# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:52:09 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 4-{[4-(1-benzothiophen-4-yloxy)-3-chlorophenyl]amino}-N-(2-hydroxyethyl)-8,9-dihydro-7H-pyrimido[4,5-b]azepine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCNC(=O)C1=Cc2c(NCC1)ncnc2Nc3ccc(Oc4cccc5sccc45)c(Cl)c3
#
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
 W19  W19  4-{[4-(1-benzothiophen-4-yloxy)-3-chlorophenyl]amino}-N-(2-hydroxyethyl)-8,9-dihydro-7H-pyrimido[4,5-b]azepine-6-carboxamide  ligand  57  35  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W19
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
 W19  C1   C   CR16  0  -0.275  -6.4961  -2.0904  -2.1583
 W19  C2   C   CR16  0  -0.349  -1.0504  -0.2501  -0.7160
 W19  C3   C   CR16  0  -0.332  -5.6851  -0.9671  -2.3669
 W19  C4   C   CR16  0  -0.321  -2.3877  -0.3128  -1.0604
 W19  C5   C   CR16  0  -0.280  -6.8232  -2.5093  -0.8849
 W19  C6   C   CR15  0  -0.194  -5.1534  -0.0368   1.2647
 W19  C7   C   CR16  0  -0.261  -1.1737   2.1403  -0.5740
 W19  C8   C   CR15  0  -0.462  -5.6623  -0.7045   2.3234
 W19  C9   C   CR16  0   0.071   1.9619   3.7732   1.5636
 W19  C10  C   CR56  0   0.158  -5.5233  -0.6389   0.0173
 W19  C11  C   CR6   0  -0.133   3.1470   1.6396   0.4456
 W19  C12  C   CR6   0   0.369  -0.4207   0.9714  -0.4697
 W19  C13  C   CR6   0   0.280  -5.2078  -0.2529  -1.2922
 W19  C14  C   CR6   0   0.404  -3.1424   0.8476  -1.1558
 W19  C15  C   CR56  0  -0.244  -6.3313  -1.7747   0.1928
 W19  C16  C   CR6   0  -0.130  -2.5166   2.0619  -0.9022
 W19  C17  C   CR6   0   0.490   3.8732   2.6024   1.1850
 W19  C18  C   CR6   0   0.525   1.7458   1.8597   0.4009
 W19  C19  C   C1    0  -0.276   3.7114   0.5198  -0.2821
 W19  C20  C   C     0  -0.067   4.8387  -0.1650  -0.0323
 W19  C21  C   C     0   0.533   5.1585  -1.2803  -0.9751
 W19  C22  C   CH2   0  -0.552   5.7543   0.1961   1.0977
 W19  C23  C   CH2   0  -0.274   6.2050   1.6528   1.0010
 W19  C24  C   CH2   0  -0.291   6.3731  -3.3928  -1.2714
 W19  C25  C   CH2   0  -0.180   7.7221  -3.9089  -0.8238
 W19  N26  N   N     0  -0.478   3.2539   3.6684   1.7384
 W19  N27  N   N     0  -0.490   1.1621   2.9282   0.9359
 W19  N28  N   NH1   0  -0.648   5.1943   2.5991   1.4001
 W19  N30  N   NH1   0  -0.657   5.9992  -2.2218  -0.5104
 W19  O31  O   O     0  -0.501   4.6723  -1.3410  -2.1002
 W19  O32  O   OH1   0  -0.673   7.6387  -4.2575   0.5415
 W19  O33  O   O2    0  -0.499  -4.4560   0.8728  -1.5063
 W19  S34  S   S2    0   0.222  -6.6090  -2.0795   1.8759
 W19  CL1  CL  CL    0  -0.104  -3.4440   3.5164  -1.0072
 W19  H1   H   HCR6  0   0.270  -6.8633  -2.6414  -3.0136
 W19  H2   H   HCR6  0   0.281  -0.4856  -1.1715  -0.6440
 W19  H3   H   HCR6  0   0.276  -5.4345  -0.6562  -3.3728
 W19  H4   H   HCR6  0   0.290  -2.8366  -1.2779  -1.2564
 W19  H5   H   HCR6  0   0.273  -7.4467  -3.3795  -0.7295
 W19  H6   H   HCR5  0   0.271  -4.5433   0.8492   1.3634
