# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 17:49:03 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 2-(benzyloxy)-4-(1H-pyrazol-4-yl)-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc2CCNCCc2c1)c3ccc(cc3OCc4ccccc4)c5c[nH]nc5
#
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
 7LY  7LY  2-(benzyloxy)-4-(1H-pyrazol-4-yl)-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide  ligand  59  33  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7LY
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
 7LY  C1   C  CR6   0   0.378   2.3103  -1.5051  -0.1998
 7LY  C2   C  CR16  0  -0.352   2.8569  -2.1720  -1.2937
 7LY  C3   C  CR16  0  -0.308   4.2298  -2.2943  -1.4161
 7LY  C4   C  CR6   0   0.083   5.1018  -1.7649  -0.4704
 7LY  C5   C  CH2   0  -0.532   6.5876  -1.9064  -0.6525
 7LY  C6   C  CH2   0  -0.301   7.3444  -0.5771  -0.7780
 7LY  C7   C  CH2   0  -0.302   6.3858   0.6064   1.1543
 7LY  C8   C  CH2   0  -0.539   5.4400  -0.4849   1.6794
 7LY  N    N  NH1   0  -0.739   0.9131  -1.4377  -0.1325
 7LY  C    C  C     0   0.514   0.1238  -0.7143   0.7014
 7LY  O    O  O     0  -0.454   0.5370   0.0580   1.5465
 7LY  N1   N  NH1   0  -0.578   7.5693   0.1677   0.4445
 7LY  C9   C  CR6   0   0.125   4.5538  -1.0945   0.6284
 7LY  N2   N  NR15  0  -0.425  -7.4594  -2.7181  -0.0680
 7LY  C21  C  CR16  0  -0.263  -0.0441   5.8352  -0.6403
 7LY  C10  C  CR16  0  -0.393   3.1730  -0.9692   0.7568
 7LY  C12  C  CR16  0  -0.225  -1.8222  -2.2785   0.5855
 7LY  C13  C  CR16  0  -0.366  -3.1762  -2.5485   0.4836
 7LY  C14  C  CR6   0   0.156  -4.0798  -1.5077   0.2786
 7LY  C15  C  CR16  0  -0.501  -3.5944  -0.2007   0.1820
 7LY  C16  C  CR6   0   0.432  -2.2364   0.0715   0.3004
 7LY  C17  C  CH2   0  -0.274  -2.5511   2.3894  -0.1516
 7LY  C18  C  CR6   0   0.106  -1.6800   3.5974  -0.3193
 7LY  C11  C  CR6   0  -0.212  -1.3329  -0.9812   0.5068
 7LY  C19  C  CR16  0  -0.306  -1.7597   4.6620   0.5704
 7LY  C20  C  CR16  0  -0.240  -0.9485   5.7794   0.4100
 7LY  C22  C  CR16  0  -0.243   0.0444   4.7718  -1.5323
 7LY  C23  C  CR16  0  -0.283  -0.7698   3.6611  -1.3728
 7LY  C24  C  CR5   0  -0.111  -5.5119  -1.7626   0.1602
 7LY  C25  C  CR15  0  -0.001  -6.1487  -2.9791  -0.0092
 7LY  C26  C  CR15  0  -0.117  -6.5763  -0.8336   0.1875
 7LY  N3   N  N     0  -0.259  -7.7447  -1.4265   0.0503
 7LY  H1   H  HCR6  0   0.264   2.2103  -2.5965  -2.0529
 7LY  H2   H  HCR6  0   0.249   4.6325  -2.8141  -2.2775
 7LY  H3   H  HCH2  0   0.238   7.0246  -2.4791   0.1741
 7LY  H4   H  HCH2  0   0.246   6.7731  -2.4945  -1.5548
 7LY  H5   H  HCH2  0   0.234   8.3237  -0.7844  -1.2162
 7LY  H6   H  HCH2  0   0.219   6.8183   0.0698  -1.4877
 7LY  H7   H  HCH2  0   0.221   5.8237   1.2874   0.5075
 7LY  H8   H  HCH2  0   0.236   6.7217   1.1990   2.0088
 7LY  H9   H  HCH2  0   0.241   6.0392  -1.2623   2.1674
 7LY  H10  H  HCH2  0   0.249   4.8151  -0.0497   2.4626
 7LY  H11  H  HNH1  0   0.419   0.4308  -1.9577  -0.8506
 7LY  H12  H  HNH1  0   0.340   8.1401  -0.3895   1.0696
