# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 02:57:11 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: 4-{[9-chloro-7-(2,6-difluorophenyl)-5H-pyrimido[5,4-d][2]benzazepin-2-yl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2ncc3CN=C(c4cc(Cl)ccc4c3n2)c5c(F)cccc5F)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
 ZZL  ZZL  '4-{[9-chloro-7-(2,6-difluorophenyl)-5H-pyrimido[5,4-d][2]benzazepin-2-yl]amino}benzoic acid'  ligand  49  34  .  2021-08-25  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZZL
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
 ZZL  C13   C   CH2   0  -0.445  52.0152  30.5477  42.4775
 ZZL  C15   C   C     0   0.211  49.6898  30.6209  42.3135
 ZZL  C17   C   CR6   0   0.561  47.9902  28.7891  42.6455
 ZZL  C20   C   CR16  0  -0.225  45.9585  28.7266  41.4084
 ZZL  C21   C   CR16  0  -0.421  46.3146  29.8945  40.7485
 ZZL  C22   C   CR6   0   0.584  47.5193  30.4826  41.0715
 ZZL  C24   C   CR6   0   0.013  49.6146  32.0316  42.7749
 ZZL  C26   C   CR6   0  -0.033  48.4313  33.6674  44.0852
 ZZL  C28   C   CR16  0  -0.197  49.2746  34.6735  43.6350
 ZZL  O01   O   O     0  -0.448  50.2490  40.0604  37.8599
 ZZL  O03   O   OH1   0  -0.598  51.9777  40.2025  36.4596
 ZZL  C04   C   CR6   0  -0.102  51.7767  38.2467  37.7306
 ZZL  C05   C   CR16  0  -0.246  51.0925  37.4778  38.6685
 ZZL  C06   C   CR16  0  -0.300  51.5360  36.2240  39.0455
 ZZL  C07   C   CR6   0   0.377  52.7034  35.6991  38.4780
 ZZL  C09   C   CR6   0   0.607  52.8867  33.5095  39.6823
 ZZL  N10   N   N     0  -0.452  53.6466  32.4098  39.6489
 ZZL  C11   C   CR16  0  -0.038  53.3590  31.4756  40.5320
 ZZL  C12   C   CR6   0  -0.043  52.3322  31.5945  41.4614
 ZZL  N14   N   N     0  -0.313  50.7405  29.9298  42.1656
 ZZL  C16   C   CR6   0  -0.421  48.3920  29.9604  42.0169
 ZZL  C19   C   CR16  0  -0.424  46.7911  28.1639  42.3646
 ZZL  F23   F   F     0  -0.296  47.8888  31.6032  40.4408
 ZZL  C25   C   CR16  0  -0.233  48.5797  32.3660  43.6478
 ZZL  CL1   CL  CL    0  -0.107  47.1676  34.0499  45.1986
 ZZL  C29   C   CR16  0  -0.291  50.2813  34.3500  42.7477
 ZZL  C30   C   CR6   0   0.068  50.4844  33.0364  42.3223
 ZZL  C31   C   CR6   0   0.292  51.5900  32.7682  41.3881
 ZZL  N32   N   N     0  -0.489  51.8752  33.7219  40.5059
 ZZL  C33   C   CR16  0  -0.341  53.3938  36.4716  37.5319
 ZZL  C34   C   CR16  0  -0.249  52.9399  37.7195  37.1649
 ZZL  H131  H   HCH2  0   0.273  52.7845  29.7761  42.4746
 ZZL  H132  H   HCH2  0   0.266  52.0011  30.9902  43.4811
 ZZL  H19   H   HCR6  0   0.289  46.5143  27.2574  42.8852
 ZZL  H20   H   HCR6  0   0.286  45.0178  28.2483  41.1734
