G  N10  C11  single    1.456  0.020  1.456
 H6G  C05  C04  single    1.517  0.020  1.517
 H6G  C13  C12  single    1.528  0.020  1.528
 H6G  C11  C12  single    1.532  0.020  1.532
 H6G  C04  C02  single    1.500  0.020  1.500
 H6G  C02  O01  double    1.205  0.020  1.205
 H6G  C02  O03  single    1.329  0.020  1.329
 H6G  C13  H1   single    0.970  0.020  1.090
 H6G  C13  H2   single    0.970  0.020  1.090
 H6G  C17  H3   single    0.930  0.020  1.080
 H6G  C17  H4   single    0.930  0.020  1.080
 H6G  C20  H5   single    0.970  0.020  1.090
 H6G  C20  H6   single    0.970  0.020  1.090
 H6G  C24  H7   single    0.930  0.020  1.080
 H6G  C26  H8   single    0.930  0.020  1.080
 H6G  C04  H9   single    0.970  0.020  1.090
 H6G  C04  H10  single    0.970  0.020  1.090
 H6G  C05  H11  single    0.970  0.020  1.090
 H6G  C05  H12  single    0.970  0.020  1.090
 H6G  C08  H13  single    0.930  0.020  1.080
 H6G  C11  H14  single    0.970  0.020  1.090
 H6G  C11  H15  single    0.970  0.020  1.090
 H6G  C12  H16  single    0.970  0.020  1.090
 H6G  C12  H17  single    0.970  0.020  1.090
 H6G  C16  H18  single    0.930  0.020  1.080
 H6G  C19  H19  single    0.970  0.020  1.090
 H6G  C19  H20  single    0.970  0.020  1.090
 H6G  C25  H21  single    0.930  0.020  1.080
 H6G  C27  H22  single    0.930  0.020  1.080
 H6G  N06  H23  single    0.860  0.020  1.020
 H6G  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
 H6G  H2   C13  H1   106.58  3.000
 H6G  H2   C13  N14  110.41  3.000
 H6G  H1   C13  N14  107.25  3.000
 H6G  H2   C13  C12  109.11  3.000
 H6G  H1   C13  C12  109.03  3.000
 H6G  N14  C13  C12  114.17  3.000
 H6G  O18  C15  N14  122.15  3.000
 H6G  O18  C15  C16  120.42  3.000
 H6G  N14  C15  C16  117.42  3.000
 H6G  H4   C17  H3   117.14  3.000
 H6G  H4   C17  C16  121.85  3.000
 H6G  H3   C17  C16  121.01  3.000
 H6G  H6   C20  H5   105.84  3.000
 H6G  H6   C20  N10  110.39  3.000
 H6G  H5   C20  N10  108.28  3.000
 H6G  H6   C20  C19  109.82  3.000
 H6G  H5   C20  C19  109.03  3.000
 H6G  N10  C20  C19  113.19  3.000
 H6G  N29  C22  N21  126.92  3.000
 H6G  N21  C22  C23  117.01  3.000
 H6G  N29  C22  C23  116.07  3.000
 H6G  H7   C24  C25  121.14  3.000
 H6G  H7   C24  C23  120.03  3.000
 H6G  C25  C24  C23  118.83  3.000
 H6G  H8   C26  C27  120.42  3.000
 H6G  H8   C26  C25  121.64  3.000
 H6G  C27  C26  C25  117.94  3.000
 H6G  O03  C02  O01  122.87  3.000
 H6G  O03  C02  C04  111.86  3.000
 H6G  O01  C02  C04  125.28  3.000
 H6G  H10  C04  H9   106.32  3.000
 H6G  H10  C04  C05  110.45  3.000
 H6G  H9   C04  C05  110.93  3.000
 H6G  H10  C04  C02  108.43  3.000