 7LY  H14  H  HNR5  0   0.425  -8.2021  -3.3865  -0.1973
 7LY  H16  H  HCR6  0   0.270   2.7797  -0.4516   1.6176
 7LY  H17  H  HCR6  0   0.270  -1.1335  -3.0976   0.7529
 7LY  H18  H  HCR6  0   0.251  -3.5215  -3.5694   0.5775
 7LY  H19  H  HCR6  0   0.281  -4.2951   0.6036   0.0046
 7LY  H20  H  HCH2  0   0.245  -3.0844   2.1680  -1.0826
 7LY  H21  H  HCH2  0   0.248  -3.2980   2.5612   0.6296
 7LY  H22  H  HCR6  0   0.256  -2.4614   4.6235   1.3949
 7LY  H23  H  HCR6  0   0.258  -1.0239   6.6036   1.1072
 7LY  H24  H  HCR6  0   0.258   0.7463   4.8113  -2.3550
 7LY  H25  H  HCR6  0   0.253  -0.6994   2.8397  -2.0758
 7LY  H26  H  HCR5  0   0.294  -5.7697  -3.9840  -0.0992
 7LY  H27  H  HCR5  0   0.260  -6.5277   0.2378   0.3124
 7LY  O1   O  O2    0  -0.453  -1.7062   1.2991   0.1940
 7LY  H15  H  HCR6  0   0.258   0.5885   6.7042  -0.7676

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
 7LY  C6   C5   single    1.535  0.020  1.535
 7LY  C6   N1   single    1.449  0.020  1.449
 7LY  C5   C4   single    1.504  0.020  1.504
 7LY  N1   C7   single    1.448  0.020  1.448
 7LY  C4   C3   aromatic  1.391  0.020  1.391
 7LY  C4   C9   aromatic  1.399  0.020  1.399
 7LY  C3   C2   aromatic  1.384  0.020  1.384
 7LY  C20  C19  aromatic  1.390  0.020  1.390
 7LY  C20  C21  aromatic  1.387  0.020  1.387
 7LY  C19  C18  aromatic  1.390  0.020  1.390
 7LY  C8   C9   single    1.504  0.020  1.504
 7LY  C8   C7   single    1.537  0.020  1.537
 7LY  C9   C10  aromatic  1.392  0.020  1.392
 7LY  C2   C1   aromatic  1.393  0.020  1.393
 7LY  C10  C1   aromatic  1.395  0.020  1.395
 7LY  C1   N    single    1.400  0.020  1.400
 7LY  C17  C18  single    1.499  0.020  1.499
 7LY  C17  O1   single    1.422  0.020  1.422
 7LY  C21  C22  aromatic  1.391  0.020  1.391
 7LY  C18  C23  aromatic  1.394  0.020  1.394
 7LY  O1   C16  single    1.341  0.020  1.341
 7LY  N    C    single    1.357  0.020  1.357
 7LY  O    C    double    1.217  0.020  1.217
 7LY  C    C11  single    1.494  0.020  1.494
 7LY  C16  C11  aromatic  1.403  0.020  1.403
 7LY  C16  C15  aromatic  1.390  0.020  1.390
 7LY  C22  C23  aromatic  1.386  0.020  1.386
 7LY  C11  C12  aromatic  1.389  0.020  1.389
 7LY  C15  C14  aromatic  1.398  0.020  1.398
 7LY  C12  C13  aromatic  1.384  0.020  1.384
 7LY  C14  C13  aromatic  1.393  0.020  1.393
 7LY  C14  C24  single    1.459  0.020  1.459
 7LY  C26  C24  aromatic  1.413  0.020  1.413
 7LY  C26  N3   aromatic  1.317  0.020  1.317
 7LY  C24  C25  aromatic  1.383  0.020  1.383
 7LY  N3   N2   aromatic  1.328  0.020  1.328
 7LY  C25  N2   aromatic  1.338  0.020  1.338
 7LY  C2   H1   single    0.930  0.020  1.080
 7LY  C3   H2   single    0.930  0.020  1.080
 7LY  C5   H3   single    0.970  0.020  1.090
 7LY  C5   H4   single    0.970  0.020  1.090
 7LY  C6   H5   single    0.970  0.020  1.090
 7LY  C6   H6   single    0.970  0.020  1.090
 7LY  C7   H7   single    0.970  0.020  1.090
 7LY  C7   H8   single    0.970  0.020  1.090
 7LY  C8   H9   single    0.970  0.020  1.090
