# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:45:26 2021
#   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  46  20  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  OH1    0  -0.566  16.5372  6.8150  24.6454
 QRJ  C8   C  C      0   0.595  15.5401  7.2892  23.9336
 QRJ  O3   O  O      0  -0.417  15.6315  8.1451  23.0932
 QRJ  C7   C  CT     0  -0.063  14.2228  6.6081  24.2826
 QRJ  N    N  NT3    1  -0.793  13.1603  7.4274  23.6380
 QRJ  C6   C  CH2    0  -0.447  13.9801  6.4863  25.7967
 QRJ  C5   C  CR5    0  -0.092  14.3374  5.0253  26.1847
 QRJ  C11  C  CH2    0  -0.291  13.1450  4.3173  26.8234
 QRJ  N1   N  N      1  -0.663  13.1465  4.8093  28.2367
 QRJ  C10  C  CH2    0  -0.302  14.5534  5.2377  28.5787
 QRJ  C9   C  CH2    0  -0.473  15.3585  4.9455  27.3214
 QRJ  C4   C  CH2    0  -0.440  14.7887  4.3488  24.8837
 QRJ  C3   C  CH1    0  -0.233  14.1639  5.1572  23.7526
 QRJ  C2   C  CH2    0  -0.421  14.7734  4.9317  22.3748
 QRJ  C1   C  CH2    0  -0.452  14.5682  3.5111  21.8539
 QRJ  C    C  CH2    0  -0.667  15.1094  3.2922  20.4420
 QRJ  B    B  B     -1   0.457  14.8794  1.7880  19.7901
 QRJ  O4   O  OB     0  -0.754  13.4397  1.5050  19.5998
 QRJ  O1   O  OB     0  -0.739  15.4472  1.6950  18.4385
 QRJ  O    O  OB     0  -0.754  15.5436  0.7478  20.6248
 QRJ  H1   H  HOH1   0   0.502  17.3750  7.2337  24.3907
 QRJ  H2   H  HNT3   0   0.482  13.1404  8.3903  23.9797
 QRJ  H3   H  HNT3   0   0.474  13.2705  7.4811  22.6234
 QRJ  H4   H  HNT3   0   0.480  12.2349  7.0346  23.8151
 QRJ  H5   H  HCH2   0   0.303  14.5517  7.2256  26.3580
 QRJ  H6   H  HCH2   0   0.291  12.9296  6.7046  26.0026
 QRJ  H7   H  HCH2   0   0.309  12.1771  4.5238  26.3733
 QRJ  H8   H  HCH2   0   0.312  13.3032  3.2414  26.8569
 QRJ  H9   H  H      0   0.475  12.5024  5.5906  28.3486
 QRJ  H10  H  H      0   0.479  12.8096  4.0886  28.8734
 QRJ  H11  H  HCH2   0   0.309  14.8831  4.6862  29.4533
 QRJ  H12  H  HCH2   0   0.299  14.5205  6.2961  28.8219
 QRJ  H13  H  HCH2   0   0.277  15.7795  3.9391  27.3638
 QRJ  H14  H  HCH2   0   0.285  16.1793  5.6494  27.1992
 QRJ  H15  H  HCH2   0   0.274  14.4902  3.3013  24.8403
 QRJ  H16  H  HCH2   0   0.265  15.8778  4.3659  24.8073
 QRJ  H17  H  HCH1   0   0.280  13.0967  4.9021  23.6998
 QRJ  H18  H  HCH2   0   0.226  15.8477  5.1439  22.4005
 QRJ  H19  H  HCH2   0   0.225  14.3353  5.6281  21.6509
 QRJ  H20  H  HCH2   0   0.195  13.4947  3.2832  21.8942
 QRJ  H21  H  HCH2   0   0.203  15.0470  2.8127  22.5501
 QRJ  H22  H  HCH2   0   0.161  16.1817  3.5399  20.4570
 QRJ  H23  H  HCH2   0   0.161  14.6549  4.0511  19.7884
 QRJ  H24  H  H      0   0.416  12.9385  1.8698  20.3313
 QRJ  H25  H  H      0   0.419  16.3696  1.9564  18.4730
 QRJ  H26  H  H      0   0.413  15.3873  0.9251  21.5552

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  1.469  0.020  1.469
 QRJ  O4   B    single  1.480  0.020  1.480
 QRJ  B    C    single  1.656  0.020  1.656
 QRJ  B    O    single  1.490  0.020  1.490
 QRJ  C    C1   single  1.528  0.020  1.528
 QRJ  C1   C2   single  1.527  0.020  1.527
 QRJ  C2   C3   single  1.523  0.020  1.523
 QRJ  O3   C8   double  1.203  0.020  1.203
 QRJ  N    C7   single  1.489  0.020  1.489
 QRJ  C3   C7   single  1.546  0.020  1.546
 QRJ  C3   C4   single  1.524  0.020  1.524
 QRJ  C8   O2   single  1.314  0.020  1.314
 QRJ  C8   C7   single  1.523  0.020  1.523
 QRJ  C7   C6   single  1.538  0.020  1.538
 QRJ  C4   C5   single  1.534  0.020  1.534
 QRJ  C6   C5   single  1.553  0.020  1.553
 QRJ  C5   C11  single  1.527  0.020  1.527
 QRJ  C5   C9   single  1.530  0.020  1.530
 QRJ  C11  N1   single  1.497  0.020  1.497
 QRJ  C9   C10  single  1.521  0.020  1.521
 QRJ  N1   C10  single  1.510  0.020  1.510
