# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 18:44:21 2020
#   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  48  34  .  2021-08-25  2021-08-25  
;
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  -0.442   1.3857  -0.2285  -2.6000
 ZZL  C15   C   C      0   0.210   2.8492  -0.6732  -0.8387
 ZZL  C17   C   CR6    0   0.560   4.8494  -2.2072  -0.7331
 ZZL  C20   C   CR16   0  -0.225   5.4282  -3.3706   1.2602
 ZZL  C21   C   CR16   0  -0.420   4.3556  -2.7886   1.9213
 ZZL  C22   C   CR6    0   0.585   3.5549  -1.9141   1.2173
 ZZL  C24   C   CR6    0   0.013   2.7064   0.6881  -0.2598
 ZZL  C26   C   CR6    0  -0.033   3.7891   2.5454   0.8208
 ZZL  C28   C   CR16   0  -0.197   2.5733   3.1976   0.9696
 ZZL  O01   O   O      0  -0.597  -9.1345  -1.1333  -0.5263
 ZZL  O03   O   OC    -1  -0.598  -9.3683   0.0602   1.3413
 ZZL  C04   C   C      0  -0.115  -7.2155  -0.1189   0.3971
 ZZL  C05   C   C1     0  -0.281  -6.3832  -0.5949  -0.6092
 ZZL  C06   C   C1     0  -0.304  -5.0204  -0.3326  -0.6336
 ZZL  C07   C   C      0   0.354  -4.4450   0.4355   0.3815
 ZZL  C09   C   CR6    0   0.604  -2.0319   0.4822  -0.3176
 ZZL  N10   N   N      0  -0.460  -2.1863  -0.2491  -1.4174
 ZZL  C11   C   CR16   0  -0.013  -1.0953  -0.4702  -2.1327
 ZZL  C12   C   CR6    0  -0.044   0.1544   0.0150  -1.7907
 ZZL  N14   N   N      0  -0.314   2.2779  -1.1159  -1.8780
 ZZL  C16   C   CR6    0  -0.418   3.7653  -1.5954  -0.1178
 ZZL  C19   C   CR16   0  -0.424   5.6872  -3.0837  -0.0718
 ZZL  C25   C   CR16   0  -0.233   3.8595   1.2975   0.2336
 ZZL  CL1   CL  CL     0  -0.109   5.2353   3.2969   1.3935
 ZZL  C29   C   CR16   0  -0.291   1.4270   2.5830   0.5061
 ZZL  C30   C   CR6    0   0.071   1.4716   1.3421  -0.1302
 ZZL  C31   C   CR6    0   0.249   0.2074   0.7519  -0.6047
 ZZL  N32   N   N      0  -0.485  -0.8753   0.9889   0.1164
 ZZL  C33   C   C1     0  -0.347  -5.2751   0.9203   1.4004
 ZZL  C34   C   C1     0  -0.280  -6.6292   0.6472   1.4031
 ZZL  H131  H   HCH2   0   0.271   1.1223  -0.6977  -3.5474
 ZZL  H132  H   HCH2   0   0.265   1.8798   0.7226  -2.8334
 ZZL  H19   H   HCR6   0   0.289   6.5255  -3.5293  -0.5894
 ZZL  H20   H   HCR6   0   0.285   6.0711  -4.0583   1.7918
 ZZL  H21   H   HCR6   0   0.290   4.1432  -3.0127   2.9576
 ZZL  H25   H   HCR6   0   0.284   4.8140   0.7943   0.1528
 ZZL  H28   H   HCR6   0   0.291   2.5208   4.1683   1.4428
 ZZL  H29   H   HCR6   0   0.275   0.4750   3.0812   0.6278
 ZZL  H05   H   H      0   0.241  -6.8092  -1.1913  -1.4055
 ZZL  H34   H   H      0   0.243  -7.2423   1.0368   2.2049
 ZZL  H06   H   H      0   0.277  -4.4147  -0.7248  -1.4336
