# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:14:05 2022
#   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  33  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.300  -45.2004  22.8325  21.1143
 EQR  C14  C  C      0   0.417  -44.8767  23.0335  15.6148
 EQR  C5   C  CR16   0  -0.273  -45.2263  24.2140  21.2568
 EQR  C6   C  CR16   0  -0.262  -45.5410  25.0463  20.1810
 EQR  C7   C  CR16   0  -0.314  -45.8424  24.5357  18.9238
 EQR  C8   C  CR6    0   0.406  -45.7466  18.8108  17.9265
 EQR  C9   C  CR6    0   0.080  -45.4469  18.8327  19.3933
 EQR  C10  C  CH2    0  -0.479  -45.2625  17.5397  20.1144
 EQR  C12  C  C      0   0.411  -43.8315  18.3871  22.0939
 EQR  N1   N  NR5    0  -0.557  -46.0821  22.3483  17.6892
 EQR  N2   N  N      0  -0.472  -45.5549  21.0480  19.3682
 EQR  C3   C  CR56   0   0.766  -45.8767  21.0655  18.0486
 EQR  N3   N  N      0  -0.528  -45.9767  19.9997  17.3075
 EQR  C1   C  CR56   0   0.354  -45.5034  22.3372  19.8619
 EQR  C2   C  CR56   0   0.309  -45.8192  23.1590  18.7788
 EQR  N4   N  N      0  -0.202  -45.3618  19.9253  20.0611
 EQR  O1   O  O      0  -0.609  -42.8020  18.1876  21.4181
 EQR  O2   O  OC    -1  -0.619  -43.9205  19.0634  23.1388
 EQR  O3   O  O      0  -0.461  -45.7880  17.7433  17.3316
 EQR  O4   O  O      0  -0.599  -44.9828  23.4922  14.4651
 EQR  O5   O  OC    -1  -0.582  -43.8524  22.7411  16.2498
 EQR  H1   H  HCR6   0   0.276  -44.9499  22.1739  21.9353
 EQR  H2   H  HCR6   0   0.262  -44.9943  24.6514  22.2183
 EQR  H3   H  HCR6   0   0.262  -45.5483  26.1181  20.3268
 EQR  H4   H  HCH2   0   0.208  -45.9954  18.1742  22.0404
 EQR  H5   H  HCH2   0   0.235  -45.1120  16.6673  22.0424
 EQR  H6   H  HCR6   0   0.278  -46.0795  25.1916  18.0972
 EQR  H7   H  HCH2   0   0.250  -46.1135  16.8971  19.8712
 EQR  H8   H  HCH2   0   0.251  -44.3892  17.0322  19.6955
 EQR  H9   H  HCH2   0   0.273  -46.8306  23.7080  16.3292
 EQR  H10  H  HCH2   0   0.276  -46.8109  22.0462  15.7836
 EQR  C13  C  CH2    0  -0.483  -46.2337  22.7949  16.3273
 EQR  C11  C  CH2    0  -0.575  -45.1177  17.6786  21.6204

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  deloc     1.242  0.020  1.242
 EQR  C14  O5   deloc     1.240  0.020  1.240
 EQR  C14  C13  single    1.551  0.020  1.551
 EQR  C13  N1   single    1.441  0.020  1.441
 EQR  N3   C8   single    1.360  0.020  1.360
 EQR  N3   C3   double    1.302  0.020  1.302
 EQR  O3   C8   double    1.223  0.020  1.223
 EQR  N1   C3   single    1.348  0.020  1.348
 EQR  N1   C2   single    1.383  0.020  1.383
 EQR  C8   C9   single    1.497  0.020  1.497
 EQR  C3   N2   single    1.358  0.020  1.358
 EQR  C2   C7   aromatic  1.385  0.020  1.385
 EQR  C2   C1   aromatic  1.396  0.020  1.396
 EQR  C7   C6   aromatic  1.390  0.020  1.390
 EQR  N2   C1   single    1.382  0.020  1.382
 EQR  N2   N4   single    1.333  0.020  1.333
