# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 13:34:54 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: {3-[(3aR,4R,5S,6aR)-4-azaniumyl-4-carboxyoctahydrocyclopenta[b]pyrrol-1-ium-5-yl]propyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@]1([C@@H](CCC[B-](O)(O)O)C[C@H]2[NH2+]CC[C@@H]12)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
 QR4  QR4  {3-[(3aR,4R,5S,6aR)-4-azaniumyl-4-carboxyoctahydrocyclopenta[b]pyrrol-1-ium-5-yl]propyl}(trihydroxy)borate(1-)  ligand  42  19  .  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_QR4
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
 QR4  O    O  O      0  -0.538  15.9995  7.6021  23.6060
 QR4  C4   C  C      0   0.524  15.6729  6.7479  24.4351
 QR4  O1   O  OC    -1  -0.577  16.4308  6.1402  25.2256
 QR4  C3   C  CT     0  -0.066  14.1681  6.3423  24.4456
 QR4  N    N  NT3    1  -0.808  13.4444  7.4173  23.7091
 QR4  C5   C  CH1    0  -0.233  13.9694  4.9780  23.7451
 QR4  C9   C  CH2    0  -0.458  14.2545  3.9516  24.8522
 QR4  C10  C  CH1    0  -0.107  13.9153  4.6624  26.1642
 QR4  C2   C  CH1    0  -0.251  13.5259  6.1050  25.8239
 QR4  C1   C  CH2    0  -0.469  13.9854  6.9670  27.0135
 QR4  N1   N  NT2    1  -0.670  15.0906  4.8678  27.0535
 QR4  C    C  CH2    0  -0.327  14.7338  6.0016  27.9397
 QR4  C6   C  CH2    0  -0.413  14.7435  4.7504  22.4550
 QR4  C7   C  CH2    0  -0.431  14.4039  3.4194  21.7871
 QR4  C8   C  CH2    0  -0.678  15.1217  3.1815  20.4623
 QR4  B    B  B     -1   0.489  14.8229  1.7022  19.7745
 QR4  O4   O  OB     0  -0.741  13.3899  1.4702  19.5217
 QR4  O3   O  OB     0  -0.749  15.3038  0.6238  20.6875
 QR4  O2   O  OB     0  -0.739  15.4452  1.6252  18.4334
 QR4  H8   H  HNT3   0   0.469  13.2066  8.2109  24.3068
 QR4  H23  H  HNT3   0   0.460  14.0736  7.7866  22.9861
 QR4  H9   H  HNT3   0   0.465  12.5771  7.0980  23.2745
 QR4  H11  H  HCH1   0   0.264  12.8980  4.9110  23.5117
 QR4  H21  H  HCH2   0   0.276  13.6501  3.0560  24.7253
 QR4  H22  H  HCH2   0   0.263  15.2985  3.6312  24.8310
 QR4  H1   H  HCH1   0   0.320  13.1474  4.1588  26.7495
 QR4  H    H  HCH1   0   0.309  12.4426  6.1604  25.6955
 QR4  H7   H  HCH2   0   0.273  14.6238  7.7941  26.7034
 QR4  H6   H  HCH2   0   0.283  13.1355  7.4011  27.5346
 QR4  H3   H  HNT2   0   0.455  15.3740  4.0296  27.5586
 QR4  H2   H  HNT2   0   0.470  15.8608  5.2073  26.4121
 QR4  H4   H  HCH2   0   0.297  15.6371  6.4137  28.3823
 QR4  H5   H  HCH2   0   0.293  14.0920  5.6224  28.7325
 QR4  H12  H  HCH2   0   0.216  15.8192  4.7801  22.6568
 QR4  H13  H  HCH2   0   0.219  14.5364  5.5616  21.7486
 QR4  H15  H  HCH2   0   0.187  13.3184  3.3746  21.6327
 QR4  H14  H  HCH2   0   0.198  14.6372  2.6038  22.4800
 QR4  H16  H  HCH2   0   0.149  16.2022  3.3219  20.6332
 QR4  H17  H  HCH2   0   0.153  14.8427  3.9898  19.7708
 QR4  H20  H  H      0   0.410  12.9294  1.4326  20.3622
 QR4  H19  H  H      0   0.404  16.0701  0.9440  21.1676
