# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:06:06 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 8-[(E)-2-cyclopropylethenyl]-2-[(dimethylamino)methyl][1]benzothieno[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CC1=Nc2c(sc3ccc(/C=C/C4CC4)cc23)C(=O)N1
#
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
 LXG  LXG  8-[(E)-2-cyclopropylethenyl]-2-[(dimethylamino)methyl][1]benzothieno[3,2-d]pyrimidin-4(3H)-one  ligand  42  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_LXG
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
 LXG  C1    C  CH3   0  -0.526  -2.5502  -3.4598   1.4734
 LXG  N1    N  NT    0  -0.398  -2.9465  -3.3219   0.0876
 LXG  O1    O  O     0  -0.459  -4.2290   2.4732   0.2067
 LXG  S1    S  S2    0   0.250  -1.1055   3.0639   0.0430
 LXG  C2    C  CH3   0  -0.522  -3.5493  -4.5406  -0.4106
 LXG  N2    N  N     0  -0.437  -1.7987  -0.7897  -0.1387
 LXG  C3    C  CH2   0  -0.367  -3.8051  -2.1898  -0.1208
 LXG  N3    N  NR16  0  -0.700  -3.8868   0.2190   0.0784
 LXG  C4    C  CR6   0   0.489  -3.0837  -0.8709  -0.0484
 LXG  C5    C  CR56  0   0.287  -1.2737   0.4618  -0.0956
 LXG  C6    C  CR56  0   0.215   0.1324   0.7590  -0.1517
 LXG  C7    C  CR16  0  -0.391   1.2067  -0.1246  -0.2469
 LXG  C8    C  CR6   0   0.161   2.5078   0.3579  -0.2668
 LXG  C9    C  C1    0  -0.320   3.6163  -0.5955  -0.3414
 LXG  C10   C  C1    0  -0.181   4.9099  -0.3266  -0.1381
 LXG  C11   C  CH1   0  -0.321   5.9831  -1.3248  -0.2162
 LXG  C12   C  CH2   0  -0.478   7.3474  -0.9021  -0.7026
 LXG  C13   C  CH2   0  -0.478   7.1489  -1.2263   0.7373
 LXG  C14   C  CR16  0  -0.327   2.7100   1.7543  -0.2134
 LXG  C15   C  CR16  0  -0.253   1.6620   2.6435  -0.1222
 LXG  C16   C  CR56  0  -0.260   0.3633   2.1395  -0.0852
 LXG  C17   C  CR56  0  -0.407  -2.0302   1.6045   0.0123
 LXG  C18   C  CR6   0   0.550  -3.4555   1.5366   0.1062
 LXG  H1    H  HCH3  0   0.197  -3.4008  -3.6548   2.1446
 LXG  H1A   H  HCH3  0   0.236  -1.8473  -4.2874   1.5757
 LXG  H1B   H  HCH3  0   0.241  -2.0448  -2.5595   1.8200
 LXG  H2    H  HCH3  0   0.197  -4.4696  -4.8250   0.1215
 LXG  H2A   H  HCH3  0   0.237  -3.7930  -4.4346  -1.4683
 LXG  H2B   H  HCH3  0   0.237  -2.8425  -5.3651  -0.3123
 LXG  H3    H  HCH2  0   0.293  -4.2427  -2.2510  -1.1234
 LXG  H3A   H  HCH2  0   0.236  -4.6604  -2.1620   0.5774
 LXG  HN3   H  HNR6  0   0.433  -4.8868   0.0731   0.1545
 LXG  H7    H  HCR6  0   0.254   1.0183  -1.1908  -0.2937
 LXG  H9    H  H     0   0.242   3.3312  -1.6195  -0.5663
 LXG  H10   H  H     0   0.249   5.2254   0.6827   0.1157
 LXG  H11   H  HCH1  0   0.261   5.6674  -2.3270  -0.4856
 LXG  H12   H  HCH2  0   0.259   7.8932  -1.6031  -1.3204
 LXG  H12A  H  HCH2  0   0.252   7.4807   0.1359  -0.9811
