# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:48:44 2021
#   Inital geometry file: a 100 line input string
#   Ligand name: 3-[5-(2-hydroxy-2-oxoethyl)-3-oxidanylidene-[1,2,4]triazino[2,3-a]benzimidazol-2-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC1=NN2c3ccccc3N(CC(O)=O)C2=NC1=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
 EQR  EQR  '3-[5-(2-hydroxy-2-oxoethyl)-3-oxidanylidene-[1,2,4]triazino[2,3-a]benzimidazol-2-yl]propanoic acid'  ligand  35  23  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EQR
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
 EQR  C4   C  CR16  0  -0.297  -45.4101  22.8539  21.1872
 EQR  C14  C  C     0   0.552  -44.9778  23.1910  15.6250
 EQR  C5   C  CR16  0  -0.269  -45.4484  24.2334  21.3451
 EQR  C6   C  CR16  0  -0.262  -45.6983  25.0799  20.2642
 EQR  C7   C  CR16  0  -0.308  -45.9211  24.5856  18.9843
 EQR  C8   C  CR6   0   0.427  -45.7665  18.8674  17.9169
 EQR  C9   C  CR6   0   0.096  -45.5000  18.8772  19.3868
 EQR  C10  C  CH2   0  -0.498  -45.2703  17.5797  20.0857
 EQR  C12  C  C     0   0.554  -43.7987  18.4877  21.9227
 EQR  N1   N  NR5   0  -0.594  -46.0707  22.4087  17.7105
 EQR  N2   N  N     0  -0.476  -45.6573  21.0878  19.4022
 EQR  C3   C  CR56  0   0.794  -45.9041  21.1154  18.0694
 EQR  N3   N  N     0  -0.525  -45.9650  20.0677  17.3061
 EQR  C1   C  CR56  0   0.367  -45.6337  22.3741  19.9132
 EQR  C2   C  CR56  0   0.317  -45.8870  23.2120  18.8278
 EQR  N4   N  N     0  -0.203  -45.4565  19.9572  20.0774
 EQR  O1   O  O     0  -0.448  -42.8244  18.5612  21.2160
 EQR  O2   O  OH1   0  -0.593  -43.8642  19.0411  23.1283
 EQR  O3   O  O     0  -0.457  -45.7984  17.8080  17.3112
 EQR  O4   O  O     0  -0.434  -44.9861  23.6385  14.5088
 EQR  O5   O  OH1   0  -0.574  -43.8956  22.9343  16.3328
 EQR  H1   H  HCR6  0   0.281  -45.2124  22.1877  22.0157
 EQR  H2   H  HCR6  0   0.270  -45.2773  24.6578  22.3249
 EQR  H3   H  HCR6  0   0.271  -45.7170  26.1495  20.4225
 EQR  H4   H  HCH2  0   0.277  -45.9119  18.1764  22.0679
 EQR  H5   H  HCH2  0   0.306  -44.9420  16.7243  22.0146
 EQR  H6   H  HCR6  0   0.285  -46.1081  25.2539  18.1547
 EQR  H7   H  HCH2  0   0.286  -46.1314  16.9305  19.9100
 EQR  H8   H  HCH2  0   0.276  -44.4244  17.0733  19.6148
 EQR  H9   H  HCH2  0   0.329  -46.9132  23.7239  16.3462
 EQR  H10  H  HCH2  0   0.335  -46.7739  22.0710  15.7984
 EQR  H12  H  HOH1  0   0.477  -43.0264  19.4828  23.3328
 EQR  H13  H  HOH1  0   0.493  -43.0991  23.1514  15.8236
 EQR  C13  C  CH2   0  -0.465  -46.2589  22.8515  16.3602
 EQR  C11  C  CH2   0  -0.592  -45.0488  17.7230  21.5800

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
 EQR  O4   C14  double    1.203  0.020  1.203
 EQR  C14  O5   single    1.318  0.020  1.318
 EQR  C14  C13  single    1.516  0.020  1.516
 EQR  C13  N1   single    1.433  0.020  1.433
 EQR  N3   C8   single    1.361  0.020  1.361
 EQR  N3   C3   double    1.298  0.020  1.298
 EQR  O3   C8   double    1.221  0.020  1.221
 EQR  N1   C3   single    1.352  0.020  1.352
