# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:45:55 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1c(CN2CCOCC2)nc(nc1c3ccc(F)cc3Br)c4sccn4
#
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
 5J6  5J6  'methyl 4-(2-bromo-4-fluorophenyl)-6-(morpholin-4-ylmethyl)-2-(1,3-thiazol-2-yl)pyrimidine-5-carboxylate'  ligand  48  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5J6
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
 5J6  F1   F   F     0  -0.305  -5.3018  -2.2831  -0.8084
 5J6  C27  C   CR6   0   0.540  -4.1455  -1.7054  -0.4651
 5J6  C26  C   CR16  0  -0.382  -3.3864  -1.1161  -1.4589
 5J6  C25  C   CR6   0  -0.122  -2.1891  -0.5220  -1.0945
 5J6  BR1  BR  BR    0  -0.010  -1.1193   0.2594  -2.4305
 5J6  C28  C   CR16  0  -0.400  -3.7538  -1.7207   0.8583
 5J6  C29  C   CR16  0  -0.264  -2.5514  -1.1183   1.1921
 5J6  C24  C   CR6   0   0.065  -1.7563  -0.5126   0.2268
 5J6  C6   C   CR6   0   0.272  -0.4776   0.1274   0.6194
 5J6  N5   N   N     0  -0.414  -0.5036   1.4331   0.8433
 5J6  C4   C   CR6   0   0.386   0.6328   2.0066   1.2059
 5J6  C15  C   CR5   0  -0.055   0.5652   3.4453   1.4622
 5J6  S19  S   S2    0   0.287  -0.9329   4.2803   1.2818
 5J6  C18  C   CR15  0  -0.493  -0.1462   5.7264   1.7264
 5J6  C17  C   CR15  0  -0.021   1.1716   5.4817   1.9758
 5J6  N16  N   N     0  -0.363   1.5628   4.1907   1.8230
 5J6  N3   N   N     0  -0.417   1.8049   1.4017   1.3338
 5J6  C7   C   CR6   0  -0.108   0.6897  -0.6110   0.7662
 5J6  C20  C   C     0   0.510   0.6839  -2.0827   0.5259
 5J6  O22  O   O2    0  -0.443   1.0587  -2.7400   1.6098
 5J6  C23  C   CH3   0  -0.436   1.1309  -4.1630   1.5180
 5J6  O21  O   O     0  -0.422   0.2864  -2.5911  -0.4887
 5J6  C2   C   CR6   0   0.313   1.8432   0.0983   1.1129
 5J6  C1   C   CH2   0  -0.366   3.1796  -0.5852   1.1884
 5J6  N9   N   NT    0  -0.442   3.3114  -1.5258   0.1033
 5J6  C14  C   CH2   0  -0.304   3.4814  -0.8746  -1.1847
 5J6  C13  C   CH2   0  -0.188   3.5067  -1.9183  -2.2834
 5J6  O12  O   O2    0  -0.484   4.5289  -2.8672  -2.0699
 5J6  C11  C   CH2   0  -0.193   4.3684  -3.5050  -0.8232
 5J6  C10  C   CH2   0  -0.305   4.3586  -2.5068   0.3193
 5J6  H1   H   HCR6  0   0.306  -3.7264  -1.1313  -2.4858
 5J6  H2   H   HCR6  0   0.294  -4.3699  -2.1904   1.6129
 5J6  H3   H   HCR6  0   0.282  -2.2271  -1.1181   2.2247
 5J6  H4   H   HCR5  0   0.316  -0.6705   6.6672   1.7825
 5J6  H5   H   HCR5  0   0.278   1.8906   6.2307   2.2745
 5J6  H6   H   HCH3  0   0.256   1.4677  -4.5086   2.4904
 5J6  H7   H   HCH3  0   0.246   0.1579  -4.5985   1.2932
 5J6  H8   H   HCH3  0   0.242   1.8469  -4.4702   0.7561
 5J6  H9   H   HCH2  0   0.247   3.9662   0.1826   1.2059
 5J6  H10  H   HCH2  0   0.285   3.2410  -1.1262   2.1375
 5J6  H12  H   HCH2  0   0.244   2.6483  -0.1916  -1.3724
 5J6  H13  H   HCH2  0   0.215   4.4042  -0.2719  -1.2116
 5J6  H14  H   HCH2  0   0.208   2.5270  -2.4128  -2.3299
 5J6  H15  H   HCH2  0   0.240   3.6948  -1.4444  -3.2477
 5J6  H16  H   HCH2  0   0.204   3.4342  -4.0851  -0.8093
 5J6  H17  H   HCH2  0   0.241   5.1978  -4.2029  -0.7018
