# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:45:16 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: 4-{[9-chloro-7-(2-fluoro-6-methoxyphenyl)-5H-pyrimido[5,4-d][2]benzazepin-2-yl]amino}-2-methoxybenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(F)c1C2=NCc3cnc(Nc4ccc(C(O)=O)c(OC)c4)nc3c5ccc(Cl)cc25
#
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
 A5B  A5B  '4-{[9-chloro-7-(2-fluoro-6-methoxyphenyl)-5H-pyrimido[5,4-d][2]benzazepin-2-yl]amino}-2-methoxybenzoic acid'  ligand  56  37  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5B
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
 A5B  C26  C   CH3    0  -0.443  -6.7297   0.8044   3.2157
 A5B  O2   O   O2     0  -0.450  -7.2379   0.3493   1.9802
 A5B  C24  C   CR6    0   0.372  -6.3901   0.1341   0.9596
 A5B  C25  C   CR16   0  -0.527  -5.0239   0.3633   1.0920
 A5B  C23  C   CR6    0  -0.212  -6.9133  -0.3561  -0.2549
 A5B  C27  C   C      0   0.392  -8.3893  -0.6213  -0.5336
 A5B  O4   O   O      0  -0.591  -9.2322  -0.1350   0.2414
 A5B  O3   O   OC    -1  -0.602  -8.6340  -1.3037  -1.5507
 A5B  C22  C   CR16   0  -0.266  -5.9957  -0.5964  -1.2701
 A5B  C21  C   CR16   0  -0.335  -4.6324  -0.3649  -1.1647
 A5B  C20  C   CR6    0   0.397  -4.1339   0.1274   0.0386
 A5B  N4   N   NH1    0  -0.778  -2.7993   0.4082   0.3037
 A5B  C12  C   CR6    0   0.602  -1.6884   0.3675  -0.4811
 A5B  N3   N   N      0  -0.487  -0.5716   0.7572   0.1373
 A5B  N2   N   N      0  -0.459  -1.7679  -0.0358  -1.7451
 A5B  C11  C   CR16   0  -0.016  -0.6380  -0.0243  -2.4348
 A5B  C10  C   CR6    0  -0.043   0.5760   0.3769  -1.9074
 A5B  C9   C   CH2    0  -0.441   1.8474   0.4036  -2.6890
 A5B  N1   N   N      0  -0.320   2.7516  -0.6206  -2.2000
 A5B  C13  C   CR6    0   0.252   0.5506   0.7556  -0.5622
 A5B  C14  C   CR6    0   0.072   1.7685   1.2265   0.1195
 A5B  C19  C   CR16   0  -0.294   1.6447   2.2415   1.0690
 A5B  C18  C   CR16   0  -0.201   2.7438   2.7412   1.7390
 A5B  C17  C   CR6    0  -0.034   3.9907   2.1928   1.4760
 A5B  CL1  CL  CL     0  -0.113   5.3815   2.8054   2.3000
 A5B  C16  C   CR16   0  -0.231   4.1381   1.1581   0.5736
 A5B  C15  C   CR6    0   0.028   3.0340   0.6726  -0.1260
 A5B  C8   C   C      0   0.203   3.2638  -0.4697  -1.0513
 A5B  C7   C   CR6    0  -0.329   4.2092  -1.5098  -0.5710
 A5B  C6   C   CR6    0   0.547   5.3812  -1.8008  -1.2448
 A5B  F1   F   F      0  -0.299   5.6710  -1.1023  -2.3503
 A5B  C5   C   CR16   0  -0.437   6.2837  -2.7538  -0.8100
 A5B  C4   C   CR16   0  -0.227   5.9806  -3.4457   0.3507
 A5B  C3   C   CR16   0  -0.396   4.8125  -3.1986   1.0606
 A5B  C2   C   CR6    0   0.423   3.9245  -2.2317   0.5984
 A5B  O1   O   O2     0  -0.455   2.7614  -1.9224   1.1837
 A5B  C1   C   CH3    0  -0.437   2.4264  -2.5386   2.4133
 A5B  H1   H   HCH3   0   0.259  -7.5839   0.8943   3.8828
