# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:42:25 2021
#   Inital geometry file: a 98 line input string
#   Ligand name: {3-[(5S,7S,8S)-8-amino-8-carboxy-1-azaspiro[4.4]nonan-7-yl]propyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(C[C@]2(CCCN2)C[C@@H]1CCC[B-](O)(O)O)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
 QRA  QRA  {3-[(5S,7S,8S)-8-amino-8-carboxy-1-azaspiro[4.4]nonan-7-yl]propyl}(trihydroxy)borate(1-)  ligand  44  20  .  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 (reasonable std)
;

data_comp_QRA
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
 QRA  N1   N  NH1    0  -0.619  12.6268  4.5149  26.3354
 QRA  C4   C  CH2    0  -0.463  14.7241  4.1533  27.3574
 QRA  C5   C  CH2    0  -0.450  13.5933  4.0505  28.3939
 QRA  C6   C  CH2    0  -0.289  12.4462  4.8160  27.7449
 QRA  C7   C  CH2    0  -0.415  14.4591  3.9334  24.7874
 QRA  C8   C  CH1    0  -0.220  13.9627  4.8212  23.6453
 QRA  O    O  OH1    0  -0.590  16.2128  6.9486  23.6437
 QRA  O1   O  O      0  -0.443  14.5427  8.0452  22.6705
 QRA  C    C  CT     0  -0.016  13.9928  6.2852  24.2354
 QRA  N    N  NH2    0  -0.783  12.6321  6.7983  24.2298
 QRA  C9   C  CH2    0  -0.421  14.6655  4.5788  22.3135
 QRA  C11  C  CH2    0  -0.665  15.0661  2.9331  20.3916
 QRA  B    B  B     -1   0.455  14.8385  1.4356  19.7274
 QRA  O4   O  OB     0  -0.740  15.4595  1.3290  18.3992
 QRA  O3   O  OB     0  -0.756  15.4484  0.3854  20.5924
 QRA  O2   O  OB     0  -0.756  13.4031  1.1730  19.4777
 QRA  C3   C  CT     0   0.104  14.0594  4.6656  26.0635
 QRA  C2   C  CH2    0  -0.423  14.4516  6.1073  25.6982
 QRA  H1   H  HNH1   0   0.350  12.0939  5.1478  25.7470
 QRA  H3   H  HCH2   0   0.236  15.2010  3.1851  27.1944
 QRA  H4   H  HCH2   0   0.232  15.5105  4.8365  27.6838
 QRA  H5   H  HCH2   0   0.226  13.3060  3.0089  28.5467
 QRA  H6   H  HCH2   0   0.228  13.8691  4.4574  29.3664
 QRA  H7   H  HCH2   0   0.189  12.5312  5.8887  27.9772
 QRA  H8   H  HCH2   0   0.222  11.4650  4.4884  28.0951
 QRA  H9   H  HCH2   0   0.234  14.0504  2.9222  24.7486
 QRA  H10  H  HCH2   0   0.219  15.5510  3.8480  24.7417
 QRA  H11  H  HCH1   0   0.237  12.8998  4.6092  23.4859
 QRA  H12  H  HCH2   0   0.185  13.3517  2.9930  21.7222
 QRA  H13  H  HCH2   0   0.197  14.8242  2.4479  22.4883
 QRA  H14  H  HOH1   0   0.480  16.7507  7.5283  23.0833
 QRA  H15  H  HNH2   0   0.348  12.6105  7.7482  24.5825
 QRA  H16  H  HNH2   0   0.350  12.2773  6.8429  23.2812
 QRA  H18  H  HCH2   0   0.210  15.7423  4.7394  22.4177
 QRA  H19  H  HCH2   0   0.211  14.3097  5.2988  21.5677
 QRA  H20  H  HCH2   0   0.156  16.1413  3.1523  20.4806
 QRA  H21  H  HCH2   0   0.156  14.6800  3.7039  19.7079
 QRA  H22  H  H      0   0.418  16.3823  1.5803  18.4718
 QRA  H23  H  H      0   0.413  15.2984  0.5983  21.5161
 QRA  H24  H  H      0   0.417  12.8820  1.5360  20.1961
 QRA  H25  H  HCH2   0   0.245  15.5328  6.2101  25.7918
 QRA  H26  H  HCH2   0   0.247  14.0007  6.8575  26.3535