 5J6  H18  H   HCH2  0   0.214   5.3504  -2.0336   0.4045
 5J6  H19  H   HCH2  0   0.248   4.1703  -3.0347   1.2572

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
 5J6  O21  C20  double    1.202  0.020  1.202
 5J6  C23  O22  single    1.428  0.020  1.428
 5J6  C14  C13  single    1.516  0.020  1.516
 5J6  C14  N9   single    1.453  0.020  1.453
 5J6  C1   N9   single    1.442  0.020  1.442
 5J6  C1   C2   single    1.503  0.020  1.503
 5J6  C20  O22  single    1.322  0.020  1.322
 5J6  C20  C7   single    1.491  0.020  1.491
 5J6  C13  O12  single    1.411  0.020  1.411
 5J6  N9   C10  single    1.451  0.020  1.451
 5J6  C2   C7   aromatic  1.398  0.020  1.398
 5J6  C2   N3   aromatic  1.323  0.020  1.323
 5J6  C7   C6   aromatic  1.389  0.020  1.389
 5J6  O12  C11  single    1.410  0.020  1.410
 5J6  N3   C4   aromatic  1.325  0.020  1.325
 5J6  C10  C11  single    1.517  0.020  1.517
 5J6  C6   N5   aromatic  1.325  0.020  1.325
 5J6  C6   C24  single    1.483  0.020  1.483
 5J6  BR1  C25  single    1.881  0.020  1.881
 5J6  C4   N5   aromatic  1.324  0.020  1.324
 5J6  C4   C15  single    1.463  0.020  1.463
 5J6  C24  C25  aromatic  1.390  0.020  1.390
 5J6  C24  C29  aromatic  1.390  0.020  1.390
 5J6  N16  C15  aromatic  1.297  0.020  1.297
 5J6  N16  C17  aromatic  1.358  0.020  1.358
 5J6  C25  C26  aromatic  1.385  0.020  1.385
 5J6  C15  S19  aromatic  1.724  0.020  1.724
 5J6  C29  C28  aromatic  1.386  0.020  1.386
 5J6  C17  C18  aromatic  1.363  0.020  1.363
 5J6  C26  C27  aromatic  1.382  0.020  1.382
 5J6  S19  C18  aromatic  1.705  0.020  1.705
 5J6  C28  C27  aromatic  1.380  0.020  1.380
 5J6  C27  F1   single    1.337  0.020  1.337
 5J6  C26  H1   single    0.930  0.020  1.080
 5J6  C28  H2   single    0.930  0.020  1.080
 5J6  C29  H3   single    0.930  0.020  1.080
 5J6  C18  H4   single    0.930  0.020  1.080
 5J6  C17  H5   single    0.930  0.020  1.080
 5J6  C23  H6   single    0.970  0.020  1.090
 5J6  C23  H7   single    0.970  0.020  1.090
 5J6  C23  H8   single    0.970  0.020  1.090
 5J6  C1   H9   single    0.970  0.020  1.090
 5J6  C1   H10  single    0.970  0.020  1.090
 5J6  C14  H12  single    0.970  0.020  1.090
 5J6  C14  H13  single    0.970  0.020  1.090
 5J6  C13  H14  single    0.970  0.020  1.090
 5J6  C13  H15  single    0.970  0.020  1.090
 5J6  C11  H16  single    0.970  0.020  1.090
 5J6  C11  H17  single    0.970  0.020  1.090
 5J6  C10  H18  single    0.970  0.020  1.090
 5J6  C10  H19  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
 5J6  C28  C27  C26  122.56  3.000
 5J6  C28  C27  F1   119.12  3.000
 5J6  C26  C27  F1   118.32  3.000
 5J6  H1   C26  C25  121.82  3.000
 5J6  H1   C26  C27  120.25  3.000
 5J6  C25  C26  C27  117.92  3.000
 5J6  C24  C25  BR1  119.67  3.000
 5J6  C24  C25  C26  121.46  3.000
 5J6  BR1  C25  C26  118.86  3.000
 5J6  H2   C28  C29  121.00  3.000
 5J6  H2   C28  C27  120.81  3.000
 5J6  C29  C28  C27  118.19  3.000
 5J6  H3   C29  C24  119.42  3.000
 5J6  H3   C29  C28  119.34  3.000
 5J6  C24  C29  C28  121.24  3.000
 5J6  C6   C24  C29  119.84  3.000
