# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 19:02:33 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (4-{[2-(5-chlorothiophen-2-yl)-5-ethyl-6-methylpyrimidin-4-yl]amino}phenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(C)nc(nc1Nc2ccc(CC(O)=O)cc2)c3sc(Cl)cc3
#
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
 19T  19T  '(4-{[2-(5-chlorothiophen-2-yl)-5-ethyl-6-methylpyrimidin-4-yl]amino}phenyl)acetic acid'  ligand  43  26  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_19T
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
 19T  C2   C   CR6    0   0.413   2.5146   0.4881   0.2262
 19T  C4   C   CR6    0   0.233   3.1450   2.6549   0.3857
 19T  C5   C   CR6    0  -0.051   1.8231   3.0695   0.3261
 19T  C9   C   CR5    0  -0.255   2.7547  -3.3697   0.0493
 19T  O26  O   OC    -1  -0.625  -7.1647  -1.5063   0.1493
 19T  C24  C   C      0   0.421  -6.1149  -0.8686   0.3658
 19T  O25  O   O      0  -0.597  -5.8491  -0.1820   1.3671
 19T  C20  C   CR6    0   0.173  -3.8297  -0.1234  -0.5262
 19T  C19  C   CR16   0  -0.309  -3.7287   1.1518  -1.0740
 19T  C18  C   CR16   0  -0.328  -2.6062   1.9389  -0.8713
 19T  C21  C   CR16   0  -0.309  -2.7630  -0.5700   0.2489
 19T  C22  C   CR16   0  -0.269  -1.6363   0.2063   0.4732
 19T  C17  C   CR6    0   0.329  -1.5432   1.4751  -0.0981
 19T  C6   C   CR6    0   0.524   0.8631   2.0390   0.1901
 19T  C14  C   CH2    0  -0.564   1.4331   4.5200   0.3427
 19T  C15  C   CH3    0  -0.651   1.2269   5.0938  -1.0607
 19T  C13  C   CH3    0  -0.759   4.2696   3.6383   0.5070
 19T  N3   N   N      0  -0.471   3.4961   1.3621   0.3426
 19T  N7   N   N      0  -0.498   1.2218   0.7622   0.1420
 19T  C7   C   CR5    0  -0.261   2.8637  -0.9269   0.1803
 19T  C11  C   CR15   0  -0.227   4.0924  -1.5168   0.2582
 19T  C10  C   CR15   0  -0.120   4.0362  -2.9302   0.1833
 19T  S8   S   S2     0   0.310   1.6042  -2.0947   0.0121
 19T  H2   H   HCH2   0   0.245  -4.7489  -2.0240  -0.8299
 19T  H3   H   HCH2   0   0.242  -5.5077  -0.7186  -1.7026
 19T  H4   H   HCR6   0   0.244  -4.5363   1.5395  -1.6841
 19T  H5   H   HCR6   0   0.257  -2.5515   2.9217  -1.3256
 19T  H6   H   HCR6   0   0.241  -2.8083  -1.5559   0.6973
 19T  H7   H   HCR6   0   0.257  -0.8383  -0.1803   1.0874
 19T  H8   H   HNH1   0   0.414  -0.6833   3.3196   0.0129
 19T  H9   H   HCH2   0   0.250   0.5274   4.6634   0.9395
 19T  H10  H   HCH2   0   0.270   2.1983   5.1013   0.8569
 19T  H11  H   HCH3   0   0.233   2.1420   5.0251  -1.6491
 19T  H12  H   HCH3   0   0.221   0.4477   4.5641  -1.6112
 19T  H13  H   HCH3   0   0.240   0.9384   6.1435  -1.0089
 19T  H14  H   HCH3   0   0.260   4.2344   4.1625   1.4638
 19T  H15  H   HCH3   0   0.261   5.2258   3.1251   0.4381
 19T  H16  H   HCH3   0   0.254   4.2272   4.3976  -0.2744
 19T  H17  H   HCR5   0   0.271   5.0084  -0.9548   0.3692
