# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 10:00:11 2022
#   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  43  20  .  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_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  -0.621  12.6205  4.4371  26.3940
 QRA  C4   C  CH2    0  -0.437  14.7120  4.0893  27.3545
 QRA  C5   C  CH2    0  -0.461  13.7096  4.3849  28.4852
 QRA  C6   C  CH2    0  -0.289  12.4588  4.9058  27.7615
 QRA  C7   C  CH2    0  -0.412  14.4160  3.8609  24.7984
 QRA  C8   C  CH1    0  -0.203  13.9411  4.7600  23.6502
 QRA  O    O  OC    -1  -0.603  16.0836  7.0947  23.6107
 QRA  O1   O  O      0  -0.605  14.2833  7.9453  22.6162
 QRA  C    C  CT     0  -0.023  13.9394  6.2198  24.2428
 QRA  N    N  NH2    0  -0.793  12.5404  6.6651  24.2850
 QRA  C9   C  CH2    0  -0.404  14.6983  4.5290  22.3462
 QRA  C11  C  CH2    0  -0.658  15.1471  2.9417  20.3802
 QRA  B    B  B     -1   0.474  14.8488  1.5039  19.6088
 QRA  O4   O  OB     0  -0.735  15.4838  1.4581  18.2800
 QRA  O3   O  OB     0  -0.751  15.3801  0.3645  20.4149
 QRA  O2   O  OB     0  -0.749  13.4043  1.3443  19.3157
 QRA  C3   C  CT     0   0.092  14.0422  4.6018  26.0763
 QRA  C2   C  CH2    0  -0.411  14.4227  6.0391  25.6907
 QRA  H1   H  HNH1   0   0.342  12.0666  4.9996  25.7547
 QRA  H3   H  HCH2   0   0.224  14.8876  3.0139  27.2729
 QRA  H4   H  HCH2   0   0.223  15.6843  4.5572  27.5163
 QRA  H5   H  HCH2   0   0.226  13.4879  3.4819  29.0548
 QRA  H6   H  HCH2   0   0.225  14.0897  5.1206  29.1940
 QRA  H7   H  HCH2   0   0.188  12.4155  6.0017  27.8383
 QRA  H8   H  HCH2   0   0.214  11.5331  4.5244  28.1992
 QRA  H9   H  HCH2   0   0.217  13.9891  2.8560  24.7684
 QRA  H10  H  HCH2   0   0.206  15.5062  3.7520  24.7532
 QRA  H11  H  HCH1   0   0.205  12.8893  4.5237  23.4489
 QRA  H12  H  HCH2   0   0.175  13.3866  2.9903  21.6435
 QRA  H13  H  HCH2   0   0.188  14.8108  2.3841  22.4499
 QRA  H15  H  HNH2   0   0.326  12.5088  7.5920  24.6968
 QRA  H16  H  HNH2   0   0.328  12.2263  6.8048  23.3308
 QRA  H18  H  HCH2   0   0.193  15.7697  4.6780  22.5083
 QRA  H19  H  HCH2   0   0.195  14.3928  5.2797  21.6095
 QRA  H20  H  HCH2   0   0.146  16.2293  3.0894  20.5224
 QRA  H21  H  HCH2   0   0.148  14.8365  3.7712  19.7278
 QRA  H22  H  H      0   0.409  16.4205  1.6293  18.3949
 QRA  H23  H  H      0   0.405  15.3517  0.5938  21.3459
 QRA  H24  H  H      0   0.408  12.8995  1.5620  20.1012
 QRA  H25  H  HCH2   0   0.219  15.5075  6.1429  25.7317
 QRA  H26  H  HCH2   0   0.219  14.0025  6.7949  26.3626
 QRA  C10  C  CH2    0  -0.447  14.4700  3.1464  21.7375
 QRA  C1   C  C      0   0.403  14.8521  7.1786  23.4217

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  1.473  0.020  1.473
 QRA  O2   B    single  1.483  0.020  1.483
 QRA  B    C11  single  1.659  0.020  1.659
 QRA  B    O3   single  1.493  0.020  1.493
 QRA  C11  C10  single  1.531  0.020  1.531
 QRA  C10  C9   single  1.528  0.020  1.528
 QRA  C9   C8   single  1.525  0.020  1.525
 QRA  O1   C1   deloc   1.249  0.020  1.249
 QRA  N    C    single  1.469  0.020  1.469
 QRA  C8   C    single  1.576  0.020  1.576
 QRA  C8   C7   single  1.534  0.020  1.534
 QRA  C1   C    single  1.558  0.020  1.558
 QRA  C1   O    deloc   1.249  0.020  1.249
 QRA  C    C2   single  1.537  0.020  1.537
 QRA  C7   C3   single  1.524  0.020  1.524
 QRA  C2   C3   single  1.536  0.020  1.536
 QRA  C3   N1   single  1.466  0.020  1.466
 QRA  C3   C4   single  1.531  0.020  1.531
 QRA  N1   C6   single  1.455  0.020  1.455
