# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:03:22 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 3-benzyl-8-chloro-2-hydroxy-4H-pyrimido[2,1-b][1,3]benzothiazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(Cc2ccccc2)C(=O)N3C(=N1)Sc4cc(Cl)ccc34
#
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
 DZJ  DZJ  3-benzyl-8-chloro-2-hydroxy-4H-pyrimido[2,1-b][1,3]benzothiazol-4-one  ligand  34  23  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DZJ
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
 DZJ  C1   C   CR6   0  -0.045  -4.4949  -0.7138  -0.0921
 DZJ  C2   C   CR16  0  -0.206  -3.6425  -1.5521  -0.7996
 DZJ  C3   C   CR16  0  -0.285  -2.2994  -1.2415  -0.9369
 DZJ  C12  C   CR6   0   0.148   3.9223  -0.7060  -0.3862
 DZJ  C13  C   CR16  0  -0.301   3.5212  -1.9640   0.0632
 DZJ  C14  C   CR16  0  -0.240   4.2601  -2.6454   1.0193
 DZJ  C15  C   CR16  0  -0.273   5.4164  -2.0795   1.5439
 DZJ  C16  C   CR16  0  -0.241   5.8261  -0.8298   1.1012
 DZJ  C17  C   CR16  0  -0.314   5.0824  -0.1494   0.1441
 DZJ  C4   C   CR56  0   0.544  -1.8187  -0.0759  -0.3526
 DZJ  C5   C   CR56  0  -0.304  -2.6938   0.7497   0.3543
 DZJ  C6   C   CR16  0  -0.231  -4.0370   0.4506   0.4980
 DZJ  N1   N   N     0  -0.667  -0.5147   0.4422  -0.3528
 DZJ  C7   C   CR56  0   0.340  -0.3892   1.6127   0.3282
 DZJ  S1   S   S2    0   0.294  -1.8905   2.1488   1.0061
 DZJ  C8   C   CR6   0   0.580   0.6164  -0.1494  -0.9787
 DZJ  C9   C   CR6   0  -0.218   1.8263   0.5860  -0.8192
 DZJ  C10  C   CR6   0   0.495   1.8065   1.7539  -0.0958
 DZJ  N2   N   N     0  -0.503   0.7042   2.2770   0.4759
 DZJ  CL1  CL  CL    0  -0.107  -6.1649  -1.1319   0.0565
 DZJ  H1   H   HCR6  0   0.294  -4.0226  -2.4576  -1.2508
 DZJ  H2   H   HCR6  0   0.306  -1.6564  -1.9035  -1.4902
 DZJ  H3   H   HCH2  0   0.269   3.6899   0.8508  -1.8357
 DZJ  H4   H   HCH2  0   0.272   2.8495  -0.6266  -2.2353
 DZJ  H5   H   HCR6  0   0.248   2.6242  -2.4168  -0.3422
 DZJ  H6   H   HCR6  0   0.252   3.9357  -3.6227   1.3534
 DZJ  H7   H   HCR6  0   0.253   5.9941  -2.6115   2.2888
 DZJ  H8   H   HCR6  0   0.252   6.7269  -0.3808   1.5003
 DZJ  H9   H   HCR6  0   0.244   5.4095   0.8263  -0.1936
 DZJ  H10  H   HCR6  0   0.305  -4.6983   1.1033   1.0508
 DZJ  H11  H   HOH1  0   0.485   2.7504   3.2313   0.5897
 DZJ  O1   O   OH1   0  -0.587   2.9279   2.4356   0.0694
 DZJ  O2   O   O     0  -0.474   0.4829  -1.2007  -1.5840
 DZJ  C11  C   CH2   0  -0.586   3.0976   0.0401  -1.4086

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
 DZJ  S1   C7   single    1.732  0.020  1.732
 DZJ  S1   C5   single    1.740  0.020  1.740
 DZJ  N2   C7   double    1.288  0.020  1.288
 DZJ  N2   C10  single    1.347  0.020  1.347
 DZJ  O1   C10  single    1.323  0.020  1.323
 DZJ  C7   N1   single    1.360  0.020  1.360
 DZJ  C6   C5   aromatic  1.384  0.020  1.384
 DZJ  C6   C1   aromatic  1.383  0.020  1.383
 DZJ  C5   C4   aromatic  1.395  0.020  1.395
 DZJ  C10  C9   double    1.374  0.020  1.374
 DZJ  CL1  C1   single    1.728  0.020  1.728