 7LY  C8   H10  single    0.970  0.020  1.090
 7LY  N    H11  single    0.860  0.020  1.020
 7LY  N1   H12  single    0.890  0.020  1.040
 7LY  N2   H14  single    0.860  0.020  1.020
 7LY  C21  H15  single    0.930  0.020  1.080
 7LY  C10  H16  single    0.930  0.020  1.080
 7LY  C12  H17  single    0.930  0.020  1.080
 7LY  C13  H18  single    0.930  0.020  1.080
 7LY  C15  H19  single    0.930  0.020  1.080
 7LY  C17  H20  single    0.970  0.020  1.090
 7LY  C17  H21  single    0.970  0.020  1.090
 7LY  C19  H22  single    0.930  0.020  1.080
 7LY  C20  H23  single    0.930  0.020  1.080
 7LY  C22  H24  single    0.930  0.020  1.080
 7LY  C23  H25  single    0.930  0.020  1.080
 7LY  C25  H26  single    0.930  0.020  1.080
 7LY  C26  H27  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
 7LY  C10  C1   N    124.44  3.000
 7LY  N    C1   C2   116.89  3.000
 7LY  C10  C1   C2   118.67  3.000
 7LY  H1   C2   C3   119.69  3.000
 7LY  H1   C2   C1   120.24  3.000
 7LY  C3   C2   C1   120.07  3.000
 7LY  H2   C3   C4   119.34  3.000
 7LY  H2   C3   C2   118.77  3.000
 7LY  C4   C3   C2   121.88  3.000
 7LY  C9   C4   C5   121.82  3.000
 7LY  C9   C4   C3   118.09  3.000
 7LY  C5   C4   C3   120.08  3.000
 7LY  H4   C5   H3   105.89  3.000
 7LY  H4   C5   C6   108.36  3.000
 7LY  H3   C5   C6   108.51  3.000
 7LY  H4   C5   C4   108.56  3.000
 7LY  H3   C5   C4   110.59  3.000
 7LY  C6   C5   C4   114.56  3.000
 7LY  H6   C6   H5   106.42  3.000
 7LY  H6   C6   N1   108.53  3.000
 7LY  H5   C6   N1   107.26  3.000
 7LY  H6   C6   C5   109.13  3.000
 7LY  H5   C6   C5   108.08  3.000
 7LY  N1   C6   C5   116.92  3.000
 7LY  H8   C7   H7   106.41  3.000
 7LY  H8   C7   N1   107.24  3.000
 7LY  H7   C7   N1   108.58  3.000
 7LY  H8   C7   C8   107.89  3.000
 7LY  H7   C7   C8   109.12  3.000
 7LY  N1   C7   C8   117.09  3.000
 7LY  H10  C8   H9   106.03  3.000
 7LY  H10  C8   C9   108.99  3.000
 7LY  H9   C8   C9   110.23  3.000
 7LY  H10  C8   C7   108.31  3.000
 7LY  H9   C8   C7   108.62  3.000
 7LY  C9   C8   C7   114.32  3.000
 7LY  H11  N    C    115.72  3.000
 7LY  H11  N    C1   114.69  3.000
 7LY  C    N    C1   129.45  3.000
 7LY  C11  C    O    122.34  3.000
 7LY  C11  C    N    113.07  3.000
 7LY  O    C    N    124.57  3.000
 7LY  H12  N1   C7   108.94  3.000
 7LY  H12  N1   C6   108.98  3.000
 7LY  C7   N1   C6   116.26  3.000
 7LY  C10  C9   C8   118.91  3.000
 7LY  C10  C9   C4   120.26  3.000
 7LY  C8   C9   C4   120.82  3.000
 7LY  H14  N2   N3   119.89  3.000
 7LY  H14  N2   C25  126.76  3.000
 7LY  N3   N2   C25  113.35  3.000
 7LY  H15  C21  C22  120.08  3.000
 7LY  H15  C21  C20  120.16  3.000
 7LY  C22  C21  C20  119.76  3.000
 7LY  H16  C10  C9   118.58  3.000
 7LY  H16  C10  C1   120.40  3.000
 7LY  C9   C10  C1   121.03  3.000
 7LY  H17  C12  C11  119.42  3.000
 7LY  H17  C12  C13  119.06  3.000
 7LY  C11  C12  C13  121.50  3.000
 7LY  H18  C13  C14  120.71  3.000
 7LY  H18  C13  C12  119.33  3.000
 7LY  C14  C13  C12  119.96  3.000
