# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 11:41:42 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  52  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  -0.279   4.0792  -0.6251   1.1877
 H6G  C15  C  C      0   0.533   4.6723  -2.7007   0.1058
 H6G  C17  C  C2     0  -0.475   5.0553  -4.9346  -0.8370
 H6G  C20  C  CH2    0  -0.331   1.7403  -1.4291  -1.0091
 H6G  C22  C  CR6    0   0.355  -0.9013   2.3439   0.0271
 H6G  C24  C  CR16   0  -0.297  -2.1248   4.4359   0.6622
 H6G  C26  C  CR16   0  -0.314  -0.9260   6.4955   0.7843
 H6G  C02  C  C      0   0.423  -5.2118  -3.4831  -0.4716
 H6G  C04  C  CH2    0  -0.632  -4.8879  -2.0022  -0.2021
 H6G  C05  C  CH2    0  -0.245  -3.4176  -1.6503  -0.3184
 H6G  C07  C  CR6    0   0.546  -2.0401   0.3941  -0.1395
 H6G  C08  C  CR16   0  -0.546  -0.8520  -0.2740  -0.4504
 H6G  C09  C  CR6    0   0.565   0.3117   0.4984  -0.5146
 H6G  C11  C  CH2    0  -0.326   2.7280   0.7545  -0.5257
 H6G  C12  C  CH2    0  -0.494   3.1600   0.5670   0.9328
 H6G  C16  C  C1     0  -0.324   4.2887  -3.8521  -0.7614
 H6G  C19  C  CH2    0  -0.356   2.2842  -2.1031   0.2537
 H6G  C23  C  CR6    0   0.142  -0.9330   3.8115   0.2997
 H6G  C25  C  CR16   0  -0.154  -2.1177   5.7991   0.9085
 H6G  C27  C  CR16   0  -0.087   0.2077   5.7838   0.4167
 H6G  N10  N  NT     0  -0.487   1.5326  -0.0088  -0.8529
 H6G  N14  N  NT     0  -0.467   3.6967  -1.8362   0.4697
 H6G  N21  N  N      0  -0.491   0.2722   1.8159  -0.2601
 H6G  N28  N  N      0  -0.402   0.2098   4.4805   0.1805
 H6G  N29  N  N      0  -0.512  -2.0601   1.7168   0.1002
 H6G  O01  O  O      0  -0.606  -4.2558  -4.2474  -0.7057
 H6G  O03  O  OC    -1  -0.624  -6.4194  -3.7910  -0.4270
 H6G  O18  O  O      0  -0.502   5.8382  -2.5496   0.4539
 H6G  H1   H  HCH2   0   0.250   5.0868  -0.3624   0.8711
 H6G  H2   H  HCH2   0   0.244   4.1266  -0.8200   2.2638
 H6G  H3   H  H      0   0.260   4.7875  -5.7619  -1.4798
 H6G  H4   H  H      0   0.257   5.9641  -5.0362  -0.2586
 H6G  H5   H  HCH2   0   0.264   2.4479  -1.5843  -1.8283
 H6G  H6   H  HCH2   0   0.269   0.8166  -1.9135  -1.3149
 H6G  H7   H  HCR6   0   0.268  -3.0339   3.8590   0.7479
 H6G  H8   H  HCR6   0   0.272  -0.8697   7.5602   0.9641
 H6G  H9   H  HCH2   0   0.236  -5.4706  -1.3854  -0.8947
 H6G  H10  H  HCH2   0   0.238  -5.2508  -1.7452   0.7993
 H6G  H11  H  HCH2   0   0.223  -2.8330  -2.2510   0.3849
 H6G  H12  H  HCH2   0   0.222  -3.0516  -1.8973  -1.3199
 H6G  H13  H  HCR6   0   0.277  -0.8576  -1.3393  -0.6137
 H6G  H14  H  HCH2   0   0.274   2.5293   1.8044  -0.7157
 H6G  H15  H  HCH2   0   0.248   3.5246   0.4451  -1.2077
 H6G  H16  H  HCH2   0   0.244   2.2704   0.5194   1.5651
 H6G  H17  H  HCH2   0   0.259   3.7069   1.4526   1.2635
