# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 13:21:36 2022
#   Inital geometry file: a 102 line input string
#   Ligand name: {3-[(5R,7S,8S)-8-azaniumyl-8-carboxy-2-azaspiro[4.4]nonan-2-ium-7-yl]propyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@]1(C[C@]2(CC[NH2+]C2)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
 QRJ  QRJ  {3-[(5R,7S,8S)-8-azaniumyl-8-carboxy-2-azaspiro[4.4]nonan-2-ium-7-yl]propyl}(trihydroxy)borate(1-)  ligand  45  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QRJ
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
 QRJ  O2   O  OC    -1  -0.547  16.5354  6.9056  24.8407
 QRJ  C8   C  C      0   0.480  15.6269  7.2381  24.0709
 QRJ  O3   O  O      0  -0.585  15.6786  8.0236  23.1030
 QRJ  C7   C  CT     0  -0.038  14.2375  6.5744  24.3123
 QRJ  N    N  NT3    1  -0.817  13.2520  7.4315  23.5890
 QRJ  C6   C  CH2    0  -0.434  13.8720  6.4208  25.7908
 QRJ  C5   C  CR5    0  -0.081  14.3152  4.9929  26.2036
 QRJ  C11  C  CH2    0  -0.291  13.1780  4.2213  26.8686
 QRJ  N1   N  N      1  -0.664  13.1636  4.7324  28.2793
 QRJ  C10  C  CH2    0  -0.305  14.5395  5.2816  28.5845
 QRJ  C9   C  CH2    0  -0.471  15.3491  4.9941  27.3310
 QRJ  C4   C  CH2    0  -0.426  14.7972  4.3247  24.9074
 QRJ  C3   C  CH1    0  -0.236  14.1880  5.1330  23.7671
 QRJ  C2   C  CH2    0  -0.404  14.8256  4.8991  22.4029
 QRJ  C1   C  CH2    0  -0.451  14.5632  3.5016  21.8438
 QRJ  C    C  CH2    0  -0.659  15.1693  3.2555  20.4612
 QRJ  B    B  B     -1   0.476  14.8114  1.8017  19.7429
 QRJ  O4   O  OB     0  -0.746  13.3604  1.6801  19.4672
 QRJ  O1   O  OB     0  -0.734  15.4289  1.6989  18.4102
 QRJ  O    O  OB     0  -0.751  15.3119  0.6726  20.5809
 QRJ  H2   H  HNT3   0   0.462  12.9022  8.1974  24.1660
 QRJ  H3   H  HNT3   0   0.451  13.7731  7.8634  22.8109
 QRJ  H4   H  HNT3   0   0.457  12.4420  6.9200  23.2388
 QRJ  H5   H  HCH2   0   0.271  14.3307  7.1977  26.4041
 QRJ  H6   H  HCH2   0   0.263  12.7890  6.5303  25.9058
 QRJ  H7   H  HCH2   0   0.304  12.1943  4.3588  26.4260
 QRJ  H8   H  HCH2   0   0.303  13.4041  3.1577  26.9182
 QRJ  H9   H  H      0   0.472  12.4583  5.4601  28.3951
 QRJ  H10  H  H      0   0.474  12.9012  3.9942  28.9319
 QRJ  H11  H  HCH2   0   0.304  14.9164  4.8029  29.4832
 QRJ  H12  H  HCH2   0   0.295  14.4276  6.3462  28.7719
 QRJ  H13  H  HCH2   0   0.264  15.8244  4.0130  27.3988
 QRJ  H14  H  HCH2   0   0.283  16.1243  5.7389  27.1697
 QRJ  H15  H  HCH2   0   0.252  14.5191  3.2711  24.8580
 QRJ  H16  H  HCH2   0   0.249  15.8856  4.3730  24.8505
 QRJ  H17  H  HCH1   0   0.247  13.1234  4.8630  23.6968
 QRJ  H18  H  HCH2   0   0.212  15.9062  5.0612  22.4721
 QRJ  H19  H  HCH2   0   0.215  14.4506  5.6347  21.6831
 QRJ  H20  H  HCH2   0   0.186  13.4769  3.3458  21.8117
 QRJ  H21  H  HCH2   0   0.195  14.9433  2.7612  22.5584
 QRJ  H22  H  HCH2   0   0.150  16.2588  3.3890  20.5485
 QRJ  H23  H  HCH2   0   0.152  14.8386  4.0703  19.8010
 QRJ  H24  H  H      0   0.408  12.8707  1.8576  20.2724