 ZZL  H21   H   HCR6  0   0.290  45.6740  30.3358  39.9971
 ZZL  H25   H   HCR6  0   0.285  47.8921  31.6039  43.9901
 ZZL  H28   H   HCR6  0   0.292  49.1479  35.6932  43.9712
 ZZL  H29   H   HCR6  0   0.275  50.9394  35.1297  42.3892
 ZZL  H03   H   HOH1  0   0.485  51.5894  41.0680  36.2647
 ZZL  H05   H   HCR6  0   0.265  50.1869  37.8600  39.1207
 ZZL  H34   H   HCR6  0   0.269  53.5065  38.2794  36.4340
 ZZL  H06   H   HCR6  0   0.294  50.9783  35.6567  39.7708
 ZZL  H08   H   HNH1  0   0.415  54.0481  34.1985  38.2222
 ZZL  H33   H   HCR6  0   0.277  54.2998  36.0841  37.0818
 ZZL  H11   H   HCR6  0   0.281  53.9776  30.5839  40.5170
 ZZL  N08   N   NH1   0  -0.776  53.2370  34.4581  38.7641
 ZZL  F18   F   F     0  -0.291  48.7850  28.2650  43.5820
 ZZL  C02   C   C     0   0.525  51.2467  39.5768  37.3754

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
 ZZL  C13  C12   single    1.493  0.020  1.493
 ZZL  C13  N14   single    1.451  0.020  1.451
 ZZL  C15  C24   single    1.486  0.020  1.486
 ZZL  C15  N14   double    1.266  0.020  1.266
 ZZL  C15  C16   single    1.486  0.020  1.486
 ZZL  C17  C16   aromatic  1.389  0.020  1.389
 ZZL  C17  F18   single    1.335  0.020  1.335
 ZZL  C17  C19   aromatic  1.381  0.020  1.381
 ZZL  C20  C21   aromatic  1.388  0.020  1.388
 ZZL  C20  C19   aromatic  1.387  0.020  1.387
 ZZL  C21  C22   aromatic  1.379  0.020  1.379
 ZZL  C22  C16   aromatic  1.389  0.020  1.389
 ZZL  C22  F23   single    1.338  0.020  1.338
 ZZL  C24  C25   aromatic  1.395  0.020  1.395
 ZZL  C24  C30   aromatic  1.404  0.020  1.404
 ZZL  C26  C28   aromatic  1.388  0.020  1.388
 ZZL  C26  C25   aromatic  1.381  0.020  1.381
 ZZL  C26  CL1   single    1.727  0.020  1.727
 ZZL  C28  C29   aromatic  1.380  0.020  1.380
 ZZL  O01  C02   double    1.210  0.020  1.210
 ZZL  C02  O03   single    1.328  0.020  1.328
 ZZL  C02  C04   single    1.475  0.020  1.475
 ZZL  C04  C05   aromatic  1.392  0.020  1.392
 ZZL  C04  C34   aromatic  1.397  0.020  1.397
 ZZL  C05  C06   aromatic  1.382  0.020  1.382
 ZZL  C06  C07   aromatic  1.400  0.020  1.400
 ZZL  C07  N08   single    1.381  0.020  1.381
 ZZL  C07  C33   aromatic  1.403  0.020  1.403
 ZZL  N08  C09   single    1.366  0.020  1.366
 ZZL  C09  N10   aromatic  1.337  0.020  1.337
 ZZL  C09  N32   aromatic  1.322  0.020  1.322
 ZZL  N10  C11   aromatic  1.317  0.020  1.317
 ZZL  C11  C12   aromatic  1.390  0.020  1.390
 ZZL  C12  C31   aromatic  1.391  0.020  1.391
 ZZL  C29  C30   aromatic  1.396  0.020  1.396
 ZZL  C30  C31   aromatic  1.472  0.020  1.472
