# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 04:23:59 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  57  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  -0.447  -6.7253   0.7665   3.1962
 A5B  O2   O   O2    0  -0.446  -7.2103   0.3113   1.9463
 A5B  C24  C   CR6   0   0.421  -6.3557   0.1265   0.9383
 A5B  C25  C   CR16  0  -0.526  -4.9933   0.3574   1.0720
 A5B  C23  C   CR6   0  -0.211  -6.8728  -0.3114  -0.3026
 A5B  C27  C   C     0   0.532  -8.3076  -0.5794  -0.5046
 A5B  O4   O   O     0  -0.444  -9.1664  -0.5451   0.3458
 A5B  O3   O   OH1   0  -0.606  -8.5920  -0.8826  -1.7734
 A5B  C22  C   CR16  0  -0.238  -5.9655  -0.4924  -1.3480
 A5B  C21  C   CR16  0  -0.331  -4.6099  -0.2701  -1.2245
 A5B  C20  C   CR6   0   0.422  -4.1079   0.1660   0.0053
 A5B  N4   N   NH1   0  -0.780  -2.7815   0.4374   0.2685
 A5B  C12  C   CR6   0   0.609  -1.6650   0.3805  -0.5189
 A5B  N3   N   N     0  -0.483  -0.5512   0.7713   0.0974
 A5B  N2   N   N     0  -0.458  -1.7478  -0.0401  -1.7741
 A5B  C11  C   CR16  0  -0.012  -0.6168  -0.0488  -2.4632
 A5B  C10  C   CR6   0  -0.039   0.5983   0.3508  -1.9378
 A5B  C9   C   CH2   0  -0.441   1.8717   0.3550  -2.7169
 A5B  N1   N   N     0  -0.319   2.7651  -0.6694  -2.2093
 A5B  C13  C   CR6   0   0.255   0.5740   0.7509  -0.5990
 A5B  C14  C   CR6   0   0.073   1.7933   1.2236   0.0775
 A5B  C19  C   CR16  0  -0.293   1.6758   2.2557   1.0089
 A5B  C18  C   CR16  0  -0.201   2.7782   2.7585   1.6711
 A5B  C17  C   CR6   0  -0.034   4.0211   2.1955   1.4196
 A5B  CL1  CL  CL    0  -0.111   5.4156   2.8121   2.2337
 A5B  C16  C   CR16  0  -0.231   4.1615   1.1436   0.5360
 A5B  C15  C   CR6   0   0.029   3.0545   0.6550  -0.1566
 A5B  C8   C   C     0   0.203   3.2757  -0.5047  -1.0618
 A5B  C7   C   CR6   0  -0.328   4.2098  -1.5458  -0.5620
 A5B  C6   C   CR6   0   0.547   5.3825  -1.8560  -1.2259
 A5B  F1   F   F     0  -0.299   5.6831  -1.1754  -2.3395
 A5B  C5   C   CR16  0  -0.437   6.2743  -2.8109  -0.7734
 A5B  C4   C   CR16  0  -0.227   5.9592  -3.4839   0.3952
 A5B  C3   C   CR16  0  -0.396   4.7901  -3.2164   1.0961
 A5B  C2   C   CR6   0   0.423   3.9133  -2.2478   0.6163
 A5B  O1   O   O2    0  -0.455   2.7511  -1.9179   1.1923
 A5B  C1   C   CH3   0  -0.437   2.4000  -2.5200   2.4245
 A5B  H1   H   HCH3  0   0.266  -7.5925   0.8452   3.8462
 A5B  H2   H   HCH3  0   0.235  -6.0150   0.0642   3.6388
 A5B  H3   H   HCH3  0   0.234  -6.2537   1.7491   3.1180
 A5B  H4   H   HCR6  0   0.299  -4.5909   0.6974   2.0170
 A5B  H5   H   HOH1  0   0.482  -9.5402  -1.0602  -1.8515
 A5B  H6   H   HCR6  0   0.271  -6.3268  -0.8280  -2.3093
 A5B  H7   H   HCR6  0   0.290  -3.9575  -0.4305  -2.0653
 A5B  H8   H   HNH1  0   0.415  -2.5808   0.7592   1.2037
 A5B  H9   H   HCR6  0   0.277  -0.6818  -0.3834  -3.4936
 A5B  H10  H   HCH2  0   0.269   1.6656   0.1461  -3.7665