 A5B  H2   H   HCH3   0   0.225  -6.0160   0.1018   3.6553
 A5B  H3   H   HCH3   0   0.225  -6.2504   1.7840   3.1324
 A5B  H4   H   HCR6   0   0.285  -4.6209   0.7361   2.0249
 A5B  H6   H   HCR6   0   0.244  -6.3760  -0.9874  -2.2041
 A5B  H7   H   HCR6   0   0.273  -3.9803  -0.5652  -1.9980
 A5B  H8   H   HNH1   0   0.409  -2.6044   0.7365   1.2374
 A5B  H9   H   HCR6   0   0.274  -0.7019  -0.3438  -3.4704
 A5B  H10  H   HCH2   0   0.267   1.6404   0.2087  -3.7413
 A5B  H11  H   HCH2   0   0.260   2.3071   1.3979  -2.6287
 A5B  H12  H   HCR6   0   0.272   0.6677   2.6570   1.2738
 A5B  H13  H   HCR6   0   0.289   2.6320   3.5439   2.4546
 A5B  H14  H   HCR6   0   0.280   5.1163   0.7259   0.4096
 A5B  H15  H   HCR6   0   0.279   7.1961  -2.9410  -1.3595
 A5B  H16  H   HCR6   0   0.275   6.6681  -4.1967   0.7159
 A5B  H17  H   HCR6   0   0.287   4.6096  -3.7643   1.9589
 A5B  H18  H   HCH3   0   0.263   1.4766  -2.1092   2.7198
 A5B  H19  H   HCH3   0   0.234   2.3092  -3.6196   2.3067
 A5B  H20  H   HCH3   0   0.233   3.1730  -2.3352   3.1843

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
 A5B  C11  N2   aromatic  1.324  0.020  1.324
 A5B  C11  C10  aromatic  1.383  0.020  1.383
 A5B  N2   C12  aromatic  1.329  0.020  1.329
 A5B  C9   C10  single    1.493  0.020  1.493
 A5B  C9   N1   single    1.451  0.020  1.451
 A5B  C10  C13  aromatic  1.398  0.020  1.398
 A5B  C12  N4   single    1.361  0.020  1.361
 A5B  C12  N3   aromatic  1.335  0.020  1.335
 A5B  N4   C20  single    1.389  0.020  1.389
 A5B  C13  N3   aromatic  1.322  0.020  1.322
 A5B  C13  C14  aromatic  1.473  0.020  1.473
 A5B  N1   C8   double    1.267  0.020  1.267
 A5B  C1   O1   single    1.416  0.020  1.416
 A5B  C21  C20  aromatic  1.392  0.020  1.392
 A5B  C21  C22  aromatic  1.387  0.020  1.387
 A5B  C20  C25  aromatic  1.399  0.020  1.399
 A5B  O1   C2   single    1.338  0.020  1.338
 A5B  C14  C19  aromatic  1.395  0.020  1.395
 A5B  C14  C15  aromatic  1.403  0.020  1.403
 A5B  C19  C18  aromatic  1.381  0.020  1.381
 A5B  C8   C15  single    1.488  0.020  1.488
 A5B  C8   C7   single    1.485  0.020  1.485
 A5B  C15  C16  aromatic  1.394  0.020  1.394
 A5B  C22  C23  aromatic  1.389  0.020  1.389
 A5B  C25  C24  aromatic  1.392  0.020  1.392
 A5B  C18  C17  aromatic  1.387  0.020  1.387
 A5B  C16  C17  aromatic  1.381  0.020  1.381
 A5B  C2   C7   aromatic  1.403  0.020  1.403
 A5B  C2   C3   aromatic  1.392  0.020  1.392
 A5B  C7   C6   aromatic  1.383  0.020  1.383
 A5B  C17  CL1  single    1.729  0.020  1.729
 A5B  C23  C24  aromatic  1.410  0.020  1.410
 A5B  C23  C27  single    1.525  0.020  1.525
 A5B  C24  O2   single    1.344  0.020  1.344
 A5B  C3   C4   aromatic  1.389  0.020  1.389
 A5B  O4   C27  deloc     1.244  0.020  1.244
 A5B  C6   F1   single    1.339  0.020  1.339
 A5B  C6   C5   aromatic  1.383  0.020  1.383