 EQR  N1   C2   single    1.388  0.020  1.388
 EQR  C8   C9   single    1.494  0.020  1.494
 EQR  C3   N2   single    1.356  0.020  1.356
 EQR  C2   C7   aromatic  1.383  0.020  1.383
 EQR  C2   C1   aromatic  1.394  0.020  1.394
 EQR  C7   C6   aromatic  1.390  0.020  1.390
 EQR  N2   C1   single    1.384  0.020  1.384
 EQR  N2   N4   single    1.332  0.020  1.332
 EQR  C9   N4   double    1.283  0.020  1.283
 EQR  C9   C10  single    1.492  0.020  1.492
 EQR  C1   C4   aromatic  1.380  0.020  1.380
 EQR  C6   C5   aromatic  1.395  0.020  1.395
 EQR  C10  C11  single    1.517  0.020  1.517
 EQR  C4   C5   aromatic  1.389  0.020  1.389
 EQR  C11  C12  single    1.505  0.020  1.505
 EQR  O1   C12  double    1.206  0.020  1.206
 EQR  C12  O2   single    1.328  0.020  1.328
 EQR  C4   H1   single    0.930  0.020  1.080
 EQR  C5   H2   single    0.930  0.020  1.080
 EQR  C6   H3   single    0.930  0.020  1.080
 EQR  C11  H4   single    0.970  0.020  1.090
 EQR  C11  H5   single    0.970  0.020  1.090
 EQR  C7   H6   single    0.930  0.020  1.080
 EQR  C10  H7   single    0.970  0.020  1.090
 EQR  C10  H8   single    0.970  0.020  1.090
 EQR  C13  H9   single    0.970  0.020  1.090
 EQR  C13  H10  single    0.970  0.020  1.090
 EQR  O2   H12  single    0.850  0.020  0.980
 EQR  O5   H13  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
 EQR  H1   C4   C1   121.53  3.000
 EQR  H1   C4   C5   121.99  3.000
 EQR  C1   C4   C5   116.48  3.000
 EQR  O5   C14  O4   125.20  3.000
 EQR  O5   C14  C13  112.94  3.000
 EQR  O4   C14  C13  121.86  3.000
 EQR  H2   C5   C6   119.47  3.000
 EQR  H2   C5   C4   119.24  3.000
 EQR  C6   C5   C4   121.29  3.000
 EQR  H3   C6   C7   118.93  3.000
 EQR  H3   C6   C5   119.32  3.000
 EQR  C7   C6   C5   121.75  3.000
 EQR  H6   C7   C2   122.08  3.000
 EQR  H6   C7   C6   120.95  3.000
 EQR  C2   C7   C6   116.97  3.000
 EQR  O3   C8   N3   122.60  3.000
 EQR  O3   C8   C9   119.90  3.000
 EQR  N3   C8   C9   117.50  3.000
 EQR  N4   C9   C10  118.36  3.000
 EQR  C10  C9   C8   118.87  3.000
 EQR  N4   C9   C8   122.77  3.000
 EQR  H8   C10  H7   105.40  3.000
 EQR  H8   C10  C9   108.69  3.000
 EQR  H7   C10  C9   108.67  3.000
 EQR  H8   C10  C11  110.80  3.000
 EQR  H7   C10  C11  109.24  3.000
 EQR  C9   C10  C11  113.68  3.000
 EQR  O2   C12  O1   123.12  3.000
 EQR  O2   C12  C11  112.18  3.000
 EQR  O1   C12  C11  124.66  3.000
 EQR  C2   N1   C3   108.87  3.000
 EQR  C2   N1   C13  126.63  3.000
 EQR  C3   N1   C13  124.16  3.000
 EQR  N4   N2   C1   126.80  3.000
 EQR  N4   N2   C3   122.89  3.000
 EQR  C1   N2   C3   110.31  3.000
 EQR  N3   C3   N2   124.78  3.000
 EQR  N2   C3   N1   107.62  3.000
 EQR  N3   C3   N1   127.60  3.000
 EQR  C3   N3   C8   116.17  3.000
 EQR  C2   C1   N2   105.54  3.000
 EQR  N2   C1   C4   131.82  3.000
 EQR  C2   C1   C4   122.63  3.000
 EQR  C1   C2   N1   107.62  3.000
 EQR  C1   C2   C7   120.88  3.000
 EQR  N1   C2   C7   131.50  3.000
 EQR  N2   N4   C9   115.89  3.000