 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  1.396  0.020  1.396
 EQR  C10  C11  single    1.519  0.020  1.519
 EQR  C4   C5   aromatic  1.389  0.020  1.389
 EQR  C11  C12  single    1.543  0.020  1.543
 EQR  O1   C12  deloc     1.248  0.020  1.248
 EQR  C12  O2   deloc     1.248  0.020  1.248
 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

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   121.39  3.000
 EQR  H1   C4   C5   122.13  3.000
 EQR  C1   C4   C5   116.47  3.000
 EQR  O5   C14  O4   129.16  3.000
 EQR  O5   C14  C13  116.82  3.000
 EQR  O4   C14  C13  114.02  3.000
 EQR  H2   C5   C6   119.49  3.000
 EQR  H2   C5   C4   119.31  3.000
 EQR  C6   C5   C4   121.20  3.000
 EQR  H3   C6   C7   118.97  3.000
 EQR  H3   C6   C5   119.24  3.000
 EQR  C7   C6   C5   121.79  3.000
 EQR  H6   C7   C2   121.77  3.000
 EQR  H6   C7   C6   121.07  3.000
 EQR  C2   C7   C6   117.15  3.000
 EQR  O3   C8   N3   122.42  3.000
 EQR  O3   C8   C9   119.74  3.000
 EQR  N3   C8   C9   117.84  3.000
 EQR  N4   C9   C10  118.56  3.000
 EQR  C10  C9   C8   119.05  3.000
 EQR  N4   C9   C8   122.38  3.000
 EQR  H8   C10  H7   105.28  3.000
 EQR  H8   C10  C9   108.41  3.000
 EQR  H7   C10  C9   107.79  3.000
 EQR  H8   C10  C11  110.24  3.000
 EQR  H7   C10  C11  110.38  3.000
 EQR  C9   C10  C11  114.31  3.000
 EQR  O2   C12  O1   126.81  3.000
 EQR  O2   C12  C11  116.51  3.000
 EQR  O1   C12  C11  116.63  3.000
 EQR  C2   N1   C3   108.59  3.000
 EQR  C2   N1   C13  125.64  3.000
 EQR  C3   N1   C13  124.25  3.000
 EQR  N4   N2   C1   126.49  3.000
 EQR  N4   N2   C3   123.37  3.000
 EQR  C1   N2   C3   110.11  3.000
 EQR  N3   C3   N2   124.09  3.000
 EQR  N2   C3   N1   107.90  3.000
 EQR  N3   C3   N1   128.00  3.000
 EQR  C3   N3   C8   116.34  3.000
 EQR  C2   C1   N2   105.29  3.000
 EQR  N2   C1   C4   131.85  3.000
 EQR  C2   C1   C4   122.85  3.000
 EQR  C1   C2   N1   108.01  3.000
 EQR  C1   C2   C7   120.53  3.000
 EQR  N1   C2   C7   131.46  3.000
 EQR  N2   N4   C9   115.91  3.000
 EQR  H10  C13  H9   106.61  3.000
 EQR  H10  C13  N1   108.30  3.000
 EQR  H9   C13  N1   108.37  3.000
 EQR  H10  C13  C14  109.86  3.000
 EQR  H9   C13  C14  110.53  3.000
 EQR  N1   C13  C14  112.93  3.000
 EQR  H5   C11  H4   105.96  3.000
 EQR  H5   C11  C12  107.54  3.000
 EQR  H4   C11  C12  110.10  3.000
 EQR  H5   C11  C10  107.33  3.000
 EQR  H4   C11  C10  110.25  3.000
 EQR  C12  C11  C10  115.19  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  Var_01    C3   N1   C13  C14   -83.69  30.0  3
 EQR  Var_02    C8   C9   C10  C11  -173.52  30.0  2
 EQR  Var_03    C12  C11  C10  C9    -67.03  30.0  3
 EQR  Var_04    O4   C14  C13  N1   -176.08  30.0  2
 EQR  Var_05    O1   C12  C11  C10   -34.86  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  C13  0.020
 EQR  plan-3  C12  0.020
 EQR  plan-3  O1   0.020
 EQR  plan-3  O2   0.020
 EQR  plan-3  C11  0.020

