# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:21:59 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: 7-(2-phenylazanylpyrimidin-4-yl)-1,3,4,5-tetrahydro-1-benzazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1CCCc2cc(ccc2N1)c3ccnc(Nc4ccccc4)n3
#
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
 S9K  S9K  7-(2-phenylazanylpyrimidin-4-yl)-1,3,4,5-tetrahydro-1-benzazepin-2-one  ligand  43  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S9K
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
 S9K  C7   C  CR16  0  -0.375   -6.4471  -29.9679   5.3252
 S9K  C9   C  CH2   0  -0.515   -7.4451  -29.5036   3.0921
 S9K  N1   N  N     0  -0.463   -3.7166  -32.3834   8.7762
 S9K  C2   C  C     0   0.514   -9.3617  -27.0077   3.3253
 S9K  N2   N  NH1   0  -0.773   -3.0430  -33.2219   6.7809
 S9K  C10  C  CR6   0   0.326   -5.3428  -30.6270   7.4545
 S9K  C4   C  CR16  0  -0.324   -7.5794  -27.7600   6.4747
 S9K  N3   N  N     0  -0.503   -4.5929  -31.4860   6.7653
 S9K  C6   C  CR6   0   0.063   -6.1988  -29.7187   6.6727
 S9K  O    O  O     0  -0.484   -9.9844  -25.9785   3.1134
 S9K  C1   C  CH2   0  -0.572   -9.4204  -28.1259   2.3184
 S9K  N    N  NH1   0  -0.748   -8.6210  -27.0771   4.4716
 S9K  C3   C  CR6   0   0.352   -7.8261  -28.0227   5.1230
 S9K  C8   C  CR6   0   0.151   -7.2395  -29.1486   4.5326
 S9K  C    C  CH2   0  -0.457   -8.9151  -29.5050   2.6897
 S9K  C5   C  CR16  0  -0.334   -6.7838  -28.5872   7.2381
 S9K  C13  C  CR6   0   0.593   -3.8199  -32.3204   7.4428
 S9K  C12  C  CR16  0  -0.019   -4.4647  -31.5298   9.4509
 S9K  C11  C  CR16  0  -0.406   -5.3105  -30.6149   8.8459
 S9K  C14  C  CR6   0   0.363   -2.8670  -33.4699   5.4235
 S9K  C19  C  CR16  0  -0.312   -3.2870  -32.6232   4.3943
 S9K  C18  C  CR16  0  -0.247   -3.0352  -32.9655   3.0719
 S9K  C17  C  CR16  0  -0.278   -2.3677  -34.1355   2.7429
 S9K  C16  C  CR16  0  -0.245   -1.9416  -34.9732   3.7666
 S9K  C15  C  CR16  0  -0.349   -2.1878  -34.6481   5.0886
 S9K  H1   H  HCR6  0   0.253   -6.0096  -30.8460   4.8682
 S9K  H2   H  HCH2  0   0.263   -7.0102  -30.4875   2.9124
 S9K  H3   H  HCH2  0   0.254   -6.8937  -28.8078   2.4493
 S9K  H4   H  HNH1  0   0.407   -2.5510  -33.8472   7.4012
 S9K  H5   H  HCR6  0   0.276   -8.0228  -26.8854   6.9354
 S9K  H6   H  HCH2  0   0.278   -8.8640  -27.7666   1.4463
 S9K  H7   H  HCH2  0   0.283  -10.4620  -28.1806   1.9964
 S9K  H8   H  HNH1  0   0.406   -8.7438  -26.2341   5.0180
 S9K  H9   H  HCH2  0   0.244   -9.5237  -29.9457   3.4828
 S9K  H10  H  HCH2  0   0.260   -9.0468  -30.1419   1.8140
 S9K  H11  H  HCR6  0   0.260   -6.6197  -28.3294   8.2755
 S9K  H12  H  HCR6  0   0.277   -4.3938  -31.5753  10.5321
 S9K  H13  H  HCR6  0   0.272   -5.9135  -29.9492   9.4436