 H6G  H9   C04  C02  108.10  3.000
 H6G  C05  C04  C02  112.38  3.000
 H6G  H12  C05  H11  107.20  3.000
 H6G  H12  C05  N06  111.22  3.000
 H6G  H11  C05  N06  109.62  3.000
 H6G  H12  C05  C04  110.12  3.000
 H6G  H11  C05  C04  109.23  3.000
 H6G  N06  C05  C04  109.40  3.000
 H6G  N29  C07  N06  115.53  3.000
 H6G  N06  C07  C08  122.50  3.000
 H6G  N29  C07  C08  121.96  3.000
 H6G  H13  C08  C09  122.83  3.000
 H6G  H13  C08  C07  120.42  3.000
 H6G  C09  C08  C07  116.75  3.000
 H6G  N21  C09  N10  115.99  3.000
 H6G  N10  C09  C08  123.56  3.000
 H6G  N21  C09  C08  120.44  3.000
 H6G  H15  C11  H14  107.42  3.000
 H6G  H15  C11  N10  108.03  3.000
 H6G  H14  C11  N10  108.50  3.000
 H6G  H15  C11  C12  110.79  3.000
 H6G  H14  C11  C12  109.64  3.000
 H6G  N10  C11  C12  112.31  3.000
 H6G  H17  C12  H16  105.34  3.000
 H6G  H17  C12  C11  109.22  3.000
 H6G  H16  C12  C11  108.80  3.000
 H6G  H17  C12  C13  106.58  3.000
 H6G  H16  C12  C13  111.19  3.000
 H6G  C11  C12  C13  115.22  3.000
 H6G  H18  C16  C17  119.07  3.000
 H6G  H18  C16  C15  120.23  3.000
 H6G  C17  C16  C15  120.68  3.000
 H6G  H20  C19  H19  105.04  3.000
 H6G  H20  C19  N14  110.10  3.000
 H6G  H19  C19  N14  108.89  3.000
 H6G  H20  C19  C20  109.77  3.000
 H6G  H19  C19  C20  109.99  3.000
 H6G  N14  C19  C20  112.77  3.000
 H6G  N28  C23  C24  122.31  3.000
 H6G  C24  C23  C22  120.30  3.000
 H6G  N28  C23  C22  117.39  3.000
 H6G  H21  C25  C26  120.78  3.000
 H6G  H21  C25  C24  120.36  3.000
 H6G  C26  C25  C24  118.86  3.000
 H6G  H22  C27  N28  116.38  3.000
 H6G  H22  C27  C26  119.99  3.000
 H6G  N28  C27  C26  123.63  3.000
 H6G  C11  N10  C09  118.99  3.000
 H6G  C11  N10  C20  115.20  3.000
 H6G  C09  N10  C20  121.81  3.000
 H6G  C19  N14  C15  123.03  3.000
 H6G  C15  N14  C13  118.08  3.000
 H6G  C19  N14  C13  118.70  3.000
 H6G  C09  N21  C22  117.68  3.000
 H6G  C27  N28  C23  118.43  3.000
 H6G  C07  N29  C22  116.23  3.000
 H6G  H24  O03  C02  109.09  3.000
 H6G  H23  N06  C07  115.17  3.000
 H6G  H23  N06  C05  118.96  3.000
 H6G  C07  N06  C05  124.23  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
 H6G  CONST_01  C27  N28  C23  C22   180.00   0.0  0
 H6G  CONST_02  C25  C24  C23  C22   180.00   0.0  0
 H6G  CONST_03  C08  C07  N29  C22     0.00   0.0  0
 H6G  CONST_04  C08  C09  N21  C22     0.00   0.0  0
 H6G  CONST_05  C27  C26  C25  C24     0.00   0.0  0
 H6G  CONST_06  C27  N28  C23  C24     0.00   0.0  0
 H6G  CONST_07  N29  C22  C23  C24     0.00   0.0  0
 H6G  CONST_08  N21  C22  C23  C24   180.00   0.0  0
 H6G  CONST_09  C23  N28  C27  C26     0.00   0.0  0