 5J6  C29  C24  C25  118.63  3.000
 5J6  C6   C24  C25  121.53  3.000
 5J6  C7   C6   N5   121.50  3.000
 5J6  N5   C6   C24  116.94  3.000
 5J6  C7   C6   C24  121.55  3.000
 5J6  C4   N5   C6   117.16  3.000
 5J6  N3   C4   C15  118.22  3.000
 5J6  C15  C4   N5   115.75  3.000
 5J6  N3   C4   N5   126.02  3.000
 5J6  N16  C15  S19  114.78  3.000
 5J6  S19  C15  C4   119.87  3.000
 5J6  N16  C15  C4   125.35  3.000
 5J6  C18  S19  C15   89.00  3.000
 5J6  H4   C18  C17  128.10  3.000
 5J6  H4   C18  S19  121.94  3.000
 5J6  C17  C18  S19  109.96  3.000
 5J6  H5   C17  N16  119.91  3.000
 5J6  H5   C17  C18  124.71  3.000
 5J6  N16  C17  C18  115.39  3.000
 5J6  C17  N16  C15  110.87  3.000
 5J6  C2   N3   C4   117.34  3.000
 5J6  C2   C7   C20  122.96  3.000
 5J6  C2   C7   C6   116.74  3.000
 5J6  C20  C7   C6   120.28  3.000
 5J6  O21  C20  O22  125.12  3.000
 5J6  O22  C20  C7   110.94  3.000
 5J6  O21  C20  C7   123.68  3.000
 5J6  C23  O22  C20  117.20  3.000
 5J6  H8   C23  H7   109.26  3.000
 5J6  H8   C23  H6   109.43  3.000
 5J6  H7   C23  H6   109.55  3.000
 5J6  H8   C23  O22  111.05  3.000
 5J6  H7   C23  O22  111.50  3.000
 5J6  H6   C23  O22  105.98  3.000
 5J6  C1   C2   C7   121.03  3.000
 5J6  C7   C2   N3   121.18  3.000
 5J6  C1   C2   N3   117.74  3.000
 5J6  H10  C1   H9   106.94  3.000
 5J6  H10  C1   N9   108.97  3.000
 5J6  H9   C1   N9   113.71  3.000
 5J6  H10  C1   C2   108.56  3.000
 5J6  H9   C1   C2   108.63  3.000
 5J6  N9   C1   C2   109.88  3.000
 5J6  C10  N9   C14  110.51  3.000
 5J6  C10  N9   C1   113.26  3.000
 5J6  C14  N9   C1   112.67  3.000
 5J6  H13  C14  H12  106.98  3.000
 5J6  H13  C14  C13  110.17  3.000
 5J6  H12  C14  C13  108.57  3.000
 5J6  H13  C14  N9   111.37  3.000
 5J6  H12  C14  N9   110.05  3.000
 5J6  C13  C14  N9   109.63  3.000
 5J6  H15  C13  H14  108.18  3.000
 5J6  H15  C13  O12  107.52  3.000
 5J6  H14  C13  O12  110.48  3.000
 5J6  H15  C13  C14  110.15  3.000
 5J6  H14  C13  C14  109.02  3.000
 5J6  O12  C13  C14  111.44  3.000
 5J6  C11  O12  C13  110.83  3.000
 5J6  H17  C11  H16  107.88  3.000
 5J6  H17  C11  C10  110.00  3.000
 5J6  H16  C11  C10  109.39  3.000
 5J6  H17  C11  O12  107.54  3.000
 5J6  H16  C11  O12  110.28  3.000
 5J6  C10  C11  O12  111.66  3.000
 5J6  H19  C10  H18  107.23  3.000
 5J6  H19  C10  C11  109.25  3.000
 5J6  H18  C10  C11  109.57  3.000
 5J6  H19  C10  N9   109.27  3.000
 5J6  H18  C10  N9   111.76  3.000
 5J6  C11  C10  N9   109.71  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
 5J6  CONST_01  C24  C25  C26  C27     0.00   0.0  0
 5J6  CONST_02  C24  C29  C28  C27     0.00   0.0  0
 5J6  CONST_03  C6   C24  C25  C26   180.00   0.0  0
 5J6  CONST_04  C29  C24  C25  C26     0.00   0.0  0
 5J6  CONST_05  C29  C28  C27  C26     0.00   0.0  0
 5J6  CONST_08  C28  C29  C24  C25     0.00   0.0  0
 5J6  CONST_09  C28  C27  C26  C25     0.00   0.0  0
 5J6  CONST_10  C6   C24  C29  C28   180.00   0.0  0
 5J6  CONST_13  C2   C7   C6   C24   180.00   0.0  0
 5J6  CONST_14  C4   N5   C6   C24   180.00   0.0  0
 5J6  CONST_15  N3   C2   C7   C6      0.00   0.0  0