 S9K  H14  H  HCR6  0   0.282   -3.8022  -31.7049   4.6220
 S9K  H15  H  HCR6  0   0.255   -3.3679  -32.2951   2.2894
 S9K  H16  H  HCR6  0   0.253   -2.1801  -34.3917   1.7088
 S9K  H17  H  HCR6  0   0.257   -1.4158  -35.8910   3.5372
 S9K  H18  H  HCR6  0   0.266   -1.8535  -35.3142   5.8760

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
 S9K  C1   C    single    1.515  0.020  1.515
 S9K  C1   C2   single    1.506  0.020  1.506
 S9K  C    C9   single    1.524  0.020  1.524
 S9K  C17  C18  aromatic  1.387  0.020  1.387
 S9K  C17  C16  aromatic  1.390  0.020  1.390
 S9K  C9   C8   single    1.498  0.020  1.498
 S9K  C18  C19  aromatic  1.389  0.020  1.389
 S9K  C2   O    double    1.221  0.020  1.221
 S9K  C2   N    single    1.367  0.020  1.367
 S9K  C16  C15  aromatic  1.383  0.020  1.383
 S9K  C19  C14  aromatic  1.397  0.020  1.397
 S9K  N    C3   single    1.397  0.020  1.397
 S9K  C8   C3   aromatic  1.400  0.020  1.400
 S9K  C8   C7   aromatic  1.388  0.020  1.388
 S9K  C3   C4   aromatic  1.399  0.020  1.399
 S9K  C15  C14  aromatic  1.401  0.020  1.401
 S9K  C7   C6   aromatic  1.393  0.020  1.393
 S9K  C14  N2   single    1.391  0.020  1.391
 S9K  C4   C5   aromatic  1.378  0.020  1.378
 S9K  C6   C5   aromatic  1.394  0.020  1.394
 S9K  C6   C10  single    1.473  0.020  1.473
 S9K  N3   C10  aromatic  1.332  0.020  1.332
 S9K  N3   C13  aromatic  1.324  0.020  1.324
 S9K  N2   C13  single    1.362  0.020  1.362
 S9K  C10  C11  aromatic  1.392  0.020  1.392
 S9K  C13  N1   aromatic  1.339  0.020  1.339
 S9K  N1   C12  aromatic  1.320  0.020  1.320
 S9K  C11  C12  aromatic  1.385  0.020  1.385
 S9K  C7   H1   single    0.930  0.020  1.080
 S9K  C9   H2   single    0.970  0.020  1.090
 S9K  C9   H3   single    0.970  0.020  1.090
 S9K  N2   H4   single    0.860  0.020  1.020
 S9K  C4   H5   single    0.930  0.020  1.080
 S9K  C1   H6   single    0.970  0.020  1.090
 S9K  C1   H7   single    0.970  0.020  1.090
 S9K  N    H8   single    0.860  0.020  1.020
 S9K  C    H9   single    0.970  0.020  1.090
 S9K  C    H10  single    0.970  0.020  1.090
 S9K  C5   H11  single    0.930  0.020  1.080
 S9K  C12  H12  single    0.930  0.020  1.080
 S9K  C11  H13  single    0.930  0.020  1.080
 S9K  C19  H14  single    0.930  0.020  1.080
 S9K  C18  H15  single    0.930  0.020  1.080
 S9K  C17  H16  single    0.930  0.020  1.080
 S9K  C16  H17  single    0.930  0.020  1.080
 S9K  C15  H18  single    0.930  0.020  1.080

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
 S9K  H1   C7   C8   117.93  3.000
 S9K  H1   C7   C6   118.79  3.000
 S9K  C8   C7   C6   123.27  3.000
 S9K  H3   C9   H2   105.99  3.000
 S9K  H3   C9   C    109.33  3.000
 S9K  H2   C9   C    109.89  3.000
