# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:42:29 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 7-[2-[(4-methoxyphenyl)amino]pyrimidin-4-yl]-1,3,4,5-tetrahydro-1-benzazepin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2nccc(n2)c3ccc4NC(=O)CCCc4c3)cc1
#
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
 S9H  S9H  7-[2-[(4-methoxyphenyl)amino]pyrimidin-4-yl]-1,3,4,5-tetrahydro-1-benzazepin-2-one  ligand  47  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S9H
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
 S9H  C7   C  CR6   0   0.594  -3.9309  -32.5416   6.8986
 S9H  C9   C  CR16  0  -0.407  -5.5558  -30.6854   7.9123
 S9H  N1   N  N     0  -0.463  -3.8660  -32.3361   8.2216
 S9H  C2   C  CR16  0  -0.371  -3.3351  -34.2997   2.8011
 S9H  N2   N  NH1   0  -0.714  -8.8762  -28.3242   2.8065
 S9H  C10  C  CR6   0   0.322  -5.5503  -30.9783   6.5526
 S9H  C4   C  CR6   0   0.339  -2.8580  -33.9940   5.1543
 S9H  N3   N  N     0  -0.503  -4.7342  -31.9064   6.0566
 S9H  C6   C  CR16  0  -0.328  -1.4670  -35.4293   3.7822
 S9H  C19  C  C     0   0.487  -9.2794  -28.7985   1.5931
 S9H  C14  C  CR6   0   0.298  -8.0491  -28.9870   3.7236
 S9H  C13  C  CR16  0  -0.281  -8.3919  -28.9941   5.0717
 S9H  C12  C  CR16  0  -0.332  -7.5809  -29.6257   5.9969
 S9H  C18  C  CH2   0  -0.602  -8.8231  -30.1949   1.2448
 S9H  C17  C  CH2   0  -0.409  -7.3314  -30.2977   0.9077
 S9H  C16  C  CH2   0  -0.543  -6.4466  -29.4905   1.8586
 S9H  C15  C  CR6   0   0.155  -6.8637  -29.5985   3.2959
 S9H  C20  C  CR16  0  -0.376  -6.0846  -30.2560   4.2345
 S9H  C11  C  CR6   0   0.070  -6.4207  -30.2807   5.5883
 S9H  C8   C  CR16  0  -0.020  -4.6773  -31.4128   8.7007
 S9H  N    N  NH1   0  -0.773  -3.0783  -33.4925   6.4376
 S9H  C3   C  CR16  0  -0.301  -3.6384  -33.7264   4.0336
 S9H  C5   C  CR16  0  -0.336  -1.7660  -34.8579   5.0007
 S9H  C1   C  CR6   0   0.362  -2.2503  -35.1553   2.6597
 S9H  O    O  O2    0  -0.475  -1.8845  -35.7557   1.5068
 S9H  C    C  CH3   0  -0.434  -2.6543  -35.5052   0.3499
 S9H  H1   H  HCR6  0   0.271  -6.1835  -29.9237   8.3490
 S9H  H2   H  HCR6  0   0.277  -3.9753  -34.0573   1.9631
 S9H  H3   H  HNH1  0   0.403  -9.3013  -27.4567   3.1054
 S9H  H4   H  HCR6  0   0.264  -0.6167  -36.0942   3.6951
 S9H  H5   H  HCR6  0   0.273  -9.3073  -28.5149   5.3948
 S9H  H6   H  HCR6  0   0.259  -7.8830  -29.6301   7.0356
 S9H  H7   H  HCH2  0   0.278  -9.4170  -30.5421   0.4003
 S9H  H8   H  HCH2  0   0.268  -9.0498  -30.8552   2.0865
 S9H  H9   H  HCH2  0   0.248  -7.0526  -31.3524   0.9396
 S9H  H10  H  HCH2  0   0.247  -7.1549  -29.9560  -0.1135
 S9H  H11  H  HCH2  0   0.265  -5.4081  -29.8048   1.7471
 S9H  H12  H  HCH2  0   0.256  -6.4789  -28.4358   1.5672
 S9H  H13  H  HCR6  0   0.251  -5.1653  -30.7284   3.9122
 S9H  H14  H  HCR6  0   0.276  -4.6272  -31.2326   9.7691
 S9H  H15  H  HNH1  0   0.406  -2.4886  -33.8804   7.1583
