# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:28:23 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-(2-{[4-(dimethylcarbamoyl)phenyl]amino}-4-methoxypyrimidin-5-yl)thiophene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nc(Nc2ccc(cc2)C(=O)N(C)C)ncc1c3scc(c3)C(O)=O
#
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
 0XG  0XG  '5-(2-{[4-(dimethylcarbamoyl)phenyl]amino}-4-methoxypyrimidin-5-yl)thiophene-3-carboxylic acid'  ligand  46  28  .  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_0XG
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
 0XG  C1   C  CH3   0  -0.525   8.8481  -1.3362   0.3201
 0XG  C3   C  CH3   0  -0.534   7.3657   0.0975   1.6233
 0XG  O5   O  O     0  -0.497   6.6416  -2.2244  -1.0116
 0XG  C7   C  CR16  0  -0.262   4.0247  -1.2715  -0.2122
 0XG  C8   C  CR16  0  -0.303   2.7804  -0.6629  -0.2378
 0XG  C9   C  CR6   0   0.369   2.6898   0.7294  -0.3231
 0XG  C10  C  CR16  0  -0.346   3.8746   1.4744  -0.3803
 0XG  C11  C  CR16  0  -0.247   5.1063   0.8540  -0.3290
 0XG  C13  C  CR6   0   0.619   0.2064   1.0633  -0.2838
 0XG  C15  C  CR16  0  -0.037  -1.4059  -0.4949  -0.0830
 0XG  C16  C  CR6   0  -0.095  -2.4158   0.4503  -0.1390
 0XG  N18  N  N     0  -0.510  -0.6689   2.0722  -0.3384
 0XG  C20  C  CH3   0  -0.418  -2.4122   4.0909  -0.4216
 0XG  C21  C  CR5   0  -0.189  -3.8227   0.0813  -0.0696
 0XG  C22  C  CR15  0  -0.256  -4.3451  -1.1792  -0.1637
 0XG  C24  C  CR15  0  -0.507  -6.2898   0.0263   0.2018
 0XG  O28  O  O     0  -0.439  -6.0121  -3.5504  -0.2577
 0XG  N2   N  NT    0  -0.442   7.5226  -0.7734   0.4751
 0XG  C4   C  C     0   0.510   6.5097  -1.2503  -0.2773
 0XG  C6   C  CR6   0  -0.079   5.2023  -0.5331  -0.2328
 0XG  N14  N  N     0  -0.476  -0.1108  -0.2159  -0.1567
 0XG  C17  C  CR6   0   0.554  -1.9411   1.7748  -0.2663
 0XG  O19  O  O2    0  -0.461  -2.8427   2.7357  -0.3051
 0XG  C23  C  CR5   0   0.044  -5.7553  -1.2150  -0.0071
 0XG  S25  S  S2    0   0.281  -5.0938   1.2328   0.2025
 0XG  C26  C  C     0   0.515  -6.5200  -2.4690  -0.0770
 0XG  O27  O  OH1   0  -0.595  -7.8238  -2.2859   0.0800
 0XG  H1   H  HCH3  0   0.245   9.5863  -0.5606   0.5231
 0XG  H2   H  HCH3  0   0.238   9.0213  -2.1605   1.0166
 0XG  H3   H  HCH3  0   0.253   9.0004  -1.6980  -0.6922
 0XG  H4   H  HCH3  0   0.254   7.8639  -0.3515   2.4843
 0XG  H5   H  HCH3  0   0.244   7.8129   1.0776   1.4473
 0XG  H6   H  HCH3  0   0.263   6.3209   0.2322   1.8836
 0XG  H7   H  HCR6  0   0.259   4.0687  -2.3519  -0.1609
 0XG  H8   H  HCR6  0   0.290   1.8907  -1.2685  -0.1967
 0XG  H9   H  HCR6  0   0.274   3.8276   2.5537  -0.4635
 0XG  H10  H  HCR6  0   0.270   5.9979   1.4664  -0.3784
 0XG  H11  H  HCR6  0   0.274  -1.6498  -1.5443   0.0362
 0XG  H12  H  HCH3  0   0.242  -1.8671   4.2533  -1.3507
 0XG  H13  H  HCH3  0   0.256  -3.3205   4.6860  -0.4229
 0XG  H14  H  HCH3  0   0.242  -1.7842   4.3815   0.4198
 0XG  H15  H  HCR5  0   0.272  -3.7514  -2.0639  -0.3435
 0XG  H16  H  HCR5  0   0.310  -7.3259   0.2941   0.3415