 ZZL  C31  N32   aromatic  1.330  0.020  1.330
 ZZL  C33  C34   aromatic  1.378  0.020  1.378
 ZZL  C13  H131  single    0.970  0.020  1.090
 ZZL  C13  H132  single    0.970  0.020  1.090
 ZZL  C19  H19   single    0.930  0.020  1.080
 ZZL  C20  H20   single    0.930  0.020  1.080
 ZZL  C21  H21   single    0.930  0.020  1.080
 ZZL  C25  H25   single    0.930  0.020  1.080
 ZZL  C28  H28   single    0.930  0.020  1.080
 ZZL  C29  H29   single    0.930  0.020  1.080
 ZZL  O03  H03   single    0.850  0.020  0.980
 ZZL  C05  H05   single    0.930  0.020  1.080
 ZZL  C34  H34   single    0.930  0.020  1.080
 ZZL  C06  H06   single    0.930  0.020  1.080
 ZZL  N08  H08   single    0.860  0.020  1.020
 ZZL  C33  H33   single    0.930  0.020  1.080
 ZZL  C11  H11   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
 ZZL  H132  C13  H131  107.29  3.000
 ZZL  H132  C13  N14   110.94  3.000
 ZZL  H131  C13  N14   108.56  3.000
 ZZL  H132  C13  C12   110.03  3.000
 ZZL  H131  C13  C12   110.17  3.000
 ZZL  N14   C13  C12   109.81  3.000
 ZZL  C16   C15  N14   117.30  3.000
 ZZL  C16   C15  C24   116.08  3.000
 ZZL  N14   C15  C24   126.61  3.000
 ZZL  C19   C17  F18   118.79  3.000
 ZZL  C19   C17  C16   122.75  3.000
 ZZL  F18   C17  C16   118.44  3.000
 ZZL  H20   C20  C19   119.51  3.000
 ZZL  H20   C20  C21   119.48  3.000
 ZZL  C19   C20  C21   121.00  3.000
 ZZL  H21   C21  C22   120.41  3.000
 ZZL  H21   C21  C20   121.45  3.000
 ZZL  C22   C21  C20   118.14  3.000
 ZZL  F23   C22  C16   117.54  3.000
 ZZL  F23   C22  C21   119.21  3.000
 ZZL  C16   C22  C21   123.25  3.000
 ZZL  C30   C24  C25   119.34  3.000
 ZZL  C30   C24  C15   123.23  3.000
 ZZL  C25   C24  C15   117.35  3.000
 ZZL  CL1   C26  C25   119.44  3.000
 ZZL  CL1   C26  C28   119.55  3.000
 ZZL  C25   C26  C28   121.01  3.000
 ZZL  H28   C28  C29   120.42  3.000
 ZZL  H28   C28  C26   120.78  3.000
 ZZL  C29   C28  C26   118.80  3.000
 ZZL  H03   O03  C02   109.82  3.000
 ZZL  C34   C04  C05   118.26  3.000
 ZZL  C34   C04  C02   122.82  3.000
 ZZL  C05   C04  C02   118.92  3.000
 ZZL  H05   C05  C06   118.35  3.000
 ZZL  H05   C05  C04   119.85  3.000
 ZZL  C06   C05  C04   121.80  3.000
 ZZL  H06   C06  C07   120.50  3.000
 ZZL  H06   C06  C05   119.70  3.000
 ZZL  C07   C06  C05   119.80  3.000
 ZZL  C33   C07  N08   116.39  3.000
 ZZL  C33   C07  C06   118.50  3.000
 ZZL  N08   C07  C06   125.11  3.000
 ZZL  N32   C09  N10   125.64  3.000
 ZZL  N32   C09  N08   120.24  3.000
 ZZL  N10   C09  N08   114.12  3.000
 ZZL  C11   N10  C09   116.26  3.000
 ZZL  H11   C11  C12   120.03  3.000
 ZZL  H11   C11  N10   116.68  3.000