 W19  H7   H   HCR6  0   0.298  -0.7311   3.1044  -0.3865
 W19  H8   H   HCR5  0   0.305  -5.5373  -0.4626   3.3679
 W19  H9   H   HCR6  0   0.255   1.4863   4.6492   1.9938
 W19  H10  H   H     0   0.260   3.1469   0.1926  -1.1495
 W19  H11  H   HCH2  0   0.271   5.2805   0.0254   2.0684
 W19  H12  H   HCH2  0   0.254   6.6594  -0.4101   1.0868
 W19  H13  H   HCH2  0   0.265   7.0498   1.8165   1.6689
 W19  H14  H   HCH2  0   0.247   6.5584   1.8524  -0.0138
 W19  H15  H   HCH2  0   0.251   6.4319  -3.1316  -2.3269
 W19  H16  H   HCH2  0   0.240   5.6176  -4.1800  -1.1755
 W19  H17  H   HCH2  0   0.213   7.9874  -4.7698  -1.4492
 W19  H18  H   HCH2  0   0.209   8.4787  -3.1345  -0.9971
 W19  H19  H   HNH1  0   0.399   5.5120   3.3911   1.9365
 W19  H20  H   HNH1  0   0.420   1.3632   0.0312  -0.3598
 W19  H21  H   HNH1  0   0.399   6.2374  -2.2339   0.4681
 W19  H22  H   HOH1  0   0.460   8.5264  -4.4306   0.8669
 W19  N29  N   NH1   0  -0.787   0.9448   0.9307  -0.1891

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
 W19  C1   C5   aromatic  1.380  0.020  1.380
 W19  C1   C3   aromatic  1.401  0.020  1.401
 W19  C5   C15  aromatic  1.394  0.020  1.394
 W19  C3   C13  aromatic  1.376  0.020  1.376
 W19  C15  S34  aromatic  1.733  0.020  1.733
 W19  C15  C10  aromatic  1.405  0.020  1.405
 W19  C13  C10  aromatic  1.401  0.020  1.401
 W19  C13  O33  single    1.371  0.020  1.371
 W19  S34  C8   aromatic  1.728  0.020  1.728
 W19  C10  C6   aromatic  1.434  0.020  1.434
 W19  O33  C14  single    1.360  0.020  1.360
 W19  C6   C8   aromatic  1.351  0.020  1.351
 W19  CL1  C16  single    1.728  0.020  1.728
 W19  C14  C16  aromatic  1.389  0.020  1.389
 W19  C14  C4   aromatic  1.388  0.020  1.388
 W19  C16  C7   aromatic  1.385  0.020  1.385
 W19  C4   C2   aromatic  1.382  0.020  1.382
 W19  C7   C12  aromatic  1.394  0.020  1.394
 W19  C2   C12  aromatic  1.396  0.020  1.396
 W19  C12  N29  single    1.395  0.020  1.395
 W19  N29  C18  single    1.361  0.020  1.361
 W19  N27  C18  aromatic  1.330  0.020  1.330
 W19  N27  C9   aromatic  1.322  0.020  1.322
 W19  C18  C11  aromatic  1.419  0.020  1.419
 W19  C9   N26  aromatic  1.308  0.020  1.308
 W19  C11  C19  single    1.450  0.020  1.450
 W19  C11  C17  aromatic  1.415  0.020  1.415
 W19  N26  C17  aromatic  1.351  0.020  1.351
 W19  C19  C20  double    1.342  0.020  1.342
 W19  C17  N28  single    1.338  0.020  1.338
 W19  C24  N30  single    1.446  0.020  1.446
 W19  C24  C25  single    1.512  0.020  1.512
 W19  N30  C21  single    1.345  0.020  1.345
 W19  C25  O32  single    1.412  0.020  1.412
 W19  C20  C21  single    1.495  0.020  1.495
 W19  C20  C22  single    1.499  0.020  1.499
 W19  N28  C23  single    1.441  0.020  1.441
 W19  C21  O31  double    1.227  0.020  1.227
 W19  C23  C22  single    1.528  0.020  1.528
 W19  C1   H1   single    0.930  0.020  1.080
 W19  C2   H2   single    0.930  0.020  1.080
 W19  C3   H3   single    0.930  0.020  1.080
 W19  C4   H4   single    0.930  0.020  1.080