 ZZL  H08   H   HNH1   0   0.409  -2.8500   1.3263   1.2792
 ZZL  H33   H   H      0   0.260  -4.8468   1.5149   2.1998
 ZZL  H11   H   HCR6   0   0.275  -1.2217  -1.0606  -3.0348
 ZZL  N08   N   NH1    0  -0.773  -3.0980   0.7680   0.4760
 ZZL  F18   F   F      0  -0.292   5.1069  -1.9122  -2.0100
 ZZL  F23   F   F      0  -0.296   2.5077  -1.3507   1.8305
 ZZL  C02   C   C      0   0.391  -8.7030  -0.4236   0.4039

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    1.336  0.020  1.336
 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  1.394  0.020  1.394
 ZZL  C24  C30   aromatic  1.403  0.020  1.403
 ZZL  C26  C28   aromatic  1.388  0.020  1.388
 ZZL  C26  C25   aromatic  1.381  0.020  1.381
 ZZL  C26  CL1   single    1.728  0.020  1.728
 ZZL  C28  C29   aromatic  1.381  0.020  1.381
 ZZL  O01  C02   deloc     1.247  0.020  1.247
 ZZL  C02  O03   deloc     1.247  0.020  1.247
 ZZL  C02  C04   single    1.518  0.020  1.518
 ZZL  C04  C05   aromatic  1.390  0.020  1.390
 ZZL  C04  C34   aromatic  1.394  0.020  1.394
 ZZL  C05  C06   aromatic  1.388  0.020  1.388
 ZZL  C06  C07   aromatic  1.397  0.020  1.397
 ZZL  C07  N08   single    1.391  0.020  1.391
 ZZL  C07  C33   aromatic  1.401  0.020  1.401
 ZZL  N08  C09   single    1.359  0.020  1.359
 ZZL  C09  N10   aromatic  1.330  0.020  1.330
 ZZL  C09  N32   aromatic  1.335  0.020  1.335
 ZZL  N10  C11   aromatic  1.323  0.020  1.323
 ZZL  C11  C12   aromatic  1.384  0.020  1.384
 ZZL  C12  C31   aromatic  1.397  0.020  1.397
 ZZL  C29  C30   aromatic  1.395  0.020  1.395
 ZZL  C30  C31   aromatic  1.474  0.020  1.474
 ZZL  C31  N32   aromatic  1.322  0.020  1.322
 ZZL  C33  C34   aromatic  1.381  0.020  1.381
 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  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   111.05  3.000
 ZZL  H131  C13  N14   108.54  3.000
 ZZL  H132  C13  C12   110.21  3.000
 ZZL  H131  C13  C12   110.01  3.000
 ZZL  N14   C13  C12   109.70  3.000
 ZZL  C16   C15  N14   117.34  3.000
 ZZL  C16   C15  C24   116.02  3.000
 ZZL  N14   C15  C24   126.64  3.000
 ZZL  C19   C17  F18   118.75  3.000
 ZZL  C19   C17  C16   122.76  3.000
 ZZL  F18   C17  C16   118.48  3.000
 ZZL  H20   C20  C19   119.53  3.000
 ZZL  H20   C20  C21   119.48  3.000
 ZZL  C19   C20  C21   121.00  3.000
 ZZL  H21   C21  C22   120.44  3.000
 ZZL  H21   C21  C20   121.42  3.000
 ZZL  C22   C21  C20   118.13  3.000
 ZZL  F23   C22  C16   117.55  3.000
 ZZL  F23   C22  C21   119.18  3.000
 ZZL  C16   C22  C21   123.26  3.000
 ZZL  C30   C24  C25   119.42  3.000
 ZZL  C30   C24  C15   123.19  3.000
 ZZL  C25   C24  C15   117.30  3.000