 S9K  H3   C9   C8   110.15  3.000
 S9K  H2   C9   C8   108.51  3.000
 S9K  C    C9   C8   112.74  3.000
 S9K  C12  N1   C13  115.77  3.000
 S9K  N    C2   C1   122.98  3.000
 S9K  N    C2   O    117.68  3.000
 S9K  C1   C2   O    119.33  3.000
 S9K  H4   N2   C14  115.33  3.000
 S9K  H4   N2   C13  112.93  3.000
 S9K  C14  N2   C13  131.65  3.000
 S9K  C11  C10  C6   122.60  3.000
 S9K  C11  C10  N3   120.64  3.000
 S9K  C6   C10  N3   116.76  3.000
 S9K  H5   C4   C5   119.03  3.000
 S9K  H5   C4   C3   119.36  3.000
 S9K  C5   C4   C3   121.61  3.000
 S9K  C13  N3   C10  118.05  3.000
 S9K  C5   C6   C10  121.97  3.000
 S9K  C10  C6   C7   120.46  3.000
 S9K  C5   C6   C7   117.58  3.000
 S9K  H7   C1   H6   105.45  3.000
 S9K  H7   C1   C    110.18  3.000
 S9K  H6   C1   C    108.93  3.000
 S9K  H7   C1   C2   105.76  3.000
 S9K  H6   C1   C2   105.61  3.000
 S9K  C    C1   C2   119.94  3.000
 S9K  H8   N    C3   112.40  3.000
 S9K  H8   N    C2   110.18  3.000
 S9K  C3   N    C2   137.24  3.000
 S9K  C8   C3   N    125.89  3.000
 S9K  C8   C3   C4   118.99  3.000
 S9K  N    C3   C4   115.08  3.000
 S9K  C3   C8   C9   122.59  3.000
 S9K  C3   C8   C7   118.22  3.000
 S9K  C9   C8   C7   119.19  3.000
 S9K  H10  C    H9   106.26  3.000
 S9K  H10  C    C1   107.12  3.000
 S9K  H9   C    C1   111.06  3.000
 S9K  H10  C    C9   109.21  3.000
 S9K  H9   C    C9   110.25  3.000
 S9K  C1   C    C9   112.68  3.000
 S9K  H11  C5   C6   121.26  3.000
 S9K  H11  C5   C4   118.41  3.000
 S9K  C6   C5   C4   120.33  3.000
 S9K  N3   C13  N2   120.10  3.000
 S9K  N2   C13  N1   114.14  3.000
 S9K  N3   C13  N1   125.76  3.000
 S9K  H12  C12  C11  120.20  3.000
 S9K  H12  C12  N1   116.44  3.000
 S9K  C11  C12  N1   123.36  3.000
 S9K  H13  C11  C12  120.46  3.000
 S9K  H13  C11  C10  123.11  3.000
 S9K  C12  C11  C10  116.43  3.000
 S9K  C15  C14  C19  118.65  3.000
 S9K  C15  C14  N2   116.40  3.000
 S9K  C19  C14  N2   124.93  3.000
 S9K  H14  C19  C18  119.87  3.000
 S9K  H14  C19  C14  120.30  3.000
 S9K  C18  C19  C14  119.83  3.000
 S9K  H15  C18  C17  119.92  3.000
 S9K  H15  C18  C19  118.67  3.000
 S9K  C17  C18  C19  121.41  3.000
 S9K  H16  C17  C16  120.55  3.000
 S9K  H16  C17  C18  120.67  3.000
 S9K  C16  C17  C18  118.77  3.000
 S9K  H17  C16  C15  119.23  3.000
 S9K  H17  C16  C17  120.26  3.000
 S9K  C15  C16  C17  120.51  3.000
 S9K  H18  C15  C16  119.65  3.000
 S9K  H18  C15  C14  119.52  3.000
 S9K  C16  C15  C14  120.83  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
 S9K  CONST_01  C4   C5   C6   C7      0.00   0.0  0
 S9K  CONST_02  N3   C10  C6   C7      0.00   0.0  0
 S9K  CONST_04  C10  N3   C13  N1      0.00   0.0  0
 S9K  CONST_05  C10  C11  C12  N1      0.00   0.0  0