 A5B  C27  O3   deloc     1.249  0.020  1.249
 A5B  O2   C26  single    1.411  0.020  1.411
 A5B  C4   C5   aromatic  1.385  0.020  1.385
 A5B  C26  H1   single    0.970  0.020  1.090
 A5B  C26  H2   single    0.970  0.020  1.090
 A5B  C26  H3   single    0.970  0.020  1.090
 A5B  C25  H4   single    0.930  0.020  1.080
 A5B  C22  H6   single    0.930  0.020  1.080
 A5B  C21  H7   single    0.930  0.020  1.080
 A5B  N4   H8   single    0.860  0.020  1.020
 A5B  C11  H9   single    0.930  0.020  1.080
 A5B  C9   H10  single    0.970  0.020  1.090
 A5B  C9   H11  single    0.970  0.020  1.090
 A5B  C19  H12  single    0.930  0.020  1.080
 A5B  C18  H13  single    0.930  0.020  1.080
 A5B  C16  H14  single    0.930  0.020  1.080
 A5B  C5   H15  single    0.930  0.020  1.080
 A5B  C4   H16  single    0.930  0.020  1.080
 A5B  C3   H17  single    0.930  0.020  1.080
 A5B  C1   H18  single    0.970  0.020  1.090
 A5B  C1   H19  single    0.970  0.020  1.090
 A5B  C1   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
 A5B  H3   C26  H2   108.66  3.000
 A5B  H3   C26  H1   108.47  3.000
 A5B  H2   C26  H1   108.61  3.000
 A5B  H3   C26  O2   112.33  3.000
 A5B  H2   C26  O2   112.32  3.000
 A5B  H1   C26  O2   106.31  3.000
 A5B  C24  O2   C26  119.29  3.000
 A5B  C23  C24  C25  120.22  3.000
 A5B  C23  C24  O2   118.39  3.000
 A5B  C25  C24  O2   121.37  3.000
 A5B  H4   C25  C20  118.04  3.000
 A5B  H4   C25  C24  120.28  3.000
 A5B  C20  C25  C24  121.68  3.000
 A5B  C22  C23  C27  118.39  3.000
 A5B  C27  C23  C24  125.23  3.000
 A5B  C22  C23  C24  116.38  3.000
 A5B  O3   C27  O4   126.03  3.000
 A5B  O3   C27  C23  115.68  3.000
 A5B  O4   C27  C23  118.28  3.000
 A5B  H6   C22  C21  118.14  3.000
 A5B  H6   C22  C23  117.46  3.000
 A5B  C21  C22  C23  124.39  3.000
 A5B  H7   C21  C20  121.17  3.000
 A5B  H7   C21  C22  120.36  3.000
 A5B  C20  C21  C22  118.47  3.000
 A5B  N4   C20  C21  125.47  3.000
 A5B  C21  C20  C25  118.85  3.000
 A5B  N4   C20  C25  115.68  3.000
 A5B  H8   N4   C12  112.69  3.000
 A5B  H8   N4   C20  115.34  3.000
 A5B  C12  N4   C20  131.93  3.000
 A5B  N2   C12  N3   125.40  3.000
 A5B  N3   C12  N4   114.03  3.000
 A5B  N2   C12  N4   120.57  3.000
 A5B  C13  N3   C12  117.69  3.000
 A5B  C11  N2   C12  116.21  3.000
 A5B  H9   C11  C10  120.05  3.000
 A5B  H9   C11  N2   116.37  3.000
 A5B  C10  C11  N2   123.57  3.000
 A5B  C13  C10  C9   120.97  3.000
 A5B  C13  C10  C11  115.45  3.000
 A5B  C9   C10  C11  123.58  3.000
 A5B  H11  C9   H10  107.14  3.000
 A5B  H11  C9   N1   111.10  3.000
 A5B  H10  C9   N1   108.51  3.000
 A5B  H11  C9   C10  110.14  3.000
 A5B  H10  C9   C10  109.91  3.000
 A5B  N1   C9   C10  109.98  3.000
 A5B  C8   N1   C9   118.26  3.000
 A5B  C14  C13  C10  121.13  3.000
 A5B  C14  C13  N3   117.16  3.000
 A5B  C10  C13  N3   121.66  3.000