 ZZL  CL1   C26  C25   119.43  3.000
 ZZL  CL1   C26  C28   119.57  3.000
 ZZL  C25   C26  C28   121.00  3.000
 ZZL  H28   C28  C29   120.41  3.000
 ZZL  H28   C28  C26   120.76  3.000
 ZZL  C29   C28  C26   118.83  3.000
 ZZL  C34   C04  C05   117.32  3.000
 ZZL  C34   C04  C02   121.28  3.000
 ZZL  C05   C04  C02   121.41  3.000
 ZZL  H05   C05  C06   118.53  3.000
 ZZL  H05   C05  C04   119.06  3.000
 ZZL  C06   C05  C04   122.41  3.000
 ZZL  H06   C06  C07   120.55  3.000
 ZZL  H06   C06  C05   119.75  3.000
 ZZL  C07   C06  C05   119.71  3.000
 ZZL  C33   C07  N08   116.22  3.000
 ZZL  C33   C07  C06   118.34  3.000
 ZZL  N08   C07  C06   125.44  3.000
 ZZL  N32   C09  N10   125.32  3.000
 ZZL  N32   C09  N08   114.19  3.000
 ZZL  N10   C09  N08   120.49  3.000
 ZZL  C11   N10  C09   116.31  3.000
 ZZL  H11   C11  C12   120.09  3.000
 ZZL  H11   C11  N10   116.37  3.000
 ZZL  C12   C11  N10   123.54  3.000
 ZZL  C31   C12  C11   115.40  3.000
 ZZL  C31   C12  C13   120.98  3.000
 ZZL  C11   C12  C13   123.61  3.000
 ZZL  C15   N14  C13   118.18  3.000
 ZZL  C22   C16  C17   116.30  3.000
 ZZL  C22   C16  C15   121.02  3.000
 ZZL  C17   C16  C15   122.66  3.000
 ZZL  H19   C19  C20   121.28  3.000
 ZZL  H19   C19  C17   120.17  3.000
 ZZL  C20   C19  C17   118.55  3.000
 ZZL  H25   C25  C26   119.80  3.000
 ZZL  H25   C25  C24   119.99  3.000
 ZZL  C26   C25  C24   120.21  3.000
 ZZL  H29   C29  C30   119.29  3.000
 ZZL  H29   C29  C28   119.21  3.000
 ZZL  C30   C29  C28   121.49  3.000
 ZZL  C31   C30  C29   118.40  3.000
 ZZL  C31   C30  C24   122.58  3.000
 ZZL  C29   C30  C24   119.00  3.000
 ZZL  N32   C31  C30   117.07  3.000
 ZZL  N32   C31  C12   121.76  3.000
 ZZL  C30   C31  C12   121.13  3.000
 ZZL  C31   N32  C09   117.64  3.000
 ZZL  H33   C33  C34   119.61  3.000
 ZZL  H33   C33  C07   119.47  3.000
 ZZL  C34   C33  C07   120.93  3.000
 ZZL  H34   C34  C33   119.06  3.000
 ZZL  H34   C34  C04   119.63  3.000
 ZZL  C33   C34  C04   121.31  3.000
 ZZL  H08   N08  C09   112.85  3.000
 ZZL  H08   N08  C07   115.11  3.000
 ZZL  C09   N08  C07   132.04  3.000
 ZZL  C04   C02  O03   116.62  3.000
 ZZL  C04   C02  O01   116.73  3.000
 ZZL  O03   C02  O01   126.64  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  Var_01    C09  N08  C07  C06    0.41  30.0  2
 ZZL  Var_02    N10  C09  N08  C07   -0.20  30.0  2
 ZZL  Var_03    C05  C04  C02  O01    0.86  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  H19  0.020
 ZZL  plan-1  H20  0.020
 ZZL  plan-1  H21  0.020
 ZZL  plan-1  F18  0.020
 ZZL  plan-1  F23  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  C02  0.020