 DZJ  N1   C4   single    1.403  0.020  1.403
 DZJ  N1   C8   single    1.422  0.020  1.422
 DZJ  C1   C2   aromatic  1.389  0.020  1.389
 DZJ  C4   C3   aromatic  1.390  0.020  1.390
 DZJ  C9   C8   single    1.425  0.020  1.425
 DZJ  C9   C11  single    1.504  0.020  1.504
 DZJ  C8   O2   double    1.220  0.020  1.220
 DZJ  C2   C3   aromatic  1.385  0.020  1.385
 DZJ  C11  C12  single    1.511  0.020  1.511
 DZJ  C17  C12  aromatic  1.392  0.020  1.392
 DZJ  C17  C16  aromatic  1.390  0.020  1.390
 DZJ  C12  C13  aromatic  1.395  0.020  1.395
 DZJ  C16  C15  aromatic  1.388  0.020  1.388
 DZJ  C13  C14  aromatic  1.387  0.020  1.387
 DZJ  C15  C14  aromatic  1.390  0.020  1.390
 DZJ  C2   H1   single    0.930  0.020  1.080
 DZJ  C3   H2   single    0.930  0.020  1.080
 DZJ  C11  H3   single    0.970  0.020  1.090
 DZJ  C11  H4   single    0.970  0.020  1.090
 DZJ  C13  H5   single    0.930  0.020  1.080
 DZJ  C14  H6   single    0.930  0.020  1.080
 DZJ  C15  H7   single    0.930  0.020  1.080
 DZJ  C16  H8   single    0.930  0.020  1.080
 DZJ  C17  H9   single    0.930  0.020  1.080
 DZJ  C6   H10  single    0.930  0.020  1.080
 DZJ  O1   H11  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
 DZJ  CL1  C1   C6   119.14  3.000
 DZJ  CL1  C1   C2   119.40  3.000
 DZJ  C6   C1   C2   121.47  3.000
 DZJ  H1   C2   C3   119.18  3.000
 DZJ  H1   C2   C1   120.15  3.000
 DZJ  C3   C2   C1   120.67  3.000
 DZJ  H2   C3   C4   121.71  3.000
 DZJ  H2   C3   C2   119.50  3.000
 DZJ  C4   C3   C2   118.79  3.000
 DZJ  C17  C12  C13  118.53  3.000
 DZJ  C13  C12  C11  120.43  3.000
 DZJ  C17  C12  C11  121.02  3.000
 DZJ  H5   C13  C14  119.58  3.000
 DZJ  H5   C13  C12  119.63  3.000
 DZJ  C14  C13  C12  120.79  3.000
 DZJ  H6   C14  C15  120.02  3.000
 DZJ  H6   C14  C13  119.77  3.000
 DZJ  C15  C14  C13  120.21  3.000
 DZJ  H7   C15  C16  120.30  3.000
 DZJ  H7   C15  C14  120.24  3.000
 DZJ  C16  C15  C14  119.46  3.000
 DZJ  H8   C16  C17  119.73  3.000
 DZJ  H8   C16  C15  120.10  3.000
 DZJ  C17  C16  C15  120.17  3.000
 DZJ  H9   C17  C16  119.61  3.000
 DZJ  H9   C17  C12  119.55  3.000
 DZJ  C16  C17  C12  120.84  3.000
 DZJ  N1   C4   C5   111.38  3.000
 DZJ  N1   C4   C3   129.13  3.000
 DZJ  C5   C4   C3   119.50  3.000
 DZJ  S1   C5   C6   125.67  3.000
 DZJ  C6   C5   C4   122.25  3.000
 DZJ  S1   C5   C4   112.08  3.000
 DZJ  H10  C6   C5   121.09  3.000
 DZJ  H10  C6   C1   121.58  3.000
 DZJ  C5   C6   C1   117.32  3.000
 DZJ  C8   N1   C7   120.34  3.000
 DZJ  C8   N1   C4   125.86  3.000
 DZJ  C7   N1   C4   113.79  3.000
 DZJ  N2   C7   S1   122.09  3.000
 DZJ  N2   C7   N1   125.43  3.000
 DZJ  S1   C7   N1   112.48  3.000
 DZJ  C7   S1   C5    90.27  3.000
 DZJ  C9   C8   N1   114.30  3.000
 DZJ  C9   C8   O2   126.38  3.000
 DZJ  N1   C8   O2   119.32  3.000
 DZJ  C10  C9   C8   119.04  3.000
 DZJ  C8   C9   C11  119.12  3.000
 DZJ  C10  C9   C11  121.81  3.000
 DZJ  N2   C10  C9   124.42  3.000
 DZJ  C9   C10  O1   119.45  3.000
 DZJ  N2   C10  O1   116.13  3.000
 DZJ  C10  N2   C7   116.46  3.000