 A5B  C15  C14  C19  119.10  3.000
 A5B  C15  C14  C13  122.58  3.000
 A5B  C19  C14  C13  118.30  3.000
 A5B  H12  C19  C18  119.23  3.000
 A5B  H12  C19  C14  119.25  3.000
 A5B  C18  C19  C14  121.52  3.000
 A5B  H13  C18  C17  120.78  3.000
 A5B  H13  C18  C19  120.50  3.000
 A5B  C17  C18  C19  118.71  3.000
 A5B  C16  C17  CL1  119.42  3.000
 A5B  CL1  C17  C18  119.52  3.000
 A5B  C16  C17  C18  121.07  3.000
 A5B  H14  C16  C15  120.05  3.000
 A5B  H14  C16  C17  119.66  3.000
 A5B  C15  C16  C17  120.28  3.000
 A5B  C8   C15  C16  117.20  3.000
 A5B  C16  C15  C14  119.27  3.000
 A5B  C8   C15  C14  123.45  3.000
 A5B  C7   C8   C15  115.77  3.000
 A5B  C7   C8   N1   117.85  3.000
 A5B  C15  C8   N1   126.37  3.000
 A5B  C2   C7   C6   118.02  3.000
 A5B  C6   C7   C8   121.95  3.000
 A5B  C2   C7   C8   120.03  3.000
 A5B  C5   C6   F1   118.54  3.000
 A5B  C5   C6   C7   123.02  3.000
 A5B  F1   C6   C7   118.42  3.000
 A5B  H15  C5   C4   121.61  3.000
 A5B  H15  C5   C6   120.68  3.000
 A5B  C4   C5   C6   117.71  3.000
 A5B  H16  C4   C3   119.04  3.000
 A5B  H16  C4   C5   119.39  3.000
 A5B  C3   C4   C5   121.57  3.000
 A5B  H17  C3   C2   121.33  3.000
 A5B  H17  C3   C4   119.31  3.000
 A5B  C2   C3   C4   119.37  3.000
 A5B  O1   C2   C3   124.74  3.000
 A5B  C3   C2   C7   120.31  3.000
 A5B  O1   C2   C7   114.95  3.000
 A5B  C1   O1   C2   119.01  3.000
 A5B  H20  C1   H19  109.05  3.000
 A5B  H20  C1   H18  108.96  3.000
 A5B  H19  C1   H18  108.95  3.000
 A5B  H20  C1   O1   111.73  3.000
 A5B  H19  C1   O1   111.80  3.000
 A5B  H18  C1   O1   106.25  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
 A5B  CONST_01  C21  C20  C25  C24     0.00   0.0  0
 A5B  CONST_02  C21  C22  C23  C24     0.00   0.0  0
 A5B  CONST_03  C22  C21  C20  C25     0.00   0.0  0
 A5B  CONST_04  C22  C23  C24  C25     0.00   0.0  0
 A5B  CONST_05  C20  C21  C22  C23     0.00   0.0  0
 A5B  CONST_06  C20  C25  C24  C23     0.00   0.0  0
 A5B  CONST_07  C10  C11  N2   C12     0.00   0.0  0
 A5B  CONST_08  C11  N2   C12  N3      0.00   0.0  0
 A5B  CONST_09  C13  N3   C12  N2      0.00   0.0  0
 A5B  CONST_10  C17  C18  C19  C14     0.00   0.0  0
 A5B  CONST_11  C16  C17  C18  C19     0.00   0.0  0
 A5B  CONST_12  C15  C16  C17  C18     0.00   0.0  0
 A5B  CONST_13  C4   C3   C2   C7      0.00   0.0  0
 A5B  CONST_14  C4   C5   C6   C7      0.00   0.0  0
 A5B  CONST_15  C3   C2   C7   C6      0.00   0.0  0
 A5B  CONST_16  C3   C4   C5   C6      0.00   0.0  0
 A5B  CONST_17  C2   C7   C6   C5      0.00   0.0  0
 A5B  CONST_18  C2   C3   C4   C5      0.00   0.0  0
 A5B  CONST_19  C3   C2   C7   C8    180.00   0.0  0
 A5B  CONST_20  C5   C6   C7   C8    180.00   0.0  0
 A5B  CONST_21  C20  C25  C24  O2    180.00   0.0  0
 A5B  CONST_22  C22  C23  C24  O2    180.00   0.0  0
 A5B  CONST_23  N4   C20  C25  C24   180.00   0.0  0