 QRJ  O2   H1   single  0.850  0.020  0.980
 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  H1   O2   C8   110.93  3.000
 QRJ  C7   C8   O3   122.94  3.000
 QRJ  C7   C8   O2   111.76  3.000
 QRJ  O3   C8   O2   125.29  3.000
 QRJ  C3   C7   C6   104.90  3.000
 QRJ  C6   C7   N    110.93  3.000
 QRJ  C3   C7   N    109.93  3.000
 QRJ  C6   C7   C8   113.41  3.000
 QRJ  C3   C7   C8   111.96  3.000
 QRJ  N    C7   C8   105.78  3.000
 QRJ  H4   N    H3   106.87  3.000
 QRJ  H4   N    H2   106.67  3.000
 QRJ  H3   N    H2   106.53  3.000
 QRJ  H4   N    C7   111.11  3.000
 QRJ  H3   N    C7   112.46  3.000
 QRJ  H2   N    C7   112.81  3.000
 QRJ  H6   C6   H5   105.77  3.000
 QRJ  H6   C6   C5   111.22  3.000
 QRJ  H5   C6   C5   112.87  3.000
 QRJ  H6   C6   C7   108.75  3.000
 QRJ  H5   C6   C7   111.74  3.000
 QRJ  C5   C6   C7   106.50  3.000
 QRJ  C4   C5   C9   114.25  3.000
 QRJ  C9   C5   C11  100.73  3.000
 QRJ  C4   C5   C11  112.34  3.000
 QRJ  C9   C5   C6   112.84  3.000
 QRJ  C11  C5   C6   111.16  3.000
 QRJ  C4   C5   C6   105.70  3.000
 QRJ  H8   C11  H7   109.27  3.000
 QRJ  H8   C11  N1   107.21  3.000
 QRJ  H7   C11  N1   109.23  3.000
 QRJ  H8   C11  C5   110.97  3.000
 QRJ  H7   C11  C5   115.72  3.000
 QRJ  N1   C11  C5   103.99  3.000
 QRJ  H10  N1   H9   105.35  3.000
 QRJ  H10  N1   C10  111.54  3.000
 QRJ  H9   N1   C10  110.28  3.000
 QRJ  H10  N1   C11  110.93  3.000
 QRJ  H9   N1   C11  110.81  3.000
 QRJ  C10  N1   C11  107.95  3.000
 QRJ  H12  C10  H11  108.90  3.000
 QRJ  H12  C10  C9   112.83  3.000
 QRJ  H11  C10  C9   114.06  3.000
 QRJ  H12  C10  N1   107.39  3.000
 QRJ  H11  C10  N1   108.75  3.000
 QRJ  C9   C10  N1   104.56  3.000
 QRJ  H14  C9   H13  108.05  3.000
 QRJ  H14  C9   C10  111.58  3.000
 QRJ  H13  C9   C10  110.43  3.000
 QRJ  H14  C9   C5   112.72  3.000
 QRJ  H13  C9   C5   109.53  3.000
 QRJ  C10  C9   C5   104.52  3.000
 QRJ  H16  C4   H15  106.58  3.000
 QRJ  H16  C4   C3   110.40  3.000
 QRJ  H15  C4   C3   111.58  3.000
 QRJ  H16  C4   C5   110.24  3.000
 QRJ  H15  C4   C5   112.14  3.000
 QRJ  C3   C4   C5   105.95  3.000
 QRJ  H17  C3   C2   108.11  3.000
 QRJ  H17  C3   C4   108.10  3.000
 QRJ  C2   C3   C4   115.38  3.000
 QRJ  H17  C3   C7   105.75  3.000
 QRJ  C4   C3   C7   103.16  3.000
 QRJ  C2   C3   C7   115.71  3.000
 QRJ  H19  C2   H18  106.52  3.000
 QRJ  H19  C2   C1   108.19  3.000
 QRJ  H18  C2   C1   108.66  3.000
 QRJ  H19  C2   C3   110.09  3.000
 QRJ  H18  C2   C3   110.03  3.000
 QRJ  C1   C2   C3   113.11  3.000
 QRJ  H21  C1   H20  105.75  3.000
 QRJ  H21  C1   C    109.93  3.000
 QRJ  H20  C1   C    110.51  3.000
 QRJ  H21  C1   C2   108.50  3.000
 QRJ  H20  C1   C2   108.18  3.000
 QRJ  C    C1   C2   113.64  3.000
 QRJ  H23  C    H22  104.80  3.000
 QRJ  H23  C    B    109.61  3.000
 QRJ  H22  C    B    110.20  3.000
 QRJ  H23  C    C1   107.69  3.000
 QRJ  H22  C    C1   107.47  3.000
 QRJ  B    C    C1   116.41  3.000
 QRJ  O    B    O1   107.40  3.000
 QRJ  O    B    O4   111.86  3.000
 QRJ  O1   B    O4   104.22  3.000
 QRJ  O    B    C    110.59  3.000
 QRJ  O4   B    C    111.08  3.000
 QRJ  O1   B    C    111.48  3.000
 QRJ  H24  O4   B    109.75  3.000
 QRJ  H25  O1   B    108.74  3.000
 QRJ  H26  O    B    109.97  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  CONST_01  H1   O2   C8   C7    180.00   0.0  0
 QRJ  Var_01    C10  N1   C11  C5    -24.64  30.0  1
 QRJ  Var_02    C9   C10  N1   C11    -1.15  30.0  1
 QRJ  Var_03    C    C1   C2   C3    176.92  30.0  1
 QRJ  Var_04    B    C    C1   C2   -178.09  30.0  1
 QRJ  Var_05    O1   B    C    C1   -179.64  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
 QRJ  plan-1  H1  0.020