 LXG  H13   H  HCH2  0   0.252   7.1438  -0.4121   1.4510
 LXG  H13A  H  HCH2  0   0.259   7.5558  -2.1532   1.1199
 LXG  H14   H  HCR6  0   0.261   3.7157   2.1520  -0.2542
 LXG  H15   H  HCR6  0   0.275   1.8480   3.7086  -0.0855

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
 LXG  N1   C1    single    1.448  0.020  1.448
 LXG  C1   H1    single    0.970  0.020  1.090
 LXG  C1   H1A   single    0.970  0.020  1.090
 LXG  C1   H1B   single    0.970  0.020  1.090
 LXG  C2   N1    single    1.448  0.020  1.448
 LXG  N1   C3    single    1.436  0.020  1.436
 LXG  C18  O1    double    1.219  0.020  1.219
 LXG  C17  S1    aromatic  1.728  0.020  1.728
 LXG  C16  S1    aromatic  1.740  0.020  1.740
 LXG  C2   H2    single    0.970  0.020  1.090
 LXG  C2   H2A   single    0.970  0.020  1.090
 LXG  C2   H2B   single    0.970  0.020  1.090
 LXG  N2   C4    double    1.291  0.020  1.291
 LXG  N2   C5    single    1.358  0.020  1.358
 LXG  C3   C4    single    1.505  0.020  1.505
 LXG  C3   H3    single    0.970  0.020  1.090
 LXG  C3   H3A   single    0.970  0.020  1.090
 LXG  C4   N3    single    1.360  0.020  1.360
 LXG  N3   C18   single    1.387  0.020  1.387
 LXG  N3   HN3   single    0.860  0.020  1.020
 LXG  C5   C6    aromatic  1.438  0.020  1.438
 LXG  C5   C17   aromatic  1.375  0.020  1.375
 LXG  C7   C6    aromatic  1.394  0.020  1.394
 LXG  C6   C16   aromatic  1.401  0.020  1.401
 LXG  C7   C8    aromatic  1.388  0.020  1.388
 LXG  C7   H7    single    0.930  0.020  1.080
 LXG  C9   C8    single    1.464  0.020  1.464
 LXG  C8   C14   aromatic  1.412  0.020  1.412
 LXG  C10  C9    double    1.337  0.020  1.337
 LXG  C9   H9    single    0.930  0.020  1.080
 LXG  C11  C10   single    1.468  0.020  1.468
 LXG  C10  H10   single    0.930  0.020  1.080
 LXG  C13  C11   single    1.509  0.020  1.509
 LXG  C12  C11   single    1.509  0.020  1.509
 LXG  C11  H11   single    0.970  0.020  1.090
 LXG  C13  C12   single    1.489  0.020  1.489
 LXG  C12  H12   single    0.970  0.020  1.090
 LXG  C12  H12A  single    0.970  0.020  1.090
 LXG  C13  H13   single    0.970  0.020  1.090
 LXG  C13  H13A  single    0.970  0.020  1.090
 LXG  C14  C15   aromatic  1.377  0.020  1.377
 LXG  C14  H14   single    0.930  0.020  1.080
 LXG  C16  C15   aromatic  1.394  0.020  1.394
 LXG  C15  H15   single    0.930  0.020  1.080
 LXG  C17  C18   single    1.430  0.020  1.430

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
 LXG  H1B   C1   H1A  107.36  3.000
 LXG  H1B   C1   H1   108.11  3.000
 LXG  H1A   C1   H1   107.84  3.000
 LXG  H1B   C1   N1   110.66  3.000
 LXG  H1A   C1   N1   109.78  3.000
 LXG  H1    C1   N1   112.89  3.000
 LXG  C3    N1   C2   111.39  3.000
 LXG  C3    N1   C1   112.19  3.000
 LXG  C2    N1   C1   111.29  3.000