 19T  H18  H   HCR5   0   0.290   4.8962  -3.5816   0.2268
 19T  N16  N   NH1    0  -0.785  -0.4571   2.3425   0.0991
 19T  CL1  CL  CL     0  -0.078   2.2419  -4.9932  -0.0761
 19T  C23  C   CH2    0  -0.697  -5.0405  -0.9719  -0.7467

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
 19T  CL1  C9   single    1.707  0.020  1.707
 19T  C10  C9   aromatic  1.361  0.020  1.361
 19T  C10  C11  aromatic  1.416  0.020  1.416
 19T  C9   S8   aromatic  1.718  0.020  1.718
 19T  C11  C7   aromatic  1.365  0.020  1.365
 19T  C7   S8   aromatic  1.726  0.020  1.726
 19T  C7   C2   single    1.458  0.020  1.458
 19T  N3   C2   aromatic  1.319  0.020  1.319
 19T  N3   C4   aromatic  1.340  0.020  1.340
 19T  C2   N7   aromatic  1.324  0.020  1.324
 19T  C15  C14  single    1.530  0.020  1.530
 19T  C13  C4   single    1.499  0.020  1.499
 19T  C4   C5   aromatic  1.387  0.020  1.387
 19T  N7   C6   aromatic  1.327  0.020  1.327
 19T  C18  C19  aromatic  1.386  0.020  1.386
 19T  C18  C17  aromatic  1.394  0.020  1.394
 19T  C5   C6   aromatic  1.415  0.020  1.415
 19T  C5   C14  single    1.502  0.020  1.502
 19T  C6   N16  single    1.358  0.020  1.358
 19T  C19  C20  aromatic  1.392  0.020  1.392
 19T  N16  C17  single    1.404  0.020  1.404
 19T  C17  C22  aromatic  1.395  0.020  1.395
 19T  C20  C23  single    1.495  0.020  1.495
 19T  C20  C21  aromatic  1.392  0.020  1.392
 19T  O25  C24  deloc     1.243  0.020  1.243
 19T  C23  C24  single    1.550  0.020  1.550
 19T  C22  C21  aromatic  1.387  0.020  1.387
 19T  C24  O26  deloc     1.247  0.020  1.247
 19T  C23  H2   single    0.970  0.020  1.090
 19T  C23  H3   single    0.970  0.020  1.090
 19T  C19  H4   single    0.930  0.020  1.080
 19T  C18  H5   single    0.930  0.020  1.080
 19T  C21  H6   single    0.930  0.020  1.080
 19T  C22  H7   single    0.930  0.020  1.080
 19T  N16  H8   single    0.860  0.020  1.020
 19T  C14  H9   single    0.970  0.020  1.090
 19T  C14  H10  single    0.970  0.020  1.090
 19T  C15  H11  single    0.970  0.020  1.090
 19T  C15  H12  single    0.970  0.020  1.090
 19T  C15  H13  single    0.970  0.020  1.090
 19T  C13  H14  single    0.970  0.020  1.090
 19T  C13  H15  single    0.970  0.020  1.090
 19T  C13  H16  single    0.970  0.020  1.090
 19T  C11  H17  single    0.930  0.020  1.080
 19T  C10  H18  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
 19T  C7   C2   N7   115.63  3.000
 19T  N7   C2   N3   126.49  3.000
 19T  C7   C2   N3   117.88  3.000
 19T  N3   C4   C13  116.04  3.000
 19T  C13  C4   C5   121.50  3.000
 19T  N3   C4   C5   122.46  3.000
 19T  C14  C5   C6   121.88  3.000
 19T  C14  C5   C4   122.39  3.000
 19T  C6   C5   C4   115.67  3.000
 19T  CL1  C9   S8   120.20  3.000
 19T  S8   C9   C10  113.14  3.000
 19T  CL1  C9   C10  126.66  3.000
 19T  C23  C24  O25  117.82  3.000
 19T  C23  C24  O26  115.13  3.000