 QRA  C10  C  CH2    0  -0.451  14.4346  3.1731  21.7634
 QRA  C1   C  C      0   0.534  14.9240  7.1913  23.4346

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
 QRA  O4   B    single  1.470  0.020  1.470
 QRA  O2   B    single  1.481  0.020  1.481
 QRA  B    C11  single  1.654  0.020  1.654
 QRA  B    O3   single  1.491  0.020  1.491
 QRA  C11  C10  single  1.529  0.020  1.529
 QRA  C10  C9   single  1.527  0.020  1.527
 QRA  C9   C8   single  1.525  0.020  1.525
 QRA  O1   C1   double  1.208  0.020  1.208
 QRA  N    C    single  1.454  0.020  1.454
 QRA  C8   C    single  1.579  0.020  1.579
 QRA  C8   C7   single  1.529  0.020  1.529
 QRA  C1   C    single  1.526  0.020  1.526
 QRA  C1   O    single  1.328  0.020  1.328
 QRA  C    C2   single  1.543  0.020  1.543
 QRA  C7   C3   single  1.525  0.020  1.525
 QRA  C2   C3   single  1.538  0.020  1.538
 QRA  C3   N1   single  1.466  0.020  1.466
 QRA  C3   C4   single  1.542  0.020  1.542
 QRA  N1   C6   single  1.453  0.020  1.453
 QRA  C4   C5   single  1.537  0.020  1.537
 QRA  C6   C5   single  1.524  0.020  1.524
 QRA  N1   H1   single  0.890  0.020  1.040
 QRA  C4   H3   single  0.970  0.020  1.090
 QRA  C4   H4   single  0.970  0.020  1.090
 QRA  C5   H5   single  0.970  0.020  1.090
 QRA  C5   H6   single  0.970  0.020  1.090
 QRA  C6   H7   single  0.970  0.020  1.090
 QRA  C6   H8   single  0.970  0.020  1.090
 QRA  C7   H9   single  0.970  0.020  1.090
 QRA  C7   H10  single  0.970  0.020  1.090
 QRA  C8   H11  single  0.970  0.020  1.090
 QRA  C10  H12  single  0.970  0.020  1.090
 QRA  C10  H13  single  0.970  0.020  1.090
 QRA  O    H14  single  0.850  0.020  0.980
 QRA  N    H15  single  0.890  0.020  1.040
 QRA  N    H16  single  0.890  0.020  1.040
 QRA  C9   H18  single  0.970  0.020  1.090
 QRA  C9   H19  single  0.970  0.020  1.090
 QRA  C11  H20  single  0.970  0.020  1.090
 QRA  C11  H21  single  0.970  0.020  1.090
 QRA  O4   H22  single  0.850  0.020  0.980
 QRA  O3   H23  single  0.850  0.020  0.980
 QRA  O2   H24  single  0.850  0.020  0.980
 QRA  C2   H25  single  0.970  0.020  1.090
 QRA  C2   H26  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
 QRA  H1   N1   C3   109.96  3.000
 QRA  H1   N1   C6   111.59  3.000
 QRA  C3   N1   C6   106.28  3.000
 QRA  H4   C4   H3   106.56  3.000
 QRA  H4   C4   C3   110.70  3.000
 QRA  H3   C4   C3   110.95  3.000
 QRA  H4   C4   C5   111.73  3.000
 QRA  H3   C4   C5   111.27  3.000
 QRA  C3   C4   C5   105.72  3.000
 QRA  H6   C5   H5   107.34  3.000
 QRA  H6   C5   C6   112.51  3.000
 QRA  H5   C5   C6   109.93  3.000
 QRA  H6   C5   C4   112.99  3.000
 QRA  H5   C5   C4   110.61  3.000
 QRA  C6   C5   C4   103.47  3.000
 QRA  H8   C6   H7   107.10  3.000
 QRA  H8   C6   C5   112.89  3.000
 QRA  H7   C6   C5   109.96  3.000
 QRA  H8   C6   N1   111.14  3.000
 QRA  H7   C6   N1   113.40  3.000
 QRA  C5   C6   N1   102.44  3.000
 QRA  H10  C7   H9   107.42  3.000