 W19  C5   H5   single    0.930  0.020  1.080
 W19  C6   H6   single    0.930  0.020  1.080
 W19  C7   H7   single    0.930  0.020  1.080
 W19  C8   H8   single    0.930  0.020  1.080
 W19  C9   H9   single    0.930  0.020  1.080
 W19  C19  H10  single    0.930  0.020  1.080
 W19  C22  H11  single    0.970  0.020  1.090
 W19  C22  H12  single    0.970  0.020  1.090
 W19  C23  H13  single    0.970  0.020  1.090
 W19  C23  H14  single    0.970  0.020  1.090
 W19  C24  H15  single    0.970  0.020  1.090
 W19  C24  H16  single    0.970  0.020  1.090
 W19  C25  H17  single    0.970  0.020  1.090
 W19  C25  H18  single    0.970  0.020  1.090
 W19  N28  H19  single    0.860  0.020  1.020
 W19  N29  H20  single    0.860  0.020  1.020
 W19  N30  H21  single    0.860  0.020  1.020
 W19  O32  H22  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
 W19  H1   C1   C5   119.65  3.000
 W19  H1   C1   C3   119.15  3.000
 W19  C5   C1   C3   121.20  3.000
 W19  H2   C2   C12  119.82  3.000
 W19  H2   C2   C4   118.85  3.000
 W19  C12  C2   C4   121.33  3.000
 W19  H3   C3   C13  119.77  3.000
 W19  H3   C3   C1   120.18  3.000
 W19  C13  C3   C1   120.05  3.000
 W19  H4   C4   C14  120.51  3.000
 W19  H4   C4   C2   119.13  3.000
 W19  C14  C4   C2   120.35  3.000
 W19  H5   C5   C15  121.09  3.000
 W19  H5   C5   C1   120.89  3.000
 W19  C15  C5   C1   118.02  3.000
 W19  H6   C6   C10  124.73  3.000
 W19  H6   C6   C8   123.13  3.000
 W19  C10  C6   C8   112.15  3.000
 W19  H7   C7   C16  119.36  3.000
 W19  H7   C7   C12  121.02  3.000
 W19  C16  C7   C12  119.60  3.000
 W19  H8   C8   S34  119.49  3.000
 W19  H8   C8   C6   127.15  3.000
 W19  S34  C8   C6   113.36  3.000
 W19  H9   C9   N27  116.03  3.000
 W19  H9   C9   N26  116.39  3.000
 W19  N27  C9   N26  127.58  3.000
 W19  C15  C10  C13  117.97  3.000
 W19  C13  C10  C6   129.74  3.000
 W19  C15  C10  C6   112.29  3.000
 W19  C19  C11  C18  119.23  3.000
 W19  C19  C11  C17  126.03  3.000
 W19  C18  C11  C17  114.70  3.000
 W19  N29  C12  C7   124.63  3.000
 W19  N29  C12  C2   116.85  3.000
 W19  C7   C12  C2   118.47  3.000
 W19  O33  C13  C10  119.72  3.000
 W19  O33  C13  C3   119.65  3.000
 W19  C10  C13  C3   120.59  3.000
 W19  O33  C14  C16  117.77  3.000
 W19  C16  C14  C4   118.26  3.000
 W19  O33  C14  C4   123.96  3.000
 W19  S34  C15  C10  110.84  3.000
 W19  C10  C15  C5   122.17  3.000
 W19  S34  C15  C5   126.99  3.000
 W19  CL1  C16  C14  118.87  3.000
 W19  C14  C16  C7   121.98  3.000
 W19  CL1  C16  C7   119.16  3.000
 W19  N28  C17  N26  112.86  3.000
 W19  N28  C17  C11  126.09  3.000
 W19  N26  C17  C11  121.04  3.000
 W19  N29  C18  N27  117.67  3.000
 W19  N27  C18  C11  123.05  3.000
 W19  N29  C18  C11  119.27  3.000
 W19  H10  C19  C20  115.57  3.000
 W19  H10  C19  C11  115.56  3.000
 W19  C20  C19  C11  128.87  3.000
 W19  C22  C20  C21  121.64  3.000
 W19  C22  C20  C19  122.04  3.000
 W19  C21  C20  C19  116.28  3.000
 W19  O31  C21  N30  121.99  3.000