 EQR  H12  O2   C12  109.81  3.000
 EQR  H13  O5   C14  110.40  3.000
 EQR  H10  C13  H9   106.40  3.000
 EQR  H10  C13  N1   109.03  3.000
 EQR  H9   C13  N1   109.76  3.000
 EQR  H10  C13  C14  108.03  3.000
 EQR  H9   C13  C14  108.77  3.000
 EQR  N1   C13  C14  114.53  3.000
 EQR  H5   C11  H4   106.20  3.000
 EQR  H5   C11  C12  106.99  3.000
 EQR  H4   C11  C12  110.15  3.000
 EQR  H5   C11  C10  108.61  3.000
 EQR  H4   C11  C10  111.37  3.000
 EQR  C12  C11  C10  113.17  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
 EQR  CONST_01  C7   C2   C1   C4      0.00   0.0  0
 EQR  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 EQR  CONST_03  C2   C7   C6   C5      0.00   0.0  0
 EQR  CONST_04  C2   C1   C4   C5      0.00   0.0  0
 EQR  CONST_05  C1   C2   C7   C6      0.00   0.0  0
 EQR  CONST_06  C1   C4   C5   C6      0.00   0.0  0
 EQR  CONST_07  N1   C3   N3   C8    180.00   0.0  0
 EQR  CONST_08  N2   C3   N3   C8      0.00   0.0  0
 EQR  CONST_09  C1   N2   C3   N1      0.00   0.0  0
 EQR  CONST_10  N4   N2   C3   N1    180.00   0.0  0
 EQR  CONST_11  N2   C1   C2   N1      0.00   0.0  0
 EQR  CONST_12  C2   N1   C3   N2      0.00   0.0  0
 EQR  CONST_13  C1   C2   N1   C3      0.00   0.0  0
 EQR  CONST_14  C2   C1   N2   C3      0.00   0.0  0
 EQR  CONST_15  C2   N1   C3   N3    180.00   0.0  0
 EQR  CONST_16  C1   N2   C3   N3    180.00   0.0  0
 EQR  CONST_17  N4   N2   C3   N3      0.00   0.0  0
 EQR  CONST_18  N4   N2   C1   C2    180.00   0.0  0
 EQR  CONST_19  N3   C3   N1   C13     0.00   0.0  0
 EQR  CONST_20  N2   C3   N1   C13   180.00   0.0  0
 EQR  CONST_21  C1   C2   N1   C13   180.00   0.0  0
 EQR  CONST_22  H3   C6   C5   C4    180.00   0.0  0
 EQR  CONST_23  H6   C7   C6   C5    180.00   0.0  0
 EQR  CONST_24  H1   C4   C5   C6    180.00   0.0  0
 EQR  CONST_25  H2   C5   C6   C7    180.00   0.0  0
 EQR  CONST_26  H12  O2   C12  C11   180.00   0.0  0
 EQR  CONST_27  H13  O5   C14  C13   180.00   0.0  0
 EQR  Var_01    C3   N1   C13  C14   -90.43  30.0  3
 EQR  Var_02    C8   C9   C10  C11  -178.43  30.0  2
 EQR  Var_03    C12  C11  C10  C9    -64.27  30.0  3
 EQR  Var_04    O4   C14  C13  N1   -176.23  30.0  3
 EQR  Var_05    O1   C12  C11  C10   -26.42  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
 EQR  plan-1  C4   0.020
 EQR  plan-1  C5   0.020
 EQR  plan-1  C6   0.020
 EQR  plan-1  C7   0.020
 EQR  plan-1  C8   0.020
 EQR  plan-1  C9   0.020
 EQR  plan-1  C10  0.020
 EQR  plan-1  N1   0.020
 EQR  plan-1  N2   0.020
 EQR  plan-1  C3   0.020
 EQR  plan-1  N3   0.020
 EQR  plan-1  C1   0.020
 EQR  plan-1  C2   0.020
 EQR  plan-1  N4   0.020
 EQR  plan-1  O3   0.020
 EQR  plan-1  H1   0.020
 EQR  plan-1  H2   0.020
 EQR  plan-1  H3   0.020
 EQR  plan-1  H6   0.020
 EQR  plan-1  C13  0.020
 EQR  plan-2  C14  0.020
 EQR  plan-2  O4   0.020
 EQR  plan-2  O5   0.020
 EQR  plan-2  H13  0.020
 EQR  plan-2  C13  0.020
 EQR  plan-3  C12  0.020
 EQR  plan-3  O1   0.020
 EQR  plan-3  O2   0.020
 EQR  plan-3  H12  0.020
 EQR  plan-3  C11  0.020