 S9H  H16  H  HCR6  0   0.288  -4.4895  -33.0700   4.1041
 S9H  H17  H  HCR6  0   0.269  -1.1386  -35.0874   5.8544
 S9H  H18  H  HCH3  0   0.258  -2.2095  -36.0893  -0.4522
 S9H  H19  H  HCH3  0   0.225  -3.6950  -35.8173   0.4744
 S9H  H20  H  HCH3  0   0.226  -2.6367  -34.4492   0.0661
 S9H  O1   O  O     0  -0.466  -9.9925  -28.1270   0.8673

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
 S9H  C    O    single    1.412  0.020  1.412
 S9H  C17  C18  single    1.533  0.020  1.533
 S9H  C17  C16  single    1.529  0.020  1.529
 S9H  O1   C19  double    1.219  0.020  1.219
 S9H  C18  C19  single    1.510  0.020  1.510
 S9H  O    C1   single    1.350  0.020  1.350
 S9H  C19  N2   single    1.364  0.020  1.364
 S9H  C16  C15  single    1.501  0.020  1.501
 S9H  C1   C2   aromatic  1.389  0.020  1.389
 S9H  C1   C6   aromatic  1.396  0.020  1.396
 S9H  N2   C14  single    1.402  0.020  1.402
 S9H  C2   C3   aromatic  1.393  0.020  1.393
 S9H  C15  C14  aromatic  1.401  0.020  1.401
 S9H  C15  C20  aromatic  1.386  0.020  1.386
 S9H  C14  C13  aromatic  1.391  0.020  1.391
 S9H  C6   C5   aromatic  1.379  0.020  1.379
 S9H  C3   C4   aromatic  1.392  0.020  1.392
 S9H  C20  C11  aromatic  1.395  0.020  1.395
 S9H  C13  C12  aromatic  1.383  0.020  1.383
 S9H  C5   C4   aromatic  1.401  0.020  1.401
 S9H  C4   N    single    1.395  0.020  1.395
 S9H  C11  C12  aromatic  1.394  0.020  1.394
 S9H  C11  C10  single    1.474  0.020  1.474
 S9H  N3   C10  aromatic  1.332  0.020  1.332
 S9H  N3   C7   aromatic  1.326  0.020  1.326
 S9H  C10  C9   aromatic  1.391  0.020  1.391
 S9H  N    C7   single    1.358  0.020  1.358
 S9H  C7   N1   aromatic  1.340  0.020  1.340
 S9H  C9   C8   aromatic  1.387  0.020  1.387
 S9H  N1   C8   aromatic  1.319  0.020  1.319
 S9H  C9   H1   single    0.930  0.020  1.080
 S9H  C2   H2   single    0.930  0.020  1.080
 S9H  N2   H3   single    0.860  0.020  1.020
 S9H  C6   H4   single    0.930  0.020  1.080
 S9H  C13  H5   single    0.930  0.020  1.080
 S9H  C12  H6   single    0.930  0.020  1.080
 S9H  C18  H7   single    0.970  0.020  1.090
 S9H  C18  H8   single    0.970  0.020  1.090
 S9H  C17  H9   single    0.970  0.020  1.090
 S9H  C17  H10  single    0.970  0.020  1.090
 S9H  C16  H11  single    0.970  0.020  1.090
 S9H  C16  H12  single    0.970  0.020  1.090
 S9H  C20  H13  single    0.930  0.020  1.080
 S9H  C8   H14  single    0.930  0.020  1.080
 S9H  N    H15  single    0.860  0.020  1.020
 S9H  C3   H16  single    0.930  0.020  1.080
 S9H  C5   H17  single    0.930  0.020  1.080
 S9H  C    H18  single    0.970  0.020  1.090
 S9H  C    H19  single    0.970  0.020  1.090
 S9H  C    H20  single    0.970  0.020  1.090

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
 S9H  N    C7   N3   120.02  3.000
 S9H  N    C7   N1   114.34  3.000
 S9H  N3   C7   N1   125.64  3.000
 S9H  H1   C9   C8   120.57  3.000
 S9H  H1   C9   C10  123.13  3.000