 7LY  C24  C14  C15  119.90  3.000
 7LY  C24  C14  C13  121.18  3.000
 7LY  C15  C14  C13  118.91  3.000
 7LY  H19  C15  C16  120.09  3.000
 7LY  H19  C15  C14  118.81  3.000
 7LY  C16  C15  C14  121.10  3.000
 7LY  C11  C16  C15  119.66  3.000
 7LY  C15  C16  O1   123.96  3.000
 7LY  C11  C16  O1   116.36  3.000
 7LY  H21  C17  H20  107.83  3.000
 7LY  H21  C17  C18  110.49  3.000
 7LY  H20  C17  C18  110.53  3.000
 7LY  H21  C17  O1   110.64  3.000
 7LY  H20  C17  O1   109.93  3.000
 7LY  C18  C17  O1   107.45  3.000
 7LY  C23  C18  C19  119.10  3.000
 7LY  C23  C18  C17  120.07  3.000
 7LY  C19  C18  C17  120.83  3.000
 7LY  C16  C11  C12  118.86  3.000
 7LY  C12  C11  C    120.20  3.000
 7LY  C16  C11  C    120.88  3.000
 7LY  H22  C19  C20  119.63  3.000
 7LY  H22  C19  C18  119.81  3.000
 7LY  C20  C19  C18  120.56  3.000
 7LY  H23  C20  C19  119.82  3.000
 7LY  H23  C20  C21  120.17  3.000
 7LY  C19  C20  C21  120.01  3.000
 7LY  H24  C22  C23  119.84  3.000
 7LY  H24  C22  C21  120.06  3.000
 7LY  C23  C22  C21  120.10  3.000
 7LY  H25  C23  C22  119.65  3.000
 7LY  H25  C23  C18  119.88  3.000
 7LY  C22  C23  C18  120.47  3.000
 7LY  C26  C24  C25  103.52  3.000
 7LY  C25  C24  C14  127.96  3.000
 7LY  C26  C24  C14  128.52  3.000
 7LY  H26  C25  C24  131.94  3.000
 7LY  H26  C25  N2   121.52  3.000
 7LY  C24  C25  N2   106.54  3.000
 7LY  H27  C26  N3   119.90  3.000
 7LY  H27  C26  C24  128.37  3.000
 7LY  N3   C26  C24  111.73  3.000
 7LY  C26  N3   N2   104.86  3.000
 7LY  C17  O1   C16  119.08  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
 7LY  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 7LY  CONST_02  C9   C10  C1   C2      0.00   0.0  0
 7LY  CONST_03  C10  C1   C2   C3      0.00   0.0  0
 7LY  CONST_04  C24  C26  N3   N2      0.00   0.0  0
 7LY  CONST_05  C14  C24  C25  N2    180.00   0.0  0
 7LY  CONST_06  C26  C24  C25  N2      0.00   0.0  0
 7LY  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 7LY  CONST_08  C18  C23  C22  C21     0.00   0.0  0
 7LY  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 7LY  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 7LY  CONST_11  C24  C14  C13  C12   180.00   0.0  0
 7LY  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 7LY  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 7LY  CONST_14  C26  C24  C14  C13   180.00   0.0  0
 7LY  CONST_15  C25  C24  C14  C13     0.00   0.0  0
 7LY  CONST_16  C11  C16  C15  C14     0.00   0.0  0
 7LY  CONST_17  C11  C12  C13  C14     0.00   0.0  0
 7LY  CONST_18  N3   C26  C24  C14   180.00   0.0  0
 7LY  CONST_19  C26  C24  C14  C15     0.00   0.0  0
 7LY  CONST_20  C25  C24  C14  C15   180.00   0.0  0
 7LY  CONST_21  C24  C14  C15  C16   180.00   0.0  0
 7LY  CONST_22  C22  C21  C20  C19     0.00   0.0  0
 7LY  CONST_23  C22  C23  C18  C19     0.00   0.0  0
 7LY  CONST_24  C23  C18  C19  C20     0.00   0.0  0
 7LY  CONST_25  C23  C22  C21  C20     0.00   0.0  0
 7LY  CONST_26  N3   N2   C25  C24     0.00   0.0  0
 7LY  CONST_27  N3   C26  C24  C25     0.00   0.0  0