 0XG  H17  H  HNH1  0   0.415   1.6159   2.4525  -0.4438
 0XG  H18  H  HOH1  0   0.488  -8.2874  -3.1350   0.0294
 0XG  N12  N  NH1   0  -0.765   1.5068   1.4522  -0.3636

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
 0XG  C8   C7   aromatic  1.385  0.020  1.385
 0XG  C8   C9   aromatic  1.398  0.020  1.398
 0XG  N14  C15  aromatic  1.327  0.020  1.327
 0XG  N14  C13  aromatic  1.324  0.020  1.324
 0XG  N12  C13  single    1.360  0.020  1.360
 0XG  N12  C9   single    1.387  0.020  1.387
 0XG  C15  C16  aromatic  1.384  0.020  1.384
 0XG  C7   C6   aromatic  1.390  0.020  1.390
 0XG  S25  C24  aromatic  1.699  0.020  1.699
 0XG  S25  C21  aromatic  1.737  0.020  1.737
 0XG  C1   N2   single    1.448  0.020  1.448
 0XG  C13  N18  aromatic  1.337  0.020  1.337
 0XG  C9   C10  aromatic  1.401  0.020  1.401
 0XG  C16  C21  single    1.456  0.020  1.456
 0XG  C16  C17  aromatic  1.413  0.020  1.413
 0XG  N2   C4   single    1.349  0.020  1.349
 0XG  N2   C3   single    1.450  0.020  1.450
 0XG  C24  C23  aromatic  1.368  0.020  1.368
 0XG  C6   C4   single    1.492  0.020  1.492
 0XG  C6   C11  aromatic  1.394  0.020  1.394
 0XG  N18  C17  aromatic  1.309  0.020  1.309
 0XG  C21  C22  aromatic  1.368  0.020  1.368
 0XG  C10  C11  aromatic  1.380  0.020  1.380
 0XG  C17  O19  single    1.318  0.020  1.318
 0XG  C4   O5   double    1.227  0.020  1.227
 0XG  C23  C22  aromatic  1.419  0.020  1.419
 0XG  C23  C26  single    1.470  0.020  1.470
 0XG  O19  C20  single    1.427  0.020  1.427
 0XG  O28  C26  double    1.208  0.020  1.208
 0XG  C26  O27  single    1.326  0.020  1.326
 0XG  C1   H1   single    0.970  0.020  1.090
 0XG  C1   H2   single    0.970  0.020  1.090
 0XG  C1   H3   single    0.970  0.020  1.090
 0XG  C3   H4   single    0.970  0.020  1.090
 0XG  C3   H5   single    0.970  0.020  1.090
 0XG  C3   H6   single    0.970  0.020  1.090
 0XG  C7   H7   single    0.930  0.020  1.080
 0XG  C8   H8   single    0.930  0.020  1.080
 0XG  C10  H9   single    0.930  0.020  1.080
 0XG  C11  H10  single    0.930  0.020  1.080
 0XG  C15  H11  single    0.930  0.020  1.080
 0XG  C20  H12  single    0.970  0.020  1.090
 0XG  C20  H13  single    0.970  0.020  1.090
 0XG  C20  H14  single    0.970  0.020  1.090
 0XG  C22  H15  single    0.930  0.020  1.080
 0XG  C24  H16  single    0.930  0.020  1.080
 0XG  N12  H17  single    0.860  0.020  1.020
 0XG  O27  H18  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
 0XG  H3   C1   H2   108.70  3.000
 0XG  H3   C1   H1   108.41  3.000
 0XG  H2   C1   H1   108.10  3.000
 0XG  H3   C1   N2   110.95  3.000
 0XG  H2   C1   N2   111.71  3.000
 0XG  H1   C1   N2   108.87  3.000
 0XG  H6   C3   H5   108.76  3.000
 0XG  H6   C3   H4   107.54  3.000
 0XG  H5   C3   H4   108.04  3.000
 0XG  H6   C3   N2   111.64  3.000
 0XG  H5   C3   N2   111.55  3.000
 0XG  H4   C3   N2   109.16  3.000
 0XG  H7   C7   C6   119.76  3.000
 0XG  H7   C7   C8   118.41  3.000
 0XG  C6   C7   C8   121.82  3.000
 0XG  H8   C8   C9   120.59  3.000