 S9K  CONST_06  C8   C7   C6   C10   180.00   0.0  0
 S9K  CONST_07  C4   C5   C6   C10   180.00   0.0  0
 S9K  CONST_09  C12  C11  C10  N3      0.00   0.0  0
 S9K  CONST_10  C12  N1   C13  N3      0.00   0.0  0
 S9K  CONST_11  C3   C4   C5   C6      0.00   0.0  0
 S9K  CONST_12  C13  N3   C10  C6    180.00   0.0  0
 S9K  CONST_13  C12  C11  C10  C6    180.00   0.0  0
 S9K  CONST_14  C5   C6   C7   C8      0.00   0.0  0
 S9K  CONST_16  C11  C10  N3   C13     0.00   0.0  0
 S9K  CONST_17  C11  C12  N1   C13     0.00   0.0  0
 S9K  CONST_18  C17  C18  C19  C14     0.00   0.0  0
 S9K  CONST_19  C17  C16  C15  C14     0.00   0.0  0
 S9K  CONST_20  C16  C17  C18  C19     0.00   0.0  0
 S9K  CONST_21  C16  C15  C14  C19     0.00   0.0  0
 S9K  CONST_22  C15  C16  C17  C18     0.00   0.0  0
 S9K  CONST_23  C15  C14  C19  C18     0.00   0.0  0
 S9K  CONST_24  C18  C19  C14  N2    180.00   0.0  0
 S9K  CONST_25  C16  C15  C14  N2    180.00   0.0  0
 S9K  CONST_26  C10  N3   C13  N2    180.00   0.0  0
 S9K  CONST_27  C12  N1   C13  N2    180.00   0.0  0
 S9K  CONST_28  H11  C5   C6   C7    180.00   0.0  0
 S9K  CONST_29  H13  C11  C12  N1    180.00   0.0  0
 S9K  CONST_30  H1   C7   C6   C10     0.00   0.0  0
 S9K  CONST_31  H12  C12  C11  C10   180.00   0.0  0
 S9K  CONST_32  H5   C4   C5   C6    180.00   0.0  0
 S9K  CONST_33  H15  C18  C19  C14   180.00   0.0  0
 S9K  CONST_34  H17  C16  C15  C14   180.00   0.0  0
 S9K  CONST_35  H16  C17  C18  C19   180.00   0.0  0
 S9K  CONST_36  H18  C15  C14  C19   180.00   0.0  0
 S9K  CONST_37  H14  C19  C18  C17   180.00   0.0  0
 S9K  Var_01    C14  N2   C13  N1   -179.83  30.0  1
 S9K  Var_02    C19  C14  N2   C13    13.71  30.0  3

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
 S9K  plan-1  N1   0.020
 S9K  plan-1  N2   0.020
 S9K  plan-1  C10  0.020
 S9K  plan-1  N3   0.020
 S9K  plan-1  C6   0.020
 S9K  plan-1  C13  0.020
 S9K  plan-1  C12  0.020
 S9K  plan-1  C11  0.020
 S9K  plan-1  H12  0.020
 S9K  plan-1  H13  0.020
 S9K  plan-2  N2   0.020
 S9K  plan-2  C14  0.020
 S9K  plan-2  C19  0.020
 S9K  plan-2  C18  0.020
 S9K  plan-2  C17  0.020
 S9K  plan-2  C16  0.020
 S9K  plan-2  C15  0.020
 S9K  plan-2  H14  0.020
 S9K  plan-2  H15  0.020
 S9K  plan-2  H16  0.020
 S9K  plan-2  H17  0.020
 S9K  plan-2  H18  0.020
 S9K  plan-3  C7   0.020
 S9K  plan-3  C9   0.020
 S9K  plan-3  C10  0.020
 S9K  plan-3  C4   0.020
 S9K  plan-3  C6   0.020
 S9K  plan-3  N    0.020
 S9K  plan-3  C3   0.020
 S9K  plan-3  C8   0.020
 S9K  plan-3  C5   0.020
 S9K  plan-3  H1   0.020
 S9K  plan-3  H5   0.020
 S9K  plan-3  H11  0.020
 S9K  plan-4  C2   0.020
 S9K  plan-4  O    0.020
 S9K  plan-4  C1   0.020
 S9K  plan-4  N    0.020
 S9K  plan-4  C3   0.020
 S9K  plan-4  H8   0.020