 DZJ  H11  O1   C10  109.61  3.000
 DZJ  H4   C11  H3   106.32  3.000
 DZJ  H4   C11  C9   109.07  3.000
 DZJ  H3   C11  C9   110.04  3.000
 DZJ  H4   C11  C12  109.59  3.000
 DZJ  H3   C11  C12  109.61  3.000
 DZJ  C9   C11  C12  112.06  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
 DZJ  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 DZJ  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 DZJ  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 DZJ  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 DZJ  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 DZJ  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 DZJ  CONST_07  C15  C16  C17  C12    0.00   0.0  0
 DZJ  CONST_08  C15  C14  C13  C12    0.00   0.0  0
 DZJ  CONST_09  C16  C17  C12  C13    0.00   0.0  0
 DZJ  CONST_10  C16  C15  C14  C13    0.00   0.0  0
 DZJ  CONST_11  C17  C12  C13  C14    0.00   0.0  0
 DZJ  CONST_12  C17  C16  C15  C14    0.00   0.0  0
 DZJ  CONST_13  S1   C7   N1   C4     0.00   0.0  0
 DZJ  CONST_14  N2   C7   N1   C4   180.00   0.0  0
 DZJ  CONST_15  C9   C8   N1   C4   180.00   0.0  0
 DZJ  CONST_16  C10  N2   C7   N1     0.00   0.0  0
 DZJ  CONST_17  C9   C8   N1   C7     0.00   0.0  0
 DZJ  CONST_18  C10  N2   C7   S1   180.00   0.0  0
 DZJ  CONST_19  C8   N1   C7   S1   180.00   0.0  0
 DZJ  CONST_20  N2   C7   N1   C8     0.00   0.0  0
 DZJ  CONST_21  CL1  C1   C2   C3   180.00   0.0  0
 DZJ  CONST_22  C16  C17  C12  C11  180.00   0.0  0
 DZJ  CONST_23  C14  C13  C12  C11  180.00   0.0  0
 DZJ  CONST_24  CL1  C1   C6   C5   180.00   0.0  0
 DZJ  CONST_25  C7   N1   C8   O2   180.00   0.0  0
 DZJ  CONST_26  C4   N1   C8   O2     0.00   0.0  0
 DZJ  CONST_27  H2   C3   C2   C1   180.00   0.0  0
 DZJ  CONST_28  H10  C6   C1   C2   180.00   0.0  0
 DZJ  CONST_29  H8   C16  C17  C12  180.00   0.0  0
 DZJ  CONST_30  H6   C14  C13  C12  180.00   0.0  0
 DZJ  CONST_31  H9   C17  C12  C13  180.00   0.0  0
 DZJ  CONST_32  H7   C15  C14  C13  180.00   0.0  0
 DZJ  CONST_33  H5   C13  C14  C15  180.00   0.0  0
 DZJ  CONST_34  H1   C2   C3   C4   180.00   0.0  0
 DZJ  Var_01    C10  C9   C11  C12   80.75  30.0  3
 DZJ  Var_02    C9   C11  C12  C13   73.10  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
 DZJ  plan-1  C12  0.020
 DZJ  plan-1  C13  0.020
 DZJ  plan-1  C14  0.020
 DZJ  plan-1  C15  0.020
 DZJ  plan-1  C16  0.020
 DZJ  plan-1  C17  0.020
 DZJ  plan-1  H5   0.020
 DZJ  plan-1  H6   0.020
 DZJ  plan-1  H7   0.020
 DZJ  plan-1  H8   0.020
 DZJ  plan-1  H9   0.020
 DZJ  plan-1  C11  0.020
 DZJ  plan-2  C1   0.020
 DZJ  plan-2  C2   0.020
 DZJ  plan-2  C3   0.020
 DZJ  plan-2  C4   0.020
 DZJ  plan-2  C5   0.020
 DZJ  plan-2  C6   0.020
 DZJ  plan-2  N1   0.020
 DZJ  plan-2  C7   0.020
 DZJ  plan-2  S1   0.020
 DZJ  plan-2  C8   0.020
 DZJ  plan-2  C9   0.020
 DZJ  plan-2  C10  0.020
 DZJ  plan-2  N2   0.020
 DZJ  plan-2  CL1  0.020
 DZJ  plan-2  H1   0.020
 DZJ  plan-2  H2   0.020
 DZJ  plan-2  H10  0.020
 DZJ  plan-2  O1   0.020
 DZJ  plan-2  O2   0.020
 DZJ  plan-2  C11  0.020