 S9H  C8   C9   C10  116.29  3.000
 S9H  C8   N1   C7   115.85  3.000
 S9H  H2   C2   C1   121.42  3.000
 S9H  H2   C2   C3   117.66  3.000
 S9H  C1   C2   C3   120.92  3.000
 S9H  H3   N2   C14  117.41  3.000
 S9H  H3   N2   C19  115.91  3.000
 S9H  C14  N2   C19  126.32  3.000
 S9H  C11  C10  N3   116.61  3.000
 S9H  N3   C10  C9   120.88  3.000
 S9H  C11  C10  C9   122.50  3.000
 S9H  C5   C4   C3   117.87  3.000
 S9H  C5   C4   N    116.46  3.000
 S9H  C3   C4   N    125.66  3.000
 S9H  C10  N3   C7   117.95  3.000
 S9H  H4   C6   C1   119.76  3.000
 S9H  H4   C6   C5   119.73  3.000
 S9H  C1   C6   C5   120.51  3.000
 S9H  C18  C19  O1   123.29  3.000
 S9H  C18  C19  N2   115.95  3.000
 S9H  O1   C19  N2   120.74  3.000
 S9H  C15  C14  C13  120.15  3.000
 S9H  C13  C14  N2   119.42  3.000
 S9H  C15  C14  N2   120.40  3.000
 S9H  H5   C13  C12  119.89  3.000
 S9H  H5   C13  C14  119.70  3.000
 S9H  C12  C13  C14  120.40  3.000
 S9H  H6   C12  C11  120.80  3.000
 S9H  H6   C12  C13  118.71  3.000
 S9H  C11  C12  C13  120.45  3.000
 S9H  H8   C18  H7   106.94  3.000
 S9H  H8   C18  C17  109.30  3.000
 S9H  H7   C18  C17  109.80  3.000
 S9H  H8   C18  C19  108.56  3.000
 S9H  H7   C18  C19  107.99  3.000
 S9H  C17  C18  C19  114.01  3.000
 S9H  H10  C17  H9   106.78  3.000
 S9H  H10  C17  C16  108.85  3.000
 S9H  H9   C17  C16  110.13  3.000
 S9H  H10  C17  C18  110.01  3.000
 S9H  H9   C17  C18  107.88  3.000
 S9H  C16  C17  C18  113.01  3.000
 S9H  H12  C16  H11  106.17  3.000
 S9H  H12  C16  C15  108.42  3.000
 S9H  H11  C16  C15  109.99  3.000
 S9H  H12  C16  C17  109.02  3.000
 S9H  H11  C16  C17  109.59  3.000
 S9H  C15  C16  C17  113.38  3.000
 S9H  C20  C15  C16  121.78  3.000
 S9H  C20  C15  C14  118.43  3.000
 S9H  C16  C15  C14  119.76  3.000
 S9H  H13  C20  C11  119.06  3.000
 S9H  H13  C20  C15  118.87  3.000
 S9H  C11  C20  C15  122.02  3.000
 S9H  C20  C11  C12  118.47  3.000
 S9H  C12  C11  C10  121.47  3.000
 S9H  C20  C11  C10  120.05  3.000
 S9H  H14  C8   N1   116.47  3.000
 S9H  H14  C8   C9   120.15  3.000
 S9H  N1   C8   C9   123.39  3.000
 S9H  H15  N    C4   115.25  3.000
 S9H  H15  N    C7   113.19  3.000
 S9H  C4   N    C7   131.54  3.000
 S9H  H16  C3   C4   120.50  3.000
 S9H  H16  C3   C2   118.74  3.000
 S9H  C4   C3   C2   120.75  3.000
 S9H  H17  C5   C6   118.87  3.000
 S9H  H17  C5   C4   119.69  3.000
 S9H  C6   C5   C4   121.44  3.000
 S9H  O    C1   C6   116.57  3.000
 S9H  C6   C1   C2   118.51  3.000
 S9H  O    C1   C2   124.92  3.000
 S9H  C    O    C1   118.23  3.000
 S9H  H20  C    H19  108.69  3.000
 S9H  H20  C    H18  108.71  3.000
 S9H  H19  C    H18  108.66  3.000
 S9H  H20  C    O    112.04  3.000
 S9H  H19  C    O    112.02  3.000
 S9H  H18  C    O    106.62  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
 S9H  CONST_01  C11  C10  N3   C7    180.00   0.0  0
 S9H  CONST_02  C9   C10  N3   C7      0.00   0.0  0