 W19  O31  C21  C20  122.03  3.000
 W19  N30  C21  C20  115.98  3.000
 W19  H12  C22  H11  106.38  3.000
 W19  H12  C22  C23  106.55  3.000
 W19  H11  C22  C23  109.44  3.000
 W19  H12  C22  C20  111.47  3.000
 W19  H11  C22  C20  111.53  3.000
 W19  C23  C22  C20  111.24  3.000
 W19  H14  C23  H13  106.92  3.000
 W19  H14  C23  N28  111.35  3.000
 W19  H13  C23  N28  105.99  3.000
 W19  H14  C23  C22  109.16  3.000
 W19  H13  C23  C22  109.47  3.000
 W19  N28  C23  C22  113.69  3.000
 W19  H16  C24  H15  107.13  3.000
 W19  H16  C24  N30  110.96  3.000
 W19  H15  C24  N30  109.26  3.000
 W19  H16  C24  C25  110.13  3.000
 W19  H15  C24  C25  108.70  3.000
 W19  N30  C24  C25  110.57  3.000
 W19  H18  C25  H17  107.30  3.000
 W19  H18  C25  O32  111.60  3.000
 W19  H17  C25  O32  111.84  3.000
 W19  H18  C25  C24  109.13  3.000
 W19  H17  C25  C24  108.36  3.000
 W19  O32  C25  C24  108.54  3.000
 W19  C17  N26  C9   117.46  3.000
 W19  C18  N27  C9   116.04  3.000
 W19  H19  N28  C23  116.25  3.000
 W19  H19  N28  C17  113.25  3.000
 W19  C23  N28  C17  130.50  3.000
 W19  H21  N30  C24  116.14  3.000
 W19  H21  N30  C21  119.47  3.000
 W19  C24  N30  C21  123.14  3.000
 W19  H22  O32  C25  108.50  3.000
 W19  C14  O33  C13  118.32  3.000
 W19  C15  S34  C8    91.36  3.000
 W19  H20  N29  C18  116.02  3.000
 W19  H20  N29  C12  113.51  3.000
 W19  C18  N29  C12  130.05  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
 W19  CONST_01  S34  C15  C5   C1    180.00   0.0  0
 W19  CONST_02  C10  C15  C5   C1      0.00   0.0  0
 W19  CONST_03  C10  C13  C3   C1      0.00   0.0  0
 W19  CONST_04  C16  C14  C4   C2      0.00   0.0  0
 W19  CONST_05  C16  C7   C12  C2      0.00   0.0  0
 W19  CONST_06  C15  C5   C1   C3      0.00   0.0  0
 W19  CONST_07  C15  C10  C13  C3      0.00   0.0  0
 W19  CONST_08  C6   C10  C13  C3    180.00   0.0  0
 W19  CONST_09  C7   C16  C14  C4      0.00   0.0  0
 W19  CONST_10  C7   C12  C2   C4      0.00   0.0  0
 W19  CONST_11  C13  C3   C1   C5      0.00   0.0  0
 W19  CONST_12  C8   S34  C15  C5    180.00   0.0  0
 W19  CONST_13  C13  C10  C15  C5      0.00   0.0  0
 W19  CONST_14  C6   C10  C15  C5    180.00   0.0  0
 W19  CONST_15  S34  C15  C10  C6      0.00   0.0  0
 W19  CONST_16  C15  S34  C8   C6      0.00   0.0  0
 W19  CONST_17  C10  C15  S34  C8      0.00   0.0  0
 W19  CONST_18  C15  C10  C6   C8      0.00   0.0  0
 W19  CONST_19  C13  C10  C6   C8    180.00   0.0  0
 W19  CONST_20  C11  C18  N27  C9      0.00   0.0  0
 W19  CONST_21  C11  C17  N26  C9      0.00   0.0  0
 W19  CONST_22  S34  C8   C6   C10     0.00   0.0  0
 W19  CONST_23  C14  C16  C7   C12     0.00   0.0  0
 W19  CONST_24  C14  C4   C2   C12     0.00   0.0  0
 W19  CONST_25  S34  C15  C10  C13   180.00   0.0  0
 W19  CONST_26  N27  C18  C11  C17     0.00   0.0  0
 W19  CONST_27  N27  C9   N26  C17     0.00   0.0  0
 W19  CONST_28  N26  C9   N27  C18     0.00   0.0  0
 W19  CONST_29  N26  C17  C11  C18     0.00   0.0  0
 W19  CONST_30  O33  C13  C3   C1    180.00   0.0  0