 0XG  H8   C8   C7   119.61  3.000
 0XG  C9   C8   C7   119.80  3.000
 0XG  N12  C9   C10  116.30  3.000
 0XG  C10  C9   C8   118.52  3.000
 0XG  N12  C9   C8   125.18  3.000
 0XG  H9   C10  C11  119.30  3.000
 0XG  H9   C10  C9   119.75  3.000
 0XG  C11  C10  C9   120.95  3.000
 0XG  H10  C11  C6   120.62  3.000
 0XG  H10  C11  C10  118.61  3.000
 0XG  C6   C11  C10  120.76  3.000
 0XG  N14  C13  N12  120.74  3.000
 0XG  N12  C13  N18  114.08  3.000
 0XG  N14  C13  N18  125.19  3.000
 0XG  H11  C15  N14  115.42  3.000
 0XG  H11  C15  C16  120.09  3.000
 0XG  N14  C15  C16  124.48  3.000
 0XG  C17  C16  C21  124.51  3.000
 0XG  C17  C16  C15  113.49  3.000
 0XG  C21  C16  C15  122.00  3.000
 0XG  C17  N18  C13  117.57  3.000
 0XG  H14  C20  H13  109.69  3.000
 0XG  H14  C20  H12  109.30  3.000
 0XG  H13  C20  H12  109.62  3.000
 0XG  H14  C20  O19  111.36  3.000
 0XG  H13  C20  O19  105.56  3.000
 0XG  H12  C20  O19  111.23  3.000
 0XG  S25  C21  C22  110.02  3.000
 0XG  C22  C21  C16  126.82  3.000
 0XG  S25  C21  C16  123.13  3.000
 0XG  H15  C22  C23  122.93  3.000
 0XG  H15  C22  C21  123.79  3.000
 0XG  C23  C22  C21  113.28  3.000
 0XG  H16  C24  S25  119.97  3.000
 0XG  H16  C24  C23  128.34  3.000
 0XG  S25  C24  C23  111.69  3.000
 0XG  C4   N2   C3   124.96  3.000
 0XG  C3   N2   C1   114.66  3.000
 0XG  C4   N2   C1   119.35  3.000
 0XG  C6   C4   N2   118.13  3.000
 0XG  C6   C4   O5   119.59  3.000
 0XG  N2   C4   O5   122.26  3.000
 0XG  C4   C6   C11  122.46  3.000
 0XG  C11  C6   C7   118.12  3.000
 0XG  C4   C6   C7   119.18  3.000
 0XG  C15  N14  C13  116.25  3.000
 0XG  O19  C17  N18  119.85  3.000
 0XG  O19  C17  C16  117.14  3.000
 0XG  N18  C17  C16  123.01  3.000
 0XG  C17  O19  C20  119.24  3.000
 0XG  C26  C23  C24  125.32  3.000
 0XG  C26  C23  C22  122.21  3.000
 0XG  C24  C23  C22  112.48  3.000
 0XG  C24  S25  C21   92.54  3.000
 0XG  O27  C26  C23  112.83  3.000
 0XG  O27  C26  O28  123.69  3.000
 0XG  C23  C26  O28  123.49  3.000
 0XG  H18  O27  C26  110.08  3.000
 0XG  H17  N12  C13  113.05  3.000
 0XG  H17  N12  C9   115.25  3.000
 0XG  C13  N12  C9   131.68  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
 0XG  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 0XG  CONST_02  C10  C11  C6   C7     0.00   0.0  0
 0XG  CONST_03  C11  C6   C7   C8     0.00   0.0  0
 0XG  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 0XG  CONST_05  C6   C7   C8   C9     0.00   0.0  0
 0XG  CONST_06  C6   C11  C10  C9     0.00   0.0  0
 0XG  CONST_07  C16  C15  N14  C13    0.00   0.0  0
 0XG  CONST_08  C16  C17  N18  C13    0.00   0.0  0
 0XG  CONST_09  N18  C13  N14  C15    0.00   0.0  0
 0XG  CONST_10  S25  C21  C16  C15  180.00   0.0  0
 0XG  CONST_11  C22  C21  C16  C15    0.00   0.0  0
 0XG  CONST_12  N18  C17  C16  C15    0.00   0.0  0
 0XG  CONST_13  C24  S25  C21  C16  180.00   0.0  0
 0XG  CONST_14  C23  C22  C21  C16  180.00   0.0  0
 0XG  CONST_15  C21  C16  C17  N18  180.00   0.0  0
 0XG  CONST_16  C23  C24  S25  C21    0.00   0.0  0