 5J6  CONST_16  N3   C4   N5   C6      0.00   0.0  0
 5J6  CONST_17  C15  C4   N5   C6    180.00   0.0  0
 5J6  CONST_18  C2   C7   C6   N5      0.00   0.0  0
 5J6  CONST_19  C2   N3   C4   N5      0.00   0.0  0
 5J6  CONST_20  N16  C15  C4   N5    180.00   0.0  0
 5J6  CONST_21  S19  C15  C4   N5      0.00   0.0  0
 5J6  CONST_22  C7   C2   N3   C4      0.00   0.0  0
 5J6  CONST_23  C7   C6   N5   C4      0.00   0.0  0
 5J6  CONST_24  C17  N16  C15  C4    180.00   0.0  0
 5J6  CONST_25  C18  S19  C15  C4    180.00   0.0  0
 5J6  CONST_26  C2   N3   C4   C15   180.00   0.0  0
 5J6  CONST_27  C18  C17  N16  C15     0.00   0.0  0
 5J6  CONST_28  C17  C18  S19  C15     0.00   0.0  0
 5J6  CONST_29  N3   C4   C15  S19   180.00   0.0  0
 5J6  CONST_30  C17  N16  C15  S19     0.00   0.0  0
 5J6  CONST_31  N16  C17  C18  S19     0.00   0.0  0
 5J6  CONST_32  N16  C15  S19  C18     0.00   0.0  0
 5J6  CONST_33  N3   C4   C15  N16     0.00   0.0  0
 5J6  CONST_34  C25  C26  C27  F1    180.00   0.0  0
 5J6  CONST_35  C29  C28  C27  F1    180.00   0.0  0
 5J6  CONST_36  BR1  C25  C26  C27   180.00   0.0  0
 5J6  CONST_37  C6   C24  C25  BR1     0.00   0.0  0
 5J6  CONST_38  C29  C24  C25  BR1   180.00   0.0  0
 5J6  CONST_39  C20  C7   C6   C24     0.00   0.0  0
 5J6  CONST_40  C1   C2   C7   C6    180.00   0.0  0
 5J6  CONST_41  C20  C7   C6   N5    180.00   0.0  0
 5J6  CONST_42  C1   C2   N3   C4    180.00   0.0  0
 5J6  CONST_43  C20  C7   C2   N3    180.00   0.0  0
 5J6  CONST_44  H3   C29  C28  C27   180.00   0.0  0
 5J6  CONST_45  H2   C28  C27  C26   180.00   0.0  0
 5J6  CONST_46  H1   C26  C27  C28   180.00   0.0  0
 5J6  CONST_47  H5   C17  N16  C15   180.00   0.0  0
 5J6  CONST_48  H4   C18  S19  C15   180.00   0.0  0
 5J6  Var_01    O12  C13  C14  N9    -57.32  30.0  1
 5J6  Var_02    O12  C11  C10  N9     56.74  30.0  1
 5J6  Var_03    C11  C10  N9   C14   -56.11  30.0  1
 5J6  Var_04    C10  N9   C14  C13    56.46  30.0  1
 5J6  Var_05    C10  C11  O12  C13   -57.68  30.0  1
 5J6  Var_06    N9   C1   C2   N3   -137.42  30.0  3
 5J6  Var_07    C14  N9   C1   C2     71.50  30.0  3
 5J6  Var_08    O21  C20  C7   C6     54.05  30.0  2
 5J6  Var_09    H6   C23  O22  C20   179.07  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
 5J6  plan-1  C4   0.020
 5J6  plan-1  C15  0.020
 5J6  plan-1  S19  0.020
 5J6  plan-1  C18  0.020
 5J6  plan-1  C17  0.020
 5J6  plan-1  N16  0.020
 5J6  plan-1  H4   0.020
 5J6  plan-1  H5   0.020
 5J6  plan-2  F1   0.020
 5J6  plan-2  C27  0.020
 5J6  plan-2  C26  0.020
 5J6  plan-2  C25  0.020
 5J6  plan-2  BR1  0.020
 5J6  plan-2  C28  0.020
 5J6  plan-2  C29  0.020
 5J6  plan-2  C24  0.020
 5J6  plan-2  C6   0.020
 5J6  plan-2  H1   0.020
 5J6  plan-2  H2   0.020
 5J6  plan-2  H3   0.020
 5J6  plan-3  C24  0.020
 5J6  plan-3  C6   0.020
 5J6  plan-3  N5   0.020
 5J6  plan-3  C4   0.020
 5J6  plan-3  C15  0.020
 5J6  plan-3  N3   0.020
 5J6  plan-3  C7   0.020
 5J6  plan-3  C20  0.020
 5J6  plan-3  C2   0.020
 5J6  plan-3  C1   0.020
 5J6  plan-4  C7   0.020
 5J6  plan-4  C20  0.020
 5J6  plan-4  O22  0.020
 5J6  plan-4  O21  0.020