 LXG  C17   S1   C16   90.10  3.000
 LXG  H2B   C2   H2A  107.80  3.000
 LXG  H2B   C2   H2   107.64  3.000
 LXG  H2A   C2   H2   107.89  3.000
 LXG  H2B   C2   N1   109.61  3.000
 LXG  H2A   C2   N1   110.18  3.000
 LXG  H2    C2   N1   113.54  3.000
 LXG  C5    N2   C4   116.14  3.000
 LXG  H3A   C3   H3   105.70  3.000
 LXG  H3A   C3   C4   108.58  3.000
 LXG  H3    C3   C4   106.53  3.000
 LXG  H3A   C3   N1   113.02  3.000
 LXG  H3    C3   N1   109.12  3.000
 LXG  C4    C3   N1   113.41  3.000
 LXG  HN3   N3   C18  116.24  3.000
 LXG  HN3   N3   C4   118.32  3.000
 LXG  C18   N3   C4   125.44  3.000
 LXG  N3    C4   C3   115.08  3.000
 LXG  N3    C4   N2   122.96  3.000
 LXG  C3    C4   N2   121.93  3.000
 LXG  C17   C5   C6   111.67  3.000
 LXG  C17   C5   N2   123.77  3.000
 LXG  C6    C5   N2   124.55  3.000
 LXG  C16   C6   C7   120.05  3.000
 LXG  C16   C6   C5   111.27  3.000
 LXG  C7    C6   C5   128.68  3.000
 LXG  H7    C7   C8   120.30  3.000
 LXG  H7    C7   C6   119.50  3.000
 LXG  C8    C7   C6   120.20  3.000
 LXG  C14   C8   C9   122.51  3.000
 LXG  C14   C8   C7   118.53  3.000
 LXG  C9    C8   C7   118.96  3.000
 LXG  H9    C9   C10  118.36  3.000
 LXG  H9    C9   C8   115.19  3.000
 LXG  C10   C9   C8   126.44  3.000
 LXG  H10   C10  C11  115.57  3.000
 LXG  H10   C10  C9   120.19  3.000
 LXG  C11   C10  C9   124.23  3.000
 LXG  H11   C11  C13  116.23  3.000
 LXG  H11   C11  C12  116.23  3.000
 LXG  C13   C11  C12   59.13  3.000
 LXG  H11   C11  C10  115.40  3.000
 LXG  C12   C11  C10  119.19  3.000
 LXG  C13   C11  C10  119.12  3.000
 LXG  H12A  C12  H12  114.33  3.000
 LXG  H12A  C12  C13  118.28  3.000
 LXG  H12   C12  C13  118.57  3.000
 LXG  H12A  C12  C11  117.56  3.000
 LXG  H12   C12  C11  117.29  3.000
 LXG  C13   C12  C11   60.45  3.000
 LXG  H13A  C13  H13  114.39  3.000
 LXG  H13A  C13  C12  118.56  3.000
 LXG  H13   C13  C12  118.31  3.000
 LXG  H13A  C13  C11  117.24  3.000
 LXG  H13   C13  C11  117.51  3.000
 LXG  C12   C13  C11   60.42  3.000
 LXG  H14   C14  C15  118.18  3.000
 LXG  H14   C14  C8   119.68  3.000
 LXG  C15   C14  C8   122.14  3.000
 LXG  H15   C15  C16  121.02  3.000
 LXG  H15   C15  C14  120.46  3.000
 LXG  C16   C15  C14  118.52  3.000
 LXG  C15   C16  C6   120.57  3.000
 LXG  C15   C16  S1   126.62  3.000
 LXG  C6    C16  S1   112.82  3.000
 LXG  C18   C17  C5   120.94  3.000
 LXG  C18   C17  S1   124.91  3.000
 LXG  C5    C17  S1   114.14  3.000
 LXG  C17   C18  N3   110.72  3.000
 LXG  C17   C18  O1   126.97  3.000
 LXG  N3    C18  O1   122.31  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
 LXG  CONST_01  C6   C5   C17  S1      0.00   0.0  0
 LXG  CONST_02  C5   C6   C16  S1      0.00   0.0  0
 LXG  CONST_03  C7   C6   C16  S1    180.00   0.0  0