 H6G  CONST_10  C23  C24  C25  C26     0.00   0.0  0
 H6G  CONST_11  C23  C22  N29  C07   180.00   0.0  0
 H6G  CONST_12  N21  C22  N29  C07     0.00   0.0  0
 H6G  CONST_13  N21  C09  C08  C07     0.00   0.0  0
 H6G  CONST_14  C23  C22  N21  C09   180.00   0.0  0
 H6G  CONST_15  N29  C22  N21  C09     0.00   0.0  0
 H6G  CONST_16  N29  C07  C08  C09     0.00   0.0  0
 H6G  CONST_17  N28  C27  C26  C25     0.00   0.0  0
 H6G  CONST_18  N28  C23  C24  C25     0.00   0.0  0
 H6G  CONST_19  N28  C23  C22  N21     0.00   0.0  0
 H6G  CONST_20  N29  C22  C23  N28   180.00   0.0  0
 H6G  CONST_21  N10  C09  N21  C22   180.00   0.0  0
 H6G  CONST_22  N10  C09  C08  C07   180.00   0.0  0
 H6G  CONST_23  N06  C07  N29  C22   180.00   0.0  0
 H6G  CONST_24  N06  C07  C08  C09   180.00   0.0  0
 H6G  CONST_25  H7   C24  C23  C22     0.00   0.0  0
 H6G  CONST_26  H8   C26  C25  C24   180.00   0.0  0
 H6G  CONST_27  H22  C27  N28  C23   180.00   0.0  0
 H6G  CONST_28  H21  C25  C24  C23   180.00   0.0  0
 H6G  CONST_29  H13  C08  C09  N10     0.00   0.0  0
 H6G  CONST_30  N29  C07  N06  C05   180.00   0.0  0
 H6G  CONST_31  C08  C07  N06  C05     0.00   0.0  0
 H6G  CONST_32  H23  N06  C07  C08   180.00   0.0  0
 H6G  CONST_33  H24  O03  C02  C04   180.00   0.0  0
 H6G  Var_01    N14  C15  C16  C17  -160.52  30.0  2
 H6G  Var_02    C07  N06  C05  C04   176.13  30.0  1
 H6G  Var_03    N06  C05  C04  C02  -178.20  30.0  2
 H6G  Var_04    O01  C02  C04  C05    -0.44  30.0  3
 H6G  Var_05    H3   C17  C16  C15  -178.96   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
 H6G  plan-1  C22  0.020
 H6G  plan-1  C07  0.020
 H6G  plan-1  C08  0.020
 H6G  plan-1  C09  0.020
 H6G  plan-1  C23  0.020
 H6G  plan-1  N10  0.020
 H6G  plan-1  N21  0.020
 H6G  plan-1  N29  0.020
 H6G  plan-1  H13  0.020
 H6G  plan-1  N06  0.020
 H6G  plan-2  C22  0.020
 H6G  plan-2  C24  0.020
 H6G  plan-2  C26  0.020
 H6G  plan-2  C23  0.020
 H6G  plan-2  C25  0.020
 H6G  plan-2  C27  0.020
 H6G  plan-2  N28  0.020
 H6G  plan-2  H7   0.020
 H6G  plan-2  H8   0.020
 H6G  plan-2  H21  0.020
 H6G  plan-2  H22  0.020
 H6G  plan-3  C13  0.020
 H6G  plan-3  C15  0.020
 H6G  plan-3  C16  0.020
 H6G  plan-3  C19  0.020
 H6G  plan-3  N14  0.020
 H6G  plan-3  O18  0.020
 H6G  plan-4  C05  0.020
 H6G  plan-4  C07  0.020
 H6G  plan-4  H23  0.020
 H6G  plan-4  N06  0.020
 H6G  plan-5  C02  0.020
 H6G  plan-5  C04  0.020
 H6G  plan-5  O01  0.020
 H6G  plan-5  O03  0.020
 H6G  plan-5  H24  0.020
 H6G  plan-6  C15  0.020
 H6G  plan-6  C17  0.020
 H6G  plan-6  C16  0.020
 H6G  plan-6  H3   0.020
 H6G  plan-6  H4   0.020
 H6G  plan-6  H18  0.020