 A5B  H11  H   HCH2  0   0.263   2.3385   1.3466  -2.6697
 A5B  H12  H   HCR6  0   0.273   0.7021   2.6830   1.2049
 A5B  H13  H   HCR6  0   0.290   2.6723   3.5749   2.3718
 A5B  H14  H   HCR6  0   0.281   5.1364   0.7008   0.3811
 A5B  H15  H   HCR6  0   0.279   7.1873  -3.0144  -1.3159
 A5B  H16  H   HCR6  0   0.275   6.6379  -4.2361   0.7740
 A5B  H17  H   HCR6  0   0.287   4.5780  -3.7672   2.0014
 A5B  H18  H   HCH3  0   0.263   1.4544  -2.0751   2.7218
 A5B  H19  H   HCH3  0   0.234   2.2688  -3.6000   2.3248
 A5B  H20  H   HCH3  0   0.233   3.1443  -2.3214   3.1992

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  1.326  0.020  1.326
 A5B  C9   C10  single    1.493  0.020  1.493
 A5B  C9   N1   single    1.451  0.020  1.451
 A5B  C10  C13  aromatic  1.397  0.020  1.397
 A5B  C12  N4   single    1.367  0.020  1.367
 A5B  C12  N3   aromatic  1.332  0.020  1.332
 A5B  N4   C20  single    1.379  0.020  1.379
 A5B  C13  N3   aromatic  1.323  0.020  1.323
 A5B  C13  C14  aromatic  1.472  0.020  1.472
 A5B  N1   C8   double    1.267  0.020  1.267
 A5B  C1   O1   single    1.416  0.020  1.416
 A5B  C21  C20  aromatic  1.398  0.020  1.398
 A5B  C21  C22  aromatic  1.379  0.020  1.379
 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  1.396  0.020  1.396
 A5B  C25  C24  aromatic  1.388  0.020  1.388
 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    1.728  0.020  1.728
 A5B  C23  C24  aromatic  1.414  0.020  1.414
 A5B  C23  C27  single    1.474  0.020  1.474
 A5B  C24  O2   single    1.334  0.020  1.334
 A5B  C3   C4   aromatic  1.389  0.020  1.389
 A5B  O4   C27  double    1.209  0.020  1.209
 A5B  C6   F1   single    1.339  0.020  1.339
 A5B  C6   C5   aromatic  1.383  0.020  1.383
 A5B  C27  O3   single    1.335  0.020  1.335
 A5B  O2   C26  single    1.416  0.020  1.416
 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  O3   H5   single    0.850  0.020  0.980
 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   109.06  3.000
 A5B  H3   C26  H1   108.79  3.000
 A5B  H2   C26  H1   108.85  3.000
 A5B  H3   C26  O2   111.95  3.000
 A5B  H2   C26  O2   111.94  3.000
 A5B  H1   C26  O2   106.13  3.000
 A5B  C24  O2   C26  119.47  3.000
 A5B  C23  C24  C25  119.67  3.000
 A5B  C23  C24  O2   118.14  3.000
 A5B  C25  C24  O2   122.19  3.000
 A5B  H4   C25  C20  118.26  3.000
 A5B  H4   C25  C24  120.09  3.000
 A5B  C20  C25  C24  121.65  3.000
 A5B  C22  C23  C27  120.44  3.000
 A5B  C27  C23  C24  122.20  3.000
 A5B  C22  C23  C24  117.37  3.000
 A5B  O3   C27  O4   121.57  3.000
 A5B  O3   C27  C23  112.27  3.000
 A5B  O4   C27  C23  126.16  3.000
 A5B  H5   O3   C27  109.09  3.000
 A5B  H6   C22  C21  117.28  3.000
 A5B  H6   C22  C23  119.29  3.000
 A5B  C21  C22  C23  123.42  3.000
 A5B  H7   C21  C20  121.06  3.000
 A5B  H7   C21  C22  120.12  3.000
 A5B  C20  C21  C22  118.81  3.000