 QRJ  H25  H  H      0   0.409  16.3710  1.8497  18.5087
 QRJ  H26  H  H      0   0.406  15.3279  0.9369  21.5026

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
 QRJ  O1   B    single  1.472  0.020  1.472
 QRJ  O4   B    single  1.482  0.020  1.482
 QRJ  B    C    single  1.661  0.020  1.661
 QRJ  B    O    single  1.493  0.020  1.493
 QRJ  C    C1   single  1.529  0.020  1.529
 QRJ  C1   C2   single  1.528  0.020  1.528
 QRJ  C2   C3   single  1.524  0.020  1.524
 QRJ  O3   C8   deloc   1.248  0.020  1.248
 QRJ  N    C7   single  1.493  0.020  1.493
 QRJ  C3   C7   single  1.542  0.020  1.542
 QRJ  C3   C4   single  1.525  0.020  1.525
 QRJ  C8   O2   deloc   1.236  0.020  1.236
 QRJ  C8   C7   single  1.559  0.020  1.559
 QRJ  C7   C6   single  1.531  0.020  1.531
 QRJ  C4   C5   single  1.536  0.020  1.536
 QRJ  C6   C5   single  1.551  0.020  1.551
 QRJ  C5   C11  single  1.527  0.020  1.527
 QRJ  C5   C9   single  1.530  0.020  1.530
 QRJ  C11  N1   single  1.500  0.020  1.500
 QRJ  C9   C10  single  1.520  0.020  1.520
 QRJ  N1   C10  single  1.513  0.020  1.513
 QRJ  N    H2   single  0.890  0.020  1.040
 QRJ  N    H3   single  0.890  0.020  1.040
 QRJ  N    H4   single  0.890  0.020  1.040
 QRJ  C6   H5   single  0.970  0.020  1.090
 QRJ  C6   H6   single  0.970  0.020  1.090
 QRJ  C11  H7   single  0.970  0.020  1.090
 QRJ  C11  H8   single  0.970  0.020  1.090
 QRJ  N1   H9   single  0.890  0.020  1.040
 QRJ  N1   H10  single  0.890  0.020  1.040
 QRJ  C10  H11  single  0.970  0.020  1.090
 QRJ  C10  H12  single  0.970  0.020  1.090
 QRJ  C9   H13  single  0.970  0.020  1.090
 QRJ  C9   H14  single  0.970  0.020  1.090
 QRJ  C4   H15  single  0.970  0.020  1.090
 QRJ  C4   H16  single  0.970  0.020  1.090
 QRJ  C3   H17  single  0.970  0.020  1.090
 QRJ  C2   H18  single  0.970  0.020  1.090
 QRJ  C2   H19  single  0.970  0.020  1.090
 QRJ  C1   H20  single  0.970  0.020  1.090
 QRJ  C1   H21  single  0.970  0.020  1.090
 QRJ  C    H22  single  0.970  0.020  1.090
 QRJ  C    H23  single  0.970  0.020  1.090
 QRJ  O4   H24  single  0.850  0.020  0.980
 QRJ  O1   H25  single  0.850  0.020  0.980
 QRJ  O    H26  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
 QRJ  C7   C8   O3   115.16  3.000
 QRJ  C7   C8   O2   116.37  3.000
 QRJ  O3   C8   O2   128.46  3.000
 QRJ  C3   C7   C6   103.89  3.000
 QRJ  C6   C7   N    111.59  3.000
 QRJ  C3   C7   N    110.13  3.000
 QRJ  C6   C7   C8   113.90  3.000
 QRJ  C3   C7   C8   111.83  3.000
 QRJ  N    C7   C8   105.60  3.000
 QRJ  H4   N    H3   110.62  3.000
 QRJ  H4   N    H2   107.35  3.000
 QRJ  H3   N    H2   106.58  3.000
 QRJ  H4   N    C7   113.75  3.000
 QRJ  H3   N    C7   105.81  3.000
 QRJ  H2   N    C7   112.53  3.000
 QRJ  H6   C6   H5   106.61  3.000
 QRJ  H6   C6   C5   110.30  3.000
 QRJ  H5   C6   C5   112.70  3.000
 QRJ  H6   C6   C7   109.13  3.000
 QRJ  H5   C6   C7   111.78  3.000
 QRJ  C5   C6   C7   106.33  3.000
 QRJ  C4   C5   C9   114.22  3.000