 ZZL  C12   C11  N10   123.28  3.000
 ZZL  C31   C12  C11   115.54  3.000
 ZZL  C31   C12  C13   120.96  3.000
 ZZL  C11   C12  C13   123.50  3.000
 ZZL  C15   N14  C13   118.13  3.000
 ZZL  C22   C16  C17   116.33  3.000
 ZZL  C22   C16  C15   121.17  3.000
 ZZL  C17   C16  C15   122.49  3.000
 ZZL  H19   C19  C20   121.22  3.000
 ZZL  H19   C19  C17   120.25  3.000
 ZZL  C20   C19  C17   118.53  3.000
 ZZL  H25   C25  C26   119.69  3.000
 ZZL  H25   C25  C24   120.04  3.000
 ZZL  C26   C25  C24   120.26  3.000
 ZZL  H29   C29  C30   119.27  3.000
 ZZL  H29   C29  C28   119.21  3.000
 ZZL  C30   C29  C28   121.51  3.000
 ZZL  C31   C30  C29   118.31  3.000
 ZZL  C31   C30  C24   122.65  3.000
 ZZL  C29   C30  C24   119.03  3.000
 ZZL  N32   C31  C30   116.83  3.000
 ZZL  N32   C31  C12   121.72  3.000
 ZZL  C30   C31  C12   121.41  3.000
 ZZL  C31   N32  C09   117.52  3.000
 ZZL  H33   C33  C34   119.27  3.000
 ZZL  H33   C33  C07   119.65  3.000
 ZZL  C34   C33  C07   121.08  3.000
 ZZL  H34   C34  C33   118.46  3.000
 ZZL  H34   C34  C04   120.98  3.000
 ZZL  C33   C34  C04   120.56  3.000
 ZZL  H08   N08  C09   112.85  3.000
 ZZL  H08   N08  C07   115.49  3.000
 ZZL  C09   N08  C07   131.63  3.000
 ZZL  C04   C02  O03   113.14  3.000
 ZZL  C04   C02  O01   124.07  3.000
 ZZL  O03   C02  O01   122.79  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
 ZZL  CONST_01  C21  C22  C16  C17    0.00   0.0  0
 ZZL  CONST_02  C21  C20  C19  C17    0.00   0.0  0
 ZZL  CONST_03  C16  C22  C21  C20    0.00   0.0  0
 ZZL  CONST_04  C16  C17  C19  C20    0.00   0.0  0
 ZZL  CONST_05  C19  C20  C21  C22    0.00   0.0  0
 ZZL  CONST_06  C19  C17  C16  C22    0.00   0.0  0
 ZZL  CONST_07  C28  C26  C25  C24    0.00   0.0  0
 ZZL  CONST_08  C30  C29  C28  C26    0.00   0.0  0
 ZZL  CONST_09  C07  C06  C05  C04    0.00   0.0  0
 ZZL  CONST_10  C07  C33  C34  C04    0.00   0.0  0
 ZZL  CONST_11  C33  C34  C04  C05    0.00   0.0  0
 ZZL  CONST_12  C33  C07  C06  C05    0.00   0.0  0
 ZZL  CONST_13  C34  C04  C05  C06    0.00   0.0  0
 ZZL  CONST_14  C34  C33  C07  C06    0.00   0.0  0
 ZZL  CONST_15  C12  C11  N10  C09    0.00   0.0  0
 ZZL  CONST_16  C31  N32  C09  N10    0.00   0.0  0
 ZZL  CONST_17  N32  C09  N10  C11    0.00   0.0  0
 ZZL  CONST_18  C29  C28  C26  C25    0.00   0.0  0
 ZZL  CONST_19  C19  C17  C16  C15  180.00   0.0  0
 ZZL  CONST_20  C21  C22  C16  C15  180.00   0.0  0
 ZZL  CONST_21  F18  C17  C16  C15    0.00   0.0  0
 ZZL  CONST_22  F23  C22  C16  C15    0.00   0.0  0
 ZZL  CONST_23  F23  C22  C16  C17  180.00   0.0  0
 ZZL  CONST_24  F23  C22  C21  C20  180.00   0.0  0