 H6G  H18  H  H      0   0.275   3.3884  -3.8004  -1.3598
 H6G  H19  H  HCH2   0   0.280   1.7264  -1.7639   1.1295
 H6G  H20  H  HCH2   0   0.281   2.1142  -3.1768   0.2021
 H6G  H21  H  HCR6   0   0.273  -3.0294   6.3075   1.1931
 H6G  H22  H  HCR6   0   0.260   1.1587   6.2946   0.3082
 H6G  H23  H  HNH1   0   0.384  -4.0186   0.3287   0.1682
 H6G  N06  N  NH1    0  -0.667  -3.2189  -0.2411  -0.0560

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  1.386  0.020  1.386
 H6G  C27  N28  aromatic  1.325  0.020  1.325
 H6G  C25  C24  aromatic  1.385  0.020  1.385
 H6G  N28  C23  aromatic  1.330  0.020  1.330
 H6G  C24  C23  aromatic  1.393  0.020  1.393
 H6G  C23  C22  single    1.493  0.020  1.493
 H6G  C17  C16  double    1.329  0.020  1.329
 H6G  C22  N29  aromatic  1.320  0.020  1.320
 H6G  C22  N21  aromatic  1.318  0.020  1.318
 H6G  C16  C15  single    1.492  0.020  1.492
 H6G  N29  C07  aromatic  1.344  0.020  1.344
 H6G  N21  C09  aromatic  1.342  0.020  1.342
 H6G  C19  C20  single    1.531  0.020  1.531
 H6G  C19  N14  single    1.454  0.020  1.454
 H6G  C07  N06  single    1.342  0.020  1.342
 H6G  C07  C08  aromatic  1.398  0.020  1.398
 H6G  C15  N14  single    1.353  0.020  1.353
 H6G  C15  O18  double    1.226  0.020  1.226
 H6G  C09  C08  aromatic  1.398  0.020  1.398
 H6G  C09  N10  single    1.365  0.020  1.365
 H6G  C20  N10  single    1.444  0.020  1.444
 H6G  N06  C05  single    1.447  0.020  1.447
 H6G  N14  C13  single    1.459  0.020  1.459
 H6G  N10  C11  single    1.456  0.020  1.456
 H6G  C05  C04  single    1.516  0.020  1.516
 H6G  C13  C12  single    1.527  0.020  1.527
 H6G  C11  C12  single    1.533  0.020  1.533
 H6G  C04  C02  single    1.540  0.020  1.540
 H6G  C02  O01  deloc     1.246  0.020  1.246
 H6G  C02  O03  deloc     1.247  0.020  1.247
 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

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   106.79  3.000
 H6G  H2   C13  N14  110.32  3.000
 H6G  H1   C13  N14  107.45  3.000
 H6G  H2   C13  C12  109.22  3.000
 H6G  H1   C13  C12  108.69  3.000
 H6G  N14  C13  C12  114.09  3.000
 H6G  O18  C15  N14  122.03  3.000
 H6G  O18  C15  C16  120.31  3.000
 H6G  N14  C15  C16  117.65  3.000
 H6G  H4   C17  H3   117.00  3.000
 H6G  H4   C17  C16  122.05  3.000
 H6G  H3   C17  C16  120.95  3.000
 H6G  H6   C20  H5   106.02  3.000
 H6G  H6   C20  N10  110.28  3.000
 H6G  H5   C20  N10  108.28  3.000
 H6G  H6   C20  C19  109.74  3.000
 H6G  H5   C20  C19  108.99  3.000
 H6G  N10  C20  C19  113.26  3.000
 H6G  N29  C22  N21  127.11  3.000
 H6G  N21  C22  C23  116.89  3.000
 H6G  N29  C22  C23  115.99  3.000
 H6G  H7   C24  C25  121.05  3.000
 H6G  H7   C24  C23  120.08  3.000
 H6G  C25  C24  C23  118.88  3.000
 H6G  H8   C26  C27  120.42  3.000