 A5B  CONST_24  C27  C23  C24  C25   180.00   0.0  0
 A5B  CONST_25  C21  C22  C23  C27   180.00   0.0  0
 A5B  CONST_26  N4   C20  C21  C22   180.00   0.0  0
 A5B  CONST_27  C11  N2   C12  N4    180.00   0.0  0
 A5B  CONST_28  C13  N3   C12  N4    180.00   0.0  0
 A5B  CONST_29  CL1  C17  C18  C19   180.00   0.0  0
 A5B  CONST_30  C15  C16  C17  CL1   180.00   0.0  0
 A5B  CONST_31  O1   C2   C7   C8      0.00   0.0  0
 A5B  CONST_32  F1   C6   C7   C8      0.00   0.0  0
 A5B  CONST_33  O1   C2   C7   C6    180.00   0.0  0
 A5B  CONST_34  C2   C7   C6   F1    180.00   0.0  0
 A5B  CONST_35  C4   C5   C6   F1    180.00   0.0  0
 A5B  CONST_36  O1   C2   C3   C4    180.00   0.0  0
 A5B  CONST_37  H6   C22  C23  C24   180.00   0.0  0
 A5B  CONST_38  H7   C21  C20  C25   180.00   0.0  0
 A5B  CONST_39  H4   C25  C24  C23   180.00   0.0  0
 A5B  CONST_40  H9   C11  N2   C12   180.00   0.0  0
 A5B  CONST_41  H13  C18  C19  C14   180.00   0.0  0
 A5B  CONST_42  H14  C16  C17  C18   180.00   0.0  0
 A5B  CONST_43  H12  C19  C18  C17   180.00   0.0  0
 A5B  CONST_44  H17  C3   C2   C7    180.00   0.0  0
 A5B  CONST_45  H15  C5   C6   C7    180.00   0.0  0
 A5B  CONST_46  H16  C4   C5   C6    180.00   0.0  0
 A5B  Var_01    C12  N4   C20  C25  -176.21  30.0  2
 A5B  Var_02    N2   C12  N4   C20    -2.19  30.0  2
 A5B  Var_03    C25  C24  O2   C26    -0.65  30.0  3
 A5B  Var_04    O4   C27  C23  C24    15.17  30.0  2
 A5B  Var_05    H1   C26  O2   C24  -179.34  30.0  3
 A5B  Var_06    H18  C1   O1   C2    177.43  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
 A5B  plan-1  O2   0.020
 A5B  plan-1  C24  0.020
 A5B  plan-1  C25  0.020
 A5B  plan-1  C23  0.020
 A5B  plan-1  C27  0.020
 A5B  plan-1  C22  0.020
 A5B  plan-1  C21  0.020
 A5B  plan-1  C20  0.020
 A5B  plan-1  N4   0.020
 A5B  plan-1  H4   0.020
 A5B  plan-1  H6   0.020
 A5B  plan-1  H7   0.020
 A5B  plan-2  C8   0.020
 A5B  plan-2  C7   0.020
 A5B  plan-2  C6   0.020
 A5B  plan-2  F1   0.020
 A5B  plan-2  C5   0.020
 A5B  plan-2  C4   0.020
 A5B  plan-2  C3   0.020
 A5B  plan-2  C2   0.020
 A5B  plan-2  O1   0.020
 A5B  plan-2  H15  0.020
 A5B  plan-2  H16  0.020
 A5B  plan-2  H17  0.020
 A5B  plan-3  N4   0.020
 A5B  plan-3  C12  0.020
 A5B  plan-3  N3   0.020
 A5B  plan-3  N2   0.020
 A5B  plan-3  C11  0.020
 A5B  plan-3  C10  0.020
 A5B  plan-3  C9   0.020
 A5B  plan-3  C13  0.020
 A5B  plan-3  C14  0.020
 A5B  plan-3  H9   0.020
 A5B  plan-4  C13  0.020
 A5B  plan-4  C14  0.020
 A5B  plan-4  C19  0.020
 A5B  plan-4  C18  0.020
 A5B  plan-4  C17  0.020
 A5B  plan-4  CL1  0.020
 A5B  plan-4  C16  0.020
 A5B  plan-4  C15  0.020
 A5B  plan-4  C8   0.020
 A5B  plan-4  H12  0.020
 A5B  plan-4  H13  0.020
 A5B  plan-4  H14  0.020
 A5B  plan-5  C23  0.020
 A5B  plan-5  C27  0.020
 A5B  plan-5  O4   0.020
 A5B  plan-5  O3   0.020