 W19  CONST_31  O33  C14  C4   C2    180.00   0.0  0
 W19  CONST_32  CL1  C16  C14  C4    180.00   0.0  0
 W19  CONST_33  N29  C12  C2   C4    180.00   0.0  0
 W19  CONST_34  O33  C13  C10  C6      0.00   0.0  0
 W19  CONST_35  O33  C14  C16  C7    180.00   0.0  0
 W19  CONST_36  N29  C18  N27  C9    180.00   0.0  0
 W19  CONST_37  CL1  C16  C7   C12   180.00   0.0  0
 W19  CONST_38  O33  C13  C10  C15   180.00   0.0  0
 W19  CONST_39  N29  C12  C7   C16   180.00   0.0  0
 W19  CONST_40  N29  C18  C11  C17   180.00   0.0  0
 W19  CONST_41  N29  C18  C11  C19     0.00   0.0  0
 W19  CONST_42  H7   C7   C12  C2    180.00   0.0  0
 W19  CONST_43  H5   C5   C1   C3    180.00   0.0  0
 W19  CONST_44  H3   C3   C1   C5    180.00   0.0  0
 W19  CONST_45  H2   C2   C12  C7    180.00   0.0  0
 W19  CONST_46  H8   C8   C6   C10   180.00   0.0  0
 W19  CONST_47  H4   C4   C2   C12   180.00   0.0  0
 W19  CONST_48  H1   C1   C3   C13   180.00   0.0  0
 W19  CONST_49  H6   C6   C10  C13     0.00   0.0  0
 W19  CONST_50  H9   C9   N26  C17   180.00   0.0  0
 W19  CONST_51  C24  N30  C21  C20   180.00   0.0  0
 W19  CONST_52  H21  N30  C21  C20     0.00   0.0  0
 W19  CONST_53  O31  C21  N30  C24     0.00   0.0  0
 W19  Var_01    C22  C20  C19  C11    -2.08  30.0  1
 W19  Var_02    C23  N28  C17  C11    -1.92  30.0  1
 W19  Var_03    C20  C19  C11  C17    29.10  30.0  1
 W19  Var_04    C22  C23  N28  C17   -39.22  30.0  1
 W19  Var_05    C23  C22  C20  C19   -55.93  30.0  1
 W19  Var_06    N28  C23  C22  C20    75.97  30.0  1
 W19  Var_07    C18  N29  C12  C2   -161.71  30.0  2
 W19  Var_08    C12  N29  C18  C11  -173.20  30.0  1
 W19  Var_09    C16  C14  O33  C13  -156.70  30.0  2
 W19  Var_10    N30  C21  C20  C19  -158.96  30.0  2
 W19  Var_11    C25  C24  N30  C21   154.36  30.0  1
 W19  Var_12    O32  C25  C24  N30    60.58  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
 W19  plan-1  C2   0.020
 W19  plan-1  C4   0.020
 W19  plan-1  C7   0.020
 W19  plan-1  C12  0.020
 W19  plan-1  C14  0.020
 W19  plan-1  C16  0.020
 W19  plan-1  O33  0.020
 W19  plan-1  CL1  0.020
 W19  plan-1  H2   0.020
 W19  plan-1  H4   0.020
 W19  plan-1  H7   0.020
 W19  plan-1  N29  0.020
 W19  plan-2  C1   0.020
 W19  plan-2  C3   0.020
 W19  plan-2  C5   0.020
 W19  plan-2  C6   0.020
 W19  plan-2  C8   0.020
 W19  plan-2  C10  0.020
 W19  plan-2  C13  0.020
 W19  plan-2  C15  0.020
 W19  plan-2  O33  0.020
 W19  plan-2  S34  0.020
 W19  plan-2  H1   0.020
 W19  plan-2  H3   0.020
 W19  plan-2  H5   0.020
 W19  plan-2  H6   0.020
 W19  plan-2  H8   0.020
 W19  plan-3  C9   0.020
 W19  plan-3  C11  0.020
 W19  plan-3  C17  0.020
 W19  plan-3  C18  0.020
 W19  plan-3  C19  0.020
 W19  plan-3  N26  0.020
 W19  plan-3  N27  0.020
 W19  plan-3  N28  0.020
 W19  plan-3  H9   0.020
 W19  plan-3  N29  0.020
 W19  plan-4  C20  0.020
 W19  plan-4  C21  0.020
 W19  plan-4  C24  0.020
 W19  plan-4  N30  0.020
 W19  plan-4  O31  0.020
 W19  plan-4  H21  0.020