 0XG  CONST_17  N14  C15  C16  C21  180.00   0.0  0
 0XG  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 0XG  CONST_19  C24  S25  C21  C22    0.00   0.0  0
 0XG  CONST_20  C17  C16  C21  C22  180.00   0.0  0
 0XG  CONST_21  S25  C24  C23  C22    0.00   0.0  0
 0XG  CONST_22  C17  C16  C15  N14    0.00   0.0  0
 0XG  CONST_23  C17  N18  C13  N14    0.00   0.0  0
 0XG  CONST_24  S25  C21  C16  C17    0.00   0.0  0
 0XG  CONST_25  S25  C21  C22  C23    0.00   0.0  0
 0XG  CONST_26  N12  C9   C8   C7   180.00   0.0  0
 0XG  CONST_27  C4   C6   C7   C8   180.00   0.0  0
 0XG  CONST_28  C4   C6   C11  C10  180.00   0.0  0
 0XG  CONST_29  N12  C9   C10  C11  180.00   0.0  0
 0XG  CONST_30  O19  C17  N18  C13  180.00   0.0  0
 0XG  CONST_31  N12  C13  N14  C15  180.00   0.0  0
 0XG  CONST_32  O19  C17  C16  C15  180.00   0.0  0
 0XG  CONST_33  O19  C17  C16  C21    0.00   0.0  0
 0XG  CONST_34  C26  C23  C22  C21  180.00   0.0  0
 0XG  CONST_35  C17  N18  C13  N12  180.00   0.0  0
 0XG  CONST_36  C26  C23  C24  S25  180.00   0.0  0
 0XG  CONST_37  H10  C11  C6   C7   180.00   0.0  0
 0XG  CONST_38  H9   C10  C9   C8   180.00   0.0  0
 0XG  CONST_39  H7   C7   C8   C9   180.00   0.0  0
 0XG  CONST_40  H8   C8   C9   C10  180.00   0.0  0
 0XG  CONST_41  H11  C15  N14  C13  180.00   0.0  0
 0XG  CONST_42  H15  C22  C21  C16    0.00   0.0  0
 0XG  CONST_43  H16  C24  S25  C21  180.00   0.0  0
 0XG  CONST_44  C6   C4   N2   C1   180.00   0.0  0
 0XG  CONST_46  H18  O27  C26  C23  180.00   0.0  0
 0XG  CONST_47  O5   C4   N2   C1     0.00   0.0  0
 0XG  Var_01    C13  N12  C9   C8     2.90  30.0  2
 0XG  Var_02    N14  C13  N12  C9    -0.84  30.0  2
 0XG  Var_03    C7   C6   C4   O5    42.20  30.0  2
 0XG  Var_04    O28  C26  C23  C22    0.72  30.0  2
 0XG  Var_05    H12  C20  O19  C17   61.71  30.0  3
 0XG  Var_06    H4   C3   N2   C1   -42.77  30.0  3
 0XG  Var_07    H1   C1   N2   C3   -42.23  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
 0XG  plan-1  C16  0.020
 0XG  plan-1  C21  0.020
 0XG  plan-1  C22  0.020
 0XG  plan-1  C24  0.020
 0XG  plan-1  C23  0.020
 0XG  plan-1  S25  0.020
 0XG  plan-1  C26  0.020
 0XG  plan-1  H15  0.020
 0XG  plan-1  H16  0.020
 0XG  plan-2  C7   0.020
 0XG  plan-2  C8   0.020
 0XG  plan-2  C9   0.020
 0XG  plan-2  C10  0.020
 0XG  plan-2  C11  0.020
 0XG  plan-2  C4   0.020
 0XG  plan-2  C6   0.020
 0XG  plan-2  H7   0.020
 0XG  plan-2  H8   0.020
 0XG  plan-2  H9   0.020
 0XG  plan-2  H10  0.020
 0XG  plan-2  N12  0.020
 0XG  plan-3  C13  0.020
 0XG  plan-3  C15  0.020
 0XG  plan-3  C16  0.020
 0XG  plan-3  N18  0.020
 0XG  plan-3  C21  0.020
 0XG  plan-3  N14  0.020
 0XG  plan-3  C17  0.020
 0XG  plan-3  O19  0.020
 0XG  plan-3  H11  0.020
 0XG  plan-3  N12  0.020
 0XG  plan-4  C1   0.020
 0XG  plan-4  C3   0.020
 0XG  plan-4  O5   0.020
 0XG  plan-4  N2   0.020
 0XG  plan-4  C4   0.020
 0XG  plan-4  C6   0.020
 0XG  plan-5  O28  0.020
 0XG  plan-5  C23  0.020
 0XG  plan-5  C26  0.020
 0XG  plan-5  O27  0.020
 0XG  plan-5  H18  0.020