 ZZL  CONST_25  F18  C17  C19  C20  180.00   0.0  0
 ZZL  CONST_26  F18  C17  C16  C22  180.00   0.0  0
 ZZL  CONST_27  CL1  C26  C25  C24  180.00   0.0  0
 ZZL  CONST_28  C06  C05  C04  C02  180.00   0.0  0
 ZZL  CONST_29  C33  C34  C04  C02  180.00   0.0  0
 ZZL  CONST_30  N08  C07  C06  C05  180.00   0.0  0
 ZZL  CONST_31  C34  C33  C07  N08  180.00   0.0  0
 ZZL  CONST_32  C11  N10  C09  N08  180.00   0.0  0
 ZZL  CONST_33  C31  N32  C09  N08  180.00   0.0  0
 ZZL  CONST_34  C29  C28  C26  CL1  180.00   0.0  0
 ZZL  CONST_35  H20  C20  C19  C17  180.00   0.0  0
 ZZL  CONST_36  H19  C19  C20  C21  180.00   0.0  0
 ZZL  CONST_37  H29  C29  C28  C26  180.00   0.0  0
 ZZL  CONST_38  H25  C25  C26  C28  180.00   0.0  0
 ZZL  CONST_39  H06  C06  C05  C04  180.00   0.0  0
 ZZL  CONST_40  H33  C33  C34  C04  180.00   0.0  0
 ZZL  CONST_41  H34  C34  C04  C05  180.00   0.0  0
 ZZL  CONST_42  H05  C05  C06  C07  180.00   0.0  0
 ZZL  CONST_43  H11  C11  N10  C09  180.00   0.0  0
 ZZL  CONST_44  H21  C21  C22  C16  180.00   0.0  0
 ZZL  CONST_45  H28  C28  C26  C25  180.00   0.0  0
 ZZL  CONST_46  H03  O03  C02  C04  180.00   0.0  0
 ZZL  Var_01    C09  N08  C07  C06   -6.04  30.0  2
 ZZL  Var_02    N10  C09  N08  C07  179.31  30.0  2
 ZZL  Var_03    C05  C04  C02  O01    0.76  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
 ZZL  plan-1  C15  0.020
 ZZL  plan-1  C17  0.020
 ZZL  plan-1  C20  0.020
 ZZL  plan-1  C21  0.020
 ZZL  plan-1  C22  0.020
 ZZL  plan-1  C16  0.020
 ZZL  plan-1  C19  0.020
 ZZL  plan-1  F23  0.020
 ZZL  plan-1  H19  0.020
 ZZL  plan-1  H20  0.020
 ZZL  plan-1  H21  0.020
 ZZL  plan-1  F18  0.020
 ZZL  plan-2  C04  0.020
 ZZL  plan-2  C05  0.020
 ZZL  plan-2  C06  0.020
 ZZL  plan-2  C07  0.020
 ZZL  plan-2  C33  0.020
 ZZL  plan-2  C34  0.020
 ZZL  plan-2  H05  0.020
 ZZL  plan-2  H34  0.020
 ZZL  plan-2  H06  0.020
 ZZL  plan-2  H33  0.020
 ZZL  plan-2  N08  0.020
 ZZL  plan-2  C02  0.020
 ZZL  plan-3  C15  0.020
 ZZL  plan-3  C24  0.020
 ZZL  plan-3  C26  0.020
 ZZL  plan-3  C28  0.020
 ZZL  plan-3  C25  0.020
 ZZL  plan-3  CL1  0.020
 ZZL  plan-3  C29  0.020
 ZZL  plan-3  C30  0.020
 ZZL  plan-3  C31  0.020
 ZZL  plan-3  H25  0.020
 ZZL  plan-3  H28  0.020
 ZZL  plan-3  H29  0.020
 ZZL  plan-4  C13  0.020
 ZZL  plan-4  C09  0.020
 ZZL  plan-4  N10  0.020
 ZZL  plan-4  C11  0.020
 ZZL  plan-4  C12  0.020
 ZZL  plan-4  C30  0.020
 ZZL  plan-4  C31  0.020
 ZZL  plan-4  N32  0.020
 ZZL  plan-4  H11  0.020
 ZZL  plan-4  N08  0.020
 ZZL  plan-5  O01  0.020
 ZZL  plan-5  O03  0.020
 ZZL  plan-5  C04  0.020
 ZZL  plan-5  H03  0.020
 ZZL  plan-5  C02  0.020