 LXG  CONST_04  C14  C15  C16  S1    180.00   0.0  0
 LXG  CONST_05  C8   C7   C6   C5    180.00   0.0  0
 LXG  CONST_06  C15  C16  C6   C5    180.00   0.0  0
 LXG  CONST_07  C16  S1   C17  C5      0.00   0.0  0
 LXG  CONST_08  C14  C8   C7   C6      0.00   0.0  0
 LXG  CONST_09  C17  S1   C16  C6      0.00   0.0  0
 LXG  CONST_10  C14  C15  C16  C6      0.00   0.0  0
 LXG  CONST_11  C17  C5   C6   C7    180.00   0.0  0
 LXG  CONST_12  C15  C16  C6   C7      0.00   0.0  0
 LXG  CONST_13  C15  C14  C8   C7      0.00   0.0  0
 LXG  CONST_14  C16  C6   C7   C8      0.00   0.0  0
 LXG  CONST_15  C16  C15  C14  C8      0.00   0.0  0
 LXG  CONST_16  C17  S1   C16  C15   180.00   0.0  0
 LXG  CONST_17  C17  C5   C6   C16     0.00   0.0  0
 LXG  CONST_18  C18  N3   C4   N2      0.00   0.0  0
 LXG  CONST_19  C5   N2   C4   N3      0.00   0.0  0
 LXG  CONST_20  C17  C18  N3   C4      0.00   0.0  0
 LXG  CONST_21  C9   C8   C7   C6    180.00   0.0  0
 LXG  CONST_22  C15  C14  C8   C9    180.00   0.0  0
 LXG  CONST_23  C4   N3   C18  O1    180.00   0.0  0
 LXG  CONST_24  C5   N2   C4   C3    180.00   0.0  0
 LXG  CONST_25  C18  N3   C4   C3    180.00   0.0  0
 LXG  CONST_26  H15  C15  C16  S1      0.00   0.0  0
 LXG  CONST_27  H7   C7   C6   C5      0.00   0.0  0
 LXG  CONST_28  H14  C14  C8   C7    180.00   0.0  0
 LXG  CONST_29  HN3  N3   C4   N2    180.00   0.0  0
 LXG  CONST_30  C11  C10  C9   C8    180.00   0.0  0
 LXG  CONST_31  H10  C10  C9   C8      0.00   0.0  0
 LXG  CONST_32  H9   C9   C10  C11     0.00   0.0  0
 LXG  Var_01    C12  C13  C11  C10  -108.50  30.0  1
 LXG  Var_02    H12  C12  C13  C11  -106.95  30.0  1
 LXG  Var_03    N2   C4   C3   N1     16.79  30.0  3
 LXG  Var_04    C10  C9   C8   C7   -167.56  30.0  1
 LXG  Var_05    C13  C11  C10  C9   -143.81  30.0  1
 LXG  Var_06    C4   C3   N1   C1     73.33  30.0  3
 LXG  Var_07    H2   C2   N1   C1     61.82  30.0  3
 LXG  Var_08    H1   C1   N1   C2    -62.07  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 LXG  chir_01  C11  C10  C13  C12  both

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
 LXG  plan-1  O1   0.020
 LXG  plan-1  S1   0.020
 LXG  plan-1  N2   0.020
 LXG  plan-1  C3   0.020
 LXG  plan-1  N3   0.020
 LXG  plan-1  C4   0.020
 LXG  plan-1  C5   0.020
 LXG  plan-1  C6   0.020
 LXG  plan-1  C7   0.020
 LXG  plan-1  C8   0.020
 LXG  plan-1  C9   0.020
 LXG  plan-1  C14  0.020
 LXG  plan-1  C15  0.020
 LXG  plan-1  C16  0.020
 LXG  plan-1  C17  0.020
 LXG  plan-1  C18  0.020
 LXG  plan-1  HN3  0.020
 LXG  plan-1  H7   0.020
 LXG  plan-1  H14  0.020
 LXG  plan-1  H15  0.020
 LXG  plan-2  C8   0.020
 LXG  plan-2  C9   0.020
 LXG  plan-2  C10  0.020
 LXG  plan-2  C11  0.020
 LXG  plan-2  H9   0.020
 LXG  plan-2  H10  0.020