 H6G  H8   C26  C25  121.65  3.000
 H6G  C27  C26  C25  117.93  3.000
 H6G  O03  C02  O01  126.74  3.000
 H6G  O03  C02  C04  115.78  3.000
 H6G  O01  C02  C04  117.47  3.000
 H6G  H10  C04  H9   105.64  3.000
 H6G  H10  C04  C05  109.69  3.000
 H6G  H9   C04  C05  109.68  3.000
 H6G  H10  C04  C02  108.41  3.000
 H6G  H9   C04  C02  108.61  3.000
 H6G  C05  C04  C02  114.45  3.000
 H6G  H12  C05  H11  106.59  3.000
 H6G  H12  C05  N06  109.86  3.000
 H6G  H11  C05  N06  110.17  3.000
 H6G  H12  C05  C04  110.00  3.000
 H6G  H11  C05  C04  109.96  3.000
 H6G  N06  C05  C04  110.20  3.000
 H6G  N29  C07  N06  116.21  3.000
 H6G  N06  C07  C08  122.29  3.000
 H6G  N29  C07  C08  121.50  3.000
 H6G  H13  C08  C09  122.92  3.000
 H6G  H13  C08  C07  120.11  3.000
 H6G  C09  C08  C07  116.97  3.000
 H6G  N21  C09  N10  115.98  3.000
 H6G  N10  C09  C08  123.41  3.000
 H6G  N21  C09  C08  120.60  3.000
 H6G  H15  C11  H14  107.33  3.000
 H6G  H15  C11  N10  108.04  3.000
 H6G  H14  C11  N10  108.52  3.000
 H6G  H15  C11  C12  110.71  3.000
 H6G  H14  C11  C12  109.66  3.000
 H6G  N10  C11  C12  112.41  3.000
 H6G  H17  C12  H16  105.54  3.000
 H6G  H17  C12  C11  109.27  3.000
 H6G  H16  C12  C11  109.06  3.000
 H6G  H17  C12  C13  106.33  3.000
 H6G  H16  C12  C13  111.08  3.000
 H6G  C11  C12  C13  115.09  3.000
 H6G  H18  C16  C17  119.18  3.000
 H6G  H18  C16  C15  119.89  3.000
 H6G  C17  C16  C15  120.91  3.000
 H6G  H20  C19  H19  105.35  3.000
 H6G  H20  C19  N14  109.88  3.000
 H6G  H19  C19  N14  108.67  3.000
 H6G  H20  C19  C20  109.85  3.000
 H6G  H19  C19  C20  110.07  3.000
 H6G  N14  C19  C20  112.76  3.000
 H6G  N28  C23  C24  122.21  3.000
 H6G  C24  C23  C22  120.41  3.000
 H6G  N28  C23  C22  117.38  3.000
 H6G  H21  C25  C26  120.80  3.000
 H6G  H21  C25  C24  120.33  3.000
 H6G  C26  C25  C24  118.88  3.000
 H6G  H22  C27  N28  116.36  3.000
 H6G  H22  C27  C26  120.07  3.000
 H6G  N28  C27  C26  123.57  3.000
 H6G  C11  N10  C09  118.96  3.000
 H6G  C11  N10  C20  114.96  3.000
 H6G  C09  N10  C20  121.41  3.000
 H6G  C19  N14  C15  122.90  3.000
 H6G  C15  N14  C13  118.27  3.000
 H6G  C19  N14  C13  118.71  3.000
 H6G  C09  N21  C22  117.42  3.000
 H6G  C27  N28  C23  118.54  3.000
 H6G  C07  N29  C22  116.40  3.000
 H6G  H23  N06  C07  116.33  3.000
 H6G  H23  N06  C05  118.83  3.000
 H6G  C07  N06  C05  124.78  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  Var_01    N14  C15  C16  C17  -159.81  30.0  2
 H6G  Var_02    C07  N06  C05  C04  -176.85  30.0  2
 H6G  Var_03    N06  C05  C04  C02   179.66  30.0  1
 H6G  Var_04    O01  C02  C04  C05     2.53  30.0  3
 H6G  Var_05    H3   C17  C16  C15  -178.83   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-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