 QRA  C4   C5   single  1.540  0.020  1.540
 QRA  C6   C5   single  1.536  0.020  1.536
 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  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   109.28  3.000
 QRA  H1   N1   C6   110.65  3.000
 QRA  C3   N1   C6   105.98  3.000
 QRA  H4   C4   H3   106.86  3.000
 QRA  H4   C4   C3   111.71  3.000
 QRA  H3   C4   C3   109.71  3.000
 QRA  H4   C4   C5   112.89  3.000
 QRA  H3   C4   C5   110.39  3.000
 QRA  C3   C4   C5   105.30  3.000
 QRA  H6   C5   H5   106.87  3.000
 QRA  H6   C5   C6   111.19  3.000
 QRA  H5   C5   C6   111.19  3.000
 QRA  H6   C5   C4   112.34  3.000
 QRA  H5   C5   C4   110.91  3.000
 QRA  C6   C5   C4   104.43  3.000
 QRA  H8   C6   H7   106.65  3.000
 QRA  H8   C6   C5   112.50  3.000
 QRA  H7   C6   C5   109.71  3.000
 QRA  H8   C6   N1   110.99  3.000
 QRA  H7   C6   N1   113.03  3.000
 QRA  C5   C6   N1   104.07  3.000
 QRA  H10  C7   H9   107.22  3.000
 QRA  H10  C7   C3   109.07  3.000
 QRA  H9   C7   C3   111.99  3.000
 QRA  H10  C7   C8   109.58  3.000
 QRA  H9   C7   C8   113.45  3.000
 QRA  C3   C7   C8   105.48  3.000
 QRA  H11  C8   C9   106.65  3.000
 QRA  H11  C8   C    105.52  3.000
 QRA  C9   C8   C    117.54  3.000
 QRA  H11  C8   C7   107.95  3.000
 QRA  C    C8   C7   105.19  3.000
 QRA  C9   C8   C7   113.42  3.000
 QRA  C2   C    N    107.95  3.000
 QRA  C2   C    C1   112.62  3.000
 QRA  N    C    C1   112.74  3.000
 QRA  C2   C    C8   104.18  3.000
 QRA  C1   C    C8   111.80  3.000
 QRA  N    C    C8   107.02  3.000
 QRA  H16  N    H15  104.26  3.000
 QRA  H16  N    C    108.04  3.000
 QRA  H15  N    C    108.56  3.000
 QRA  H19  C9   H18  106.22  3.000
 QRA  H19  C9   C10  108.10  3.000
 QRA  H18  C9   C10  109.19  3.000
 QRA  H19  C9   C8   109.44  3.000
 QRA  H18  C9   C8   109.81  3.000
 QRA  C10  C9   C8   113.79  3.000
 QRA  H21  C11  H20  104.65  3.000
 QRA  H21  C11  B    109.09  3.000
 QRA  H20  C11  B    110.67  3.000
 QRA  H21  C11  C10  107.47  3.000
 QRA  H20  C11  C10  107.59  3.000
 QRA  B    C11  C10  116.67  3.000
 QRA  O2   B    O3   111.79  3.000
 QRA  O3   B    O4   108.05  3.000
 QRA  O2   B    O4   103.79  3.000
 QRA  O3   B    C11  110.26  3.000
 QRA  O2   B    C11  111.13  3.000
 QRA  O4   B    C11  111.64  3.000
 QRA  H22  O4   B    107.90  3.000
 QRA  H23  O3   B    109.33  3.000
 QRA  H24  O2   B    109.06  3.000
 QRA  C2   C3   C7   100.59  3.000
 QRA  C2   C3   C4   114.48  3.000
 QRA  C7   C3   C4   115.47  3.000
 QRA  C4   C3   N1   101.87  3.000
 QRA  C2   C3   N1   113.56  3.000
 QRA  C7   C3   N1   111.41  3.000
 QRA  H26  C2   H25  107.03  3.000
 QRA  H26  C2   C3   113.37  3.000
 QRA  H25  C2   C3   109.03  3.000
 QRA  H26  C2   C    112.10  3.000
 QRA  H25  C2   C    109.70  3.000
 QRA  C3   C2   C    105.58  3.000
 QRA  H13  C10  H12  105.25  3.000
 QRA  H13  C10  C11  110.20  3.000
 QRA  H12  C10  C11  109.96  3.000
 QRA  H13  C10  C9   108.88  3.000
 QRA  H12  C10  C9   108.06  3.000
 QRA  C11  C10  C9   114.10  3.000
 QRA  C    C1   O1   116.81  3.000
 QRA  C    C1   O    117.17  3.000
 QRA  O1   C1   O    126.01  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  Var_01  C4   C5   C6   N1     19.55  30.0  1
 QRA  Var_02  C3   N1   C6   C5    -39.80  30.0  1
 QRA  Var_03  C3   C4   C5   C6      6.17  30.0  1
 QRA  Var_04  C11  C10  C9   C8    175.93  30.0  1
 QRA  Var_05  O4   B    C11  C10   176.43  30.0  3
 QRA  Var_06  B    C11  C10  C9   -175.60  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  C1  0.020