 S9H  CONST_03  C9   C8   N1   C7      0.00   0.0  0
 S9H  CONST_06  C10  N3   C7   N1      0.00   0.0  0
 S9H  CONST_07  C10  C9   C8   N1      0.00   0.0  0
 S9H  CONST_08  C5   C6   C1   C2      0.00   0.0  0
 S9H  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 S9H  CONST_10  C15  C20  C11  C10   180.00   0.0  0
 S9H  CONST_11  C13  C12  C11  C10   180.00   0.0  0
 S9H  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 S9H  CONST_13  C1   C6   C5   C4      0.00   0.0  0
 S9H  CONST_16  C8   C9   C10  N3      0.00   0.0  0
 S9H  CONST_17  C8   N1   C7   N3      0.00   0.0  0
 S9H  CONST_18  C3   C2   C1   C6      0.00   0.0  0
 S9H  CONST_19  C3   C4   C5   C6      0.00   0.0  0
 S9H  CONST_20  C11  C12  C13  C14     0.00   0.0  0
 S9H  CONST_21  C20  C11  C12  C13     0.00   0.0  0
 S9H  CONST_22  C15  C20  C11  C12     0.00   0.0  0
 S9H  CONST_23  C8   C9   C10  C11   180.00   0.0  0
 S9H  CONST_24  N    C4   C3   C2    180.00   0.0  0
 S9H  CONST_25  N    C7   N3   C10   180.00   0.0  0
 S9H  CONST_26  N    C4   C5   C6    180.00   0.0  0
 S9H  CONST_27  N    C7   N1   C8    180.00   0.0  0
 S9H  CONST_28  O    C1   C2   C3    180.00   0.0  0
 S9H  CONST_29  O    C1   C6   C5    180.00   0.0  0
 S9H  CONST_30  H14  C8   N1   C7    180.00   0.0  0
 S9H  CONST_31  H1   C9   C8   N1    180.00   0.0  0
 S9H  CONST_32  H4   C6   C1   C2    180.00   0.0  0
 S9H  CONST_33  H13  C20  C11  C10     0.00   0.0  0
 S9H  CONST_34  H6   C12  C11  C10     0.00   0.0  0
 S9H  CONST_35  H2   C2   C3   C4    180.00   0.0  0
 S9H  CONST_36  H5   C13  C12  C11   180.00   0.0  0
 S9H  CONST_37  H17  C5   C4   C3    180.00   0.0  0
 S9H  CONST_38  H16  C3   C4   C5    180.00   0.0  0
 S9H  Var_01    C3   C4   N    C7     -9.39  30.0  3
 S9H  Var_02    C4   N    C7   N1    179.32  30.0  1
 S9H  Var_03    H18  C    O    C1   -178.99  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
 S9H  plan-1  C7   0.020
 S9H  plan-1  C9   0.020
 S9H  plan-1  N1   0.020
 S9H  plan-1  C10  0.020
 S9H  plan-1  N3   0.020
 S9H  plan-1  C11  0.020
 S9H  plan-1  C8   0.020
 S9H  plan-1  N    0.020
 S9H  plan-1  H1   0.020
 S9H  plan-1  H14  0.020
 S9H  plan-2  C2   0.020
 S9H  plan-2  C4   0.020
 S9H  plan-2  C6   0.020
 S9H  plan-2  N    0.020
 S9H  plan-2  C3   0.020
 S9H  plan-2  C5   0.020
 S9H  plan-2  C1   0.020
 S9H  plan-2  O    0.020
 S9H  plan-2  H2   0.020
 S9H  plan-2  H4   0.020
 S9H  plan-2  H16  0.020
 S9H  plan-2  H17  0.020
 S9H  plan-3  N2   0.020
 S9H  plan-3  C10  0.020
 S9H  plan-3  C14  0.020
 S9H  plan-3  C13  0.020
 S9H  plan-3  C12  0.020
 S9H  plan-3  C16  0.020
 S9H  plan-3  C15  0.020
 S9H  plan-3  C20  0.020
 S9H  plan-3  C11  0.020
 S9H  plan-3  H5   0.020
 S9H  plan-3  H6   0.020
 S9H  plan-3  H13  0.020
 S9H  plan-4  N2   0.020
 S9H  plan-4  C19  0.020
 S9H  plan-4  C14  0.020
 S9H  plan-4  C18  0.020
 S9H  plan-4  H3   0.020
 S9H  plan-4  O1   0.020