 19T  O25  C24  O26  127.04  3.000
 19T  C21  C20  C19  117.23  3.000
 19T  C21  C20  C23  121.38  3.000
 19T  C19  C20  C23  121.39  3.000
 19T  H4   C19  C18  118.86  3.000
 19T  H4   C19  C20  119.69  3.000
 19T  C18  C19  C20  121.44  3.000
 19T  H5   C18  C17  119.71  3.000
 19T  H5   C18  C19  119.63  3.000
 19T  C17  C18  C19  120.66  3.000
 19T  H6   C21  C22  118.44  3.000
 19T  H6   C21  C20  119.34  3.000
 19T  C22  C21  C20  122.22  3.000
 19T  H7   C22  C17  120.67  3.000
 19T  H7   C22  C21  119.51  3.000
 19T  C17  C22  C21  119.82  3.000
 19T  N16  C17  C22  123.79  3.000
 19T  C22  C17  C18  118.63  3.000
 19T  N16  C17  C18  117.54  3.000
 19T  N7   C6   N16  118.39  3.000
 19T  N16  C6   C5   120.23  3.000
 19T  N7   C6   C5   121.38  3.000
 19T  H10  C14  H9   104.71  3.000
 19T  H10  C14  C15  109.10  3.000
 19T  H9   C14  C15  109.85  3.000
 19T  H10  C14  C5   109.76  3.000
 19T  H9   C14  C5   110.34  3.000
 19T  C15  C14  C5   112.76  3.000
 19T  H13  C15  H12  107.61  3.000
 19T  H13  C15  H11  107.97  3.000
 19T  H12  C15  H11  107.25  3.000
 19T  H13  C15  C14  110.69  3.000
 19T  H12  C15  C14  112.14  3.000
 19T  H11  C15  C14  110.99  3.000
 19T  H16  C13  H15  108.51  3.000
 19T  H16  C13  H14  107.01  3.000
 19T  H15  C13  H14  108.09  3.000
 19T  H16  C13  C4   111.70  3.000
 19T  H15  C13  C4   110.18  3.000
 19T  H14  C13  C4   111.21  3.000
 19T  C4   N3   C2   116.55  3.000
 19T  C6   N7   C2   117.43  3.000
 19T  S8   C7   C11  111.72  3.000
 19T  S8   C7   C2   119.01  3.000
 19T  C11  C7   C2   129.27  3.000
 19T  H17  C11  C10  123.93  3.000
 19T  H17  C11  C7   122.97  3.000
 19T  C10  C11  C7   113.10  3.000
 19T  H18  C10  C11  124.63  3.000
 19T  H18  C10  C9   123.98  3.000
 19T  C11  C10  C9   111.39  3.000
 19T  C7   S8   C9    90.65  3.000
 19T  H8   N16  C6   116.18  3.000
 19T  H8   N16  C17  114.44  3.000
 19T  C6   N16  C17  128.58  3.000
 19T  H3   C23  H2   105.66  3.000
 19T  H3   C23  C20  110.08  3.000
 19T  H2   C23  C20  109.93  3.000
 19T  H3   C23  C24  108.41  3.000
 19T  H2   C23  C24  107.65  3.000
 19T  C20  C23  C24  114.69  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
 19T  CONST_01  C10  C11  C7   C2    180.00   0.0  0
 19T  CONST_02  C9   S8   C7   C2    180.00   0.0  0
 19T  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 19T  CONST_04  C5   C6   N7   C2      0.00   0.0  0
 19T  CONST_05  C7   C2   N3   C4    180.00   0.0  0
 19T  CONST_06  N7   C2   N3   C4      0.00   0.0  0
 19T  CONST_07  N7   C6   C5   C4      0.00   0.0  0
 19T  CONST_08  C7   C11  C10  C9      0.00   0.0  0
 19T  CONST_09  C11  C7   S8   C9      0.00   0.0  0
 19T  CONST_10  C17  C18  C19  C20     0.00   0.0  0
 19T  CONST_11  C17  C22  C21  C20     0.00   0.0  0
 19T  CONST_12  C22  C17  C18  C19     0.00   0.0  0
 19T  CONST_13  C22  C21  C20  C19     0.00   0.0  0