 7LY  CONST_28  C26  N3   N2   C25     0.00   0.0  0
 7LY  CONST_29  C12  C11  C16  O1    180.00   0.0  0
 7LY  CONST_30  C14  C15  C16  O1    180.00   0.0  0
 7LY  CONST_31  N    C1   C2   C3    180.00   0.0  0
 7LY  CONST_32  C9   C10  C1   N     180.00   0.0  0
 7LY  CONST_33  C15  C16  C11  C     180.00   0.0  0
 7LY  CONST_34  C13  C12  C11  C     180.00   0.0  0
 7LY  CONST_35  C20  C19  C18  C17   180.00   0.0  0
 7LY  CONST_36  C22  C23  C18  C17   180.00   0.0  0
 7LY  CONST_37  H2   C3   C2   C1    180.00   0.0  0
 7LY  CONST_38  H16  C10  C1   C2    180.00   0.0  0
 7LY  CONST_39  H1   C2   C3   C4    180.00   0.0  0
 7LY  CONST_40  H27  C26  N3   N2    180.00   0.0  0
 7LY  CONST_41  H22  C19  C20  C21   180.00   0.0  0
 7LY  CONST_42  H25  C23  C22  C21   180.00   0.0  0
 7LY  CONST_43  H19  C15  C14  C13   180.00   0.0  0
 7LY  CONST_44  H17  C12  C13  C14   180.00   0.0  0
 7LY  CONST_45  H26  C25  C24  C14     0.00   0.0  0
 7LY  CONST_46  H18  C13  C14  C15   180.00   0.0  0
 7LY  CONST_47  H23  C20  C19  C18   180.00   0.0  0
 7LY  CONST_48  H24  C22  C23  C18   180.00   0.0  0
 7LY  CONST_49  H15  C21  C20  C19   180.00   0.0  0
 7LY  CONST_50  H14  N2   C25  C24   180.00   0.0  0
 7LY  CONST_51  C11  C    N    C1    180.00   0.0  0
 7LY  CONST_52  C    N    C1   C2    180.00   0.0  0
 7LY  CONST_53  C10  C1   N    C       0.00   0.0  0
 7LY  CONST_54  H11  N    C1   C2      0.00   0.0  0
 7LY  CONST_55  O    C    N    C1      0.00   0.0  0
 7LY  Var_01    C19  C18  C17  O1   -112.40  30.0  2
 7LY  Var_02    C16  C11  C    N    -127.73  30.0  2
 7LY  Var_03    C18  C17  O1   C16  -174.96  30.0  1
 7LY  Var_04    C11  C16  O1   C17   173.63  30.0  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
 7LY  plan-1  N2   0.020
 7LY  plan-1  C14  0.020
 7LY  plan-1  C24  0.020
 7LY  plan-1  C25  0.020
 7LY  plan-1  C26  0.020
 7LY  plan-1  N3   0.020
 7LY  plan-1  H14  0.020
 7LY  plan-1  H26  0.020
 7LY  plan-1  H27  0.020
 7LY  plan-2  C    0.020
 7LY  plan-2  C12  0.020
 7LY  plan-2  C13  0.020
 7LY  plan-2  C14  0.020
 7LY  plan-2  C15  0.020
 7LY  plan-2  C16  0.020
 7LY  plan-2  C11  0.020
 7LY  plan-2  C24  0.020
 7LY  plan-2  H17  0.020
 7LY  plan-2  H18  0.020
 7LY  plan-2  H19  0.020
 7LY  plan-2  O1   0.020
 7LY  plan-3  C1   0.020
 7LY  plan-3  C2   0.020
 7LY  plan-3  C3   0.020
 7LY  plan-3  C4   0.020
 7LY  plan-3  C5   0.020
 7LY  plan-3  C8   0.020
 7LY  plan-3  N    0.020
 7LY  plan-3  C9   0.020
 7LY  plan-3  C10  0.020
 7LY  plan-3  H1   0.020
 7LY  plan-3  H2   0.020
 7LY  plan-3  H16  0.020
 7LY  plan-4  C21  0.020
 7LY  plan-4  C17  0.020
 7LY  plan-4  C18  0.020
 7LY  plan-4  C19  0.020
 7LY  plan-4  C20  0.020
 7LY  plan-4  C22  0.020
 7LY  plan-4  C23  0.020
 7LY  plan-4  H22  0.020
 7LY  plan-4  H23  0.020
 7LY  plan-4  H24  0.020
 7LY  plan-4  H25  0.020
 7LY  plan-4  H15  0.020
 7LY  plan-5  C1   0.020
 7LY  plan-5  N    0.020
 7LY  plan-5  C    0.020
 7LY  plan-5  O    0.020
 7LY  plan-5  C11  0.020
 7LY  plan-5  H11  0.020