 QRJ  C9   C5   C11  100.53  3.000
 QRJ  C4   C5   C11  112.43  3.000
 QRJ  C9   C5   C6   112.86  3.000
 QRJ  C11  C5   C6   111.61  3.000
 QRJ  C4   C5   C6   105.40  3.000
 QRJ  H8   C11  H7   109.27  3.000
 QRJ  H8   C11  N1   106.98  3.000
 QRJ  H7   C11  N1   109.33  3.000
 QRJ  H8   C11  C5   111.03  3.000
 QRJ  H7   C11  C5   115.63  3.000
 QRJ  N1   C11  C5   104.15  3.000
 QRJ  H10  N1   H9   105.42  3.000
 QRJ  H10  N1   C10  111.58  3.000
 QRJ  H9   N1   C10  110.31  3.000
 QRJ  H10  N1   C11  110.95  3.000
 QRJ  H9   N1   C11  110.87  3.000
 QRJ  C10  N1   C11  107.74  3.000
 QRJ  H12  C10  H11  108.96  3.000
 QRJ  H12  C10  C9   112.48  3.000
 QRJ  H11  C10  C9   114.49  3.000
 QRJ  H12  C10  N1   107.26  3.000
 QRJ  H11  C10  N1   108.83  3.000
 QRJ  C9   C10  N1   104.44  3.000
 QRJ  H14  C9   H13  108.31  3.000
 QRJ  H14  C9   C10  111.88  3.000
 QRJ  H13  C9   C10  110.52  3.000
 QRJ  H14  C9   C5   111.91  3.000
 QRJ  H13  C9   C5   109.82  3.000
 QRJ  C10  C9   C5   104.36  3.000
 QRJ  H16  C4   H15  107.15  3.000
 QRJ  H16  C4   C3   109.64  3.000
 QRJ  H15  C4   C3   112.11  3.000
 QRJ  H16  C4   C5   109.74  3.000
 QRJ  H15  C4   C5   112.23  3.000
 QRJ  C3   C4   C5   105.97  3.000
 QRJ  H17  C3   C2   108.06  3.000
 QRJ  H17  C3   C4   107.71  3.000
 QRJ  C2   C3   C4   114.89  3.000
 QRJ  H17  C3   C7   106.44  3.000
 QRJ  C4   C3   C7   102.61  3.000
 QRJ  C2   C3   C7   116.53  3.000
 QRJ  H19  C2   H18  106.26  3.000
 QRJ  H19  C2   C1   108.35  3.000
 QRJ  H18  C2   C1   109.15  3.000
 QRJ  H19  C2   C3   110.00  3.000
 QRJ  H18  C2   C3   109.49  3.000
 QRJ  C1   C2   C3   113.34  3.000
 QRJ  H21  C1   H20  105.43  3.000
 QRJ  H21  C1   C    110.05  3.000
 QRJ  H20  C1   C    110.05  3.000
 QRJ  H21  C1   C2   108.63  3.000
 QRJ  H20  C1   C2   108.08  3.000
 QRJ  C    C1   C2   114.20  3.000
 QRJ  H23  C    H22  104.79  3.000
 QRJ  H23  C    B    108.92  3.000
 QRJ  H22  C    B    110.71  3.000
 QRJ  H23  C    C1   107.72  3.000
 QRJ  H22  C    C1   107.51  3.000
 QRJ  B    C    C1   116.52  3.000
 QRJ  O    B    O1   108.34  3.000
 QRJ  O    B    O4   111.76  3.000
 QRJ  O1   B    O4   103.68  3.000
 QRJ  O    B    C    110.31  3.000
 QRJ  O4   B    C    111.30  3.000
 QRJ  O1   B    C    111.24  3.000
 QRJ  H24  O4   B    109.18  3.000
 QRJ  H25  O1   B    107.94  3.000
 QRJ  H26  O    B    109.68  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
 QRJ  Var_01  C10  N1   C11  C5    -23.39  30.0  1
 QRJ  Var_02  C9   C10  N1   C11    -3.04  30.0  1
 QRJ  Var_03  C    C1   C2   C3    178.76  30.0  1
 QRJ  Var_04  B    C    C1   C2   -174.98  30.0  1
 QRJ  Var_05  O1   B    C    C1    178.82  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
 QRJ  chir_01  C7  C3  C8   C6  positiv
 QRJ  chir_02  C5  C6  C11  C9  positiv
 QRJ  chir_03  C3  C4  C7   C2  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
 QRJ  plan-1  O2  0.020
 QRJ  plan-1  C8  0.020
 QRJ  plan-1  O3  0.020
 QRJ  plan-1  C7  0.020