 19T  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 19T  CONST_15  C21  C22  C17  C18     0.00   0.0  0
 19T  CONST_16  C7   C2   N7   C6    180.00   0.0  0
 19T  CONST_17  N3   C2   N7   C6      0.00   0.0  0
 19T  CONST_18  N3   C4   C5   C6      0.00   0.0  0
 19T  CONST_19  C11  C7   C2   N3      0.00   0.0  0
 19T  CONST_20  S8   C7   C2   N3    180.00   0.0  0
 19T  CONST_21  C11  C7   C2   N7    180.00   0.0  0
 19T  CONST_22  S8   C7   C2   N7      0.00   0.0  0
 19T  CONST_23  C10  C9   S8   C7      0.00   0.0  0
 19T  CONST_24  S8   C9   C10  C11     0.00   0.0  0
 19T  CONST_25  S8   C7   C11  C10     0.00   0.0  0
 19T  CONST_26  C13  C4   N3   C2    180.00   0.0  0
 19T  CONST_27  N16  C6   N7   C2    180.00   0.0  0
 19T  CONST_28  N16  C6   C5   C4    180.00   0.0  0
 19T  CONST_29  C18  C19  C20  C23   180.00   0.0  0
 19T  CONST_30  C22  C21  C20  C23   180.00   0.0  0
 19T  CONST_31  N16  C17  C18  C19   180.00   0.0  0
 19T  CONST_32  N16  C17  C22  C21   180.00   0.0  0
 19T  CONST_33  C13  C4   C5   C6    180.00   0.0  0
 19T  CONST_34  N3   C4   C5   C14   180.00   0.0  0
 19T  CONST_35  N7   C6   C5   C14   180.00   0.0  0
 19T  CONST_36  CL1  C9   S8   C7    180.00   0.0  0
 19T  CONST_37  CL1  C9   C10  C11   180.00   0.0  0
 19T  CONST_38  H17  C11  C7   C2      0.00   0.0  0
 19T  CONST_39  H5   C18  C19  C20   180.00   0.0  0
 19T  CONST_40  H7   C22  C21  C20   180.00   0.0  0
 19T  CONST_41  H6   C21  C20  C19   180.00   0.0  0
 19T  CONST_42  H4   C19  C20  C21   180.00   0.0  0
 19T  CONST_43  H18  C10  C11  C7    180.00   0.0  0
 19T  Var_01    C17  N16  C6   C5    176.88  30.0  2
 19T  Var_02    C6   N16  C17  C18  -144.57  30.0  2
 19T  Var_03    C15  C14  C5   C4     95.36  30.0  2
 19T  Var_04    C19  C20  C23  C24   -94.00  30.0  2
 19T  Var_05    H14  C13  C4   C5     65.81  30.0  2
 19T  Var_06    C20  C23  C24  O26   175.62  30.0  2
 19T  Var_07    H11  C15  C14  C5    -60.54  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
 19T  plan-1  C2   0.020
 19T  plan-1  C9   0.020
 19T  plan-1  C7   0.020
 19T  plan-1  C11  0.020
 19T  plan-1  C10  0.020
 19T  plan-1  S8   0.020
 19T  plan-1  H17  0.020
 19T  plan-1  H18  0.020
 19T  plan-1  CL1  0.020
 19T  plan-2  C20  0.020
 19T  plan-2  C19  0.020
 19T  plan-2  C18  0.020
 19T  plan-2  C21  0.020
 19T  plan-2  C22  0.020
 19T  plan-2  C17  0.020
 19T  plan-2  H4   0.020
 19T  plan-2  H5   0.020
 19T  plan-2  H6   0.020
 19T  plan-2  H7   0.020
 19T  plan-2  N16  0.020
 19T  plan-2  C23  0.020
 19T  plan-3  C2   0.020
 19T  plan-3  C4   0.020
 19T  plan-3  C5   0.020
 19T  plan-3  C6   0.020
 19T  plan-3  C14  0.020
 19T  plan-3  C13  0.020
 19T  plan-3  N3   0.020
 19T  plan-3  N7   0.020
 19T  plan-3  C7   0.020
 19T  plan-3  N16  0.020
 19T  plan-4  O26  0.020
 19T  plan-4  C24  0.020
 19T  plan-4  O25  0.020
 19T  plan-4  C23  0.020