 QRA  H10  C7   C3   109.48  3.000
 QRA  H9   C7   C3   112.12  3.000
 QRA  H10  C7   C8   109.72  3.000
 QRA  H9   C7   C8   112.94  3.000
 QRA  C3   C7   C8   105.14  3.000
 QRA  H11  C8   C9   106.81  3.000
 QRA  H11  C8   C    104.62  3.000
 QRA  C9   C8   C    117.71  3.000
 QRA  H11  C8   C7   108.14  3.000
 QRA  C    C8   C7   104.66  3.000
 QRA  C9   C8   C7   114.21  3.000
 QRA  H14  O    C1   109.77  3.000
 QRA  C2   C    N    108.81  3.000
 QRA  C2   C    C1   112.60  3.000
 QRA  N    C    C1   111.06  3.000
 QRA  C2   C    C8   104.66  3.000
 QRA  C1   C    C8   111.47  3.000
 QRA  N    C    C8   107.93  3.000
 QRA  H16  N    H15  106.08  3.000
 QRA  H16  N    C    110.28  3.000
 QRA  H15  N    C    110.44  3.000
 QRA  H19  C9   H18  106.73  3.000
 QRA  H19  C9   C10  108.09  3.000
 QRA  H18  C9   C10  108.56  3.000
 QRA  H19  C9   C8   109.88  3.000
 QRA  H18  C9   C8   110.31  3.000
 QRA  C10  C9   C8   113.03  3.000
 QRA  H21  C11  H20  104.68  3.000
 QRA  H21  C11  B    109.66  3.000
 QRA  H20  C11  B    110.31  3.000
 QRA  H21  C11  C10  107.62  3.000
 QRA  H20  C11  C10  107.43  3.000
 QRA  B    C11  C10  116.46  3.000
 QRA  O2   B    O3   111.69  3.000
 QRA  O3   B    O4   107.48  3.000
 QRA  O2   B    O4   104.14  3.000
 QRA  O3   B    C11  110.39  3.000
 QRA  O2   B    C11  111.21  3.000
 QRA  O4   B    C11  111.74  3.000
 QRA  H22  O4   B    108.60  3.000
 QRA  H23  O3   B    109.77  3.000
 QRA  H24  O2   B    109.48  3.000
 QRA  C2   C3   C7   100.64  3.000
 QRA  C2   C3   C4   113.62  3.000
 QRA  C7   C3   C4   115.45  3.000
 QRA  C4   C3   N1   103.38  3.000
 QRA  C2   C3   N1   112.93  3.000
 QRA  C7   C3   N1   111.23  3.000
 QRA  H26  C2   H25  107.03  3.000
 QRA  H26  C2   C3   113.30  3.000
 QRA  H25  C2   C3   108.72  3.000
 QRA  H26  C2   C    111.49  3.000
 QRA  H25  C2   C    111.43  3.000
 QRA  C3   C2   C    104.91  3.000
 QRA  H13  C10  H12  105.46  3.000
 QRA  H13  C10  C11  110.03  3.000
 QRA  H12  C10  C11  110.35  3.000
 QRA  H13  C10  C9   108.47  3.000
 QRA  H12  C10  C9   108.27  3.000
 QRA  C11  C10  C9   113.90  3.000
 QRA  C    C1   O1   124.00  3.000
 QRA  C    C1   O    113.64  3.000
 QRA  O1   C1   O    122.36  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
 QRA  CONST_01  H14  O    C1   C     180.00   0.0  0
 QRA  Var_01    C4   C5   C6   N1     34.57  30.0  1
 QRA  Var_02    C3   N1   C6   C5    -44.79  30.0  1
 QRA  Var_03    C3   C4   C5   C6    -13.17  30.0  1
 QRA  Var_04    C11  C10  C9   C8    176.79  30.0  2
 QRA  Var_05    O4   B    C11  C10   178.63  30.0  3
 QRA  Var_06    B    C11  C10  C9   -179.26  30.0  1

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
 QRA  chir_01  C8  C9  C   C7  positiv
 QRA  chir_02  C   C8  C1  C2  positiv
 QRA  chir_03  C3  C4  C2  C7  negativ

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
 QRA  plan-1  O    0.020
 QRA  plan-1  O1   0.020
 QRA  plan-1  C    0.020
 QRA  plan-1  H14  0.020
 QRA  plan-1  C1   0.020