 A5B  N4   C20  C21  125.07  3.000
 A5B  C21  C20  C25  119.08  3.000
 A5B  N4   C20  C25  115.85  3.000
 A5B  H8   N4   C12  112.62  3.000
 A5B  H8   N4   C20  115.52  3.000
 A5B  C12  N4   C20  131.85  3.000
 A5B  N2   C12  N3   125.68  3.000
 A5B  N3   C12  N4   113.84  3.000
 A5B  N2   C12  N4   120.48  3.000
 A5B  C13  N3   C12  117.59  3.000
 A5B  C11  N2   C12  116.18  3.000
 A5B  H9   C11  C10  120.16  3.000
 A5B  H9   C11  N2   116.42  3.000
 A5B  C10  C11  N2   123.42  3.000
 A5B  C13  C10  C9   120.93  3.000
 A5B  C13  C10  C11  115.56  3.000
 A5B  C9   C10  C11  123.51  3.000
 A5B  H11  C9   H10  107.17  3.000
 A5B  H11  C9   N1   111.17  3.000
 A5B  H10  C9   N1   108.54  3.000
 A5B  H11  C9   C10  110.06  3.000
 A5B  H10  C9   C10  109.92  3.000
 A5B  N1   C9   C10  109.92  3.000
 A5B  C8   N1   C9   118.25  3.000
 A5B  C14  C13  C10  121.18  3.000
 A5B  C14  C13  N3   117.22  3.000
 A5B  C10  C13  N3   121.55  3.000
 A5B  C15  C14  C19  119.13  3.000
 A5B  C15  C14  C13  122.52  3.000
 A5B  C19  C14  C13  118.33  3.000
 A5B  H12  C19  C18  119.22  3.000
 A5B  H12  C19  C14  119.29  3.000
 A5B  C18  C19  C14  121.48  3.000
 A5B  H13  C18  C17  120.78  3.000
 A5B  H13  C18  C19  120.50  3.000
 A5B  C17  C18  C19  118.72  3.000
 A5B  C16  C17  CL1  119.41  3.000
 A5B  CL1  C17  C18  119.51  3.000
 A5B  C16  C17  C18  121.08  3.000
 A5B  H14  C16  C15  120.06  3.000
 A5B  H14  C16  C17  119.67  3.000
 A5B  C15  C16  C17  120.27  3.000
 A5B  C8   C15  C16  117.21  3.000
 A5B  C16  C15  C14  119.27  3.000
 A5B  C8   C15  C14  123.44  3.000
 A5B  C7   C8   C15  115.80  3.000
 A5B  C7   C8   N1   117.85  3.000
 A5B  C15  C8   N1   126.34  3.000
 A5B  C2   C7   C6   118.04  3.000
 A5B  C6   C7   C8   121.94  3.000
 A5B  C2   C7   C8   120.02  3.000
 A5B  C5   C6   F1   118.58  3.000
 A5B  C5   C6   C7   123.01  3.000
 A5B  F1   C6   C7   118.39  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   119.38  3.000
 A5B  C3   C4   C5   121.58  3.000
 A5B  H17  C3   C2   121.32  3.000
 A5B  H17  C3   C4   119.32  3.000
 A5B  C2   C3   C4   119.36  3.000
 A5B  O1   C2   C3   124.76  3.000
 A5B  C3   C2   C7   120.30  3.000
 A5B  O1   C2   C7   114.93  3.000
 A5B  C1   O1   C2   119.02  3.000
 A5B  H20  C1   H19  109.04  3.000
 A5B  H20  C1   H18  108.93  3.000
 A5B  H19  C1   H18  108.98  3.000
 A5B  H20  C1   O1   111.77  3.000
 A5B  H19  C1   O1   111.77  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  CONST_47  H5   O3   C27  C23   180.00   0.0  0
 A5B  Var_01    C12  N4   C20  C25  -179.08  30.0  2
 A5B  Var_02    N2   C12  N4   C20    -2.55  30.0  2
 A5B  Var_03    C25  C24  O2   C26     0.44  30.0  2
 A5B  Var_04    O4   C27  C23  C24    -4.98  30.0  2
 A5B  Var_05    H1   C26  O2   C24   179.70  30.0  3
 A5B  Var_06    H18  C1   O1   C2    177.44  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
 A5B  plan-5  H5   0.020