 QR4  H18  H  H      0   0.408  16.2660  2.1204  18.4466

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
 QR4  O2   B    single  1.480  0.020  1.480
 QR4  O4   B    single  1.474  0.020  1.474
 QR4  B    O3   single  1.493  0.020  1.493
 QR4  B    C8   single  1.658  0.020  1.658
 QR4  C8   C7   single  1.526  0.020  1.526
 QR4  C7   C6   single  1.527  0.020  1.527
 QR4  C6   C5   single  1.522  0.020  1.522
 QR4  O    C4   deloc   1.234  0.020  1.234
 QR4  N    C3   single  1.491  0.020  1.491
 QR4  C5   C3   single  1.546  0.020  1.546
 QR4  C5   C9   single  1.536  0.020  1.536
 QR4  C4   C3   single  1.559  0.020  1.559
 QR4  C4   O1   deloc   1.252  0.020  1.252
 QR4  C3   C2   single  1.539  0.020  1.539
 QR4  C9   C10  single  1.530  0.020  1.530
 QR4  C2   C10  single  1.533  0.020  1.533
 QR4  C2   C1   single  1.539  0.020  1.539
 QR4  C10  N1   single  1.488  0.020  1.488
 QR4  C1   C    single  1.533  0.020  1.533
 QR4  N1   C    single  1.483  0.020  1.483
 QR4  N    H8   single  0.890  0.020  1.040
 QR4  N    H23  single  0.890  0.020  1.040
 QR4  N    H9   single  0.890  0.020  1.040
 QR4  C5   H11  single  0.970  0.020  1.090
 QR4  C9   H21  single  0.970  0.020  1.090
 QR4  C9   H22  single  0.970  0.020  1.090
 QR4  C10  H1   single  0.970  0.020  1.090
 QR4  C2   H    single  0.970  0.020  1.090
 QR4  C1   H7   single  0.970  0.020  1.090
 QR4  C1   H6   single  0.970  0.020  1.090
 QR4  N1   H3   single  0.890  0.020  1.040
 QR4  N1   H2   single  0.890  0.020  1.040
 QR4  C    H4   single  0.970  0.020  1.090
 QR4  C    H5   single  0.970  0.020  1.090
 QR4  C6   H12  single  0.970  0.020  1.090
 QR4  C6   H13  single  0.970  0.020  1.090
 QR4  C7   H15  single  0.970  0.020  1.090
 QR4  C7   H14  single  0.970  0.020  1.090
 QR4  C8   H16  single  0.970  0.020  1.090
 QR4  C8   H17  single  0.970  0.020  1.090
 QR4  O4   H20  single  0.850  0.020  0.980
 QR4  O3   H19  single  0.850  0.020  0.980
 QR4  O2   H18  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
 QR4  C3   C4   O1   116.99  3.000
 QR4  O1   C4   O    126.84  3.000
 QR4  C3   C4   O    116.11  3.000
 QR4  C2   C3   C5   102.48  3.000
 QR4  C2   C3   N    110.56  3.000
 QR4  C5   C3   N    110.49  3.000
 QR4  C2   C3   C4   116.68  3.000
 QR4  C5   C3   C4   110.52  3.000
 QR4  N    C3   C4   106.13  3.000
 QR4  H9   N    H23  109.45  3.000
 QR4  H9   N    H8   107.11  3.000
 QR4  H23  N    H8   105.97  3.000
 QR4  H9   N    C3   113.40  3.000
 QR4  H23  N    C3   108.04  3.000
 QR4  H8   N    C3   112.59  3.000
 QR4  H11  C5   C6   107.87  3.000
 QR4  H11  C5   C9   107.05  3.000
 QR4  C6   C5   C9   114.62  3.000
 QR4  H11  C5   C3   105.98  3.000
 QR4  C9   C5   C3   103.84  3.000
 QR4  C6   C5   C3   116.79  3.000
 QR4  H22  C9   H21  106.69  3.000
 QR4  H22  C9   C10  111.39  3.000
 QR4  H21  C9   C10  111.05  3.000
 QR4  H22  C9   C5   111.06  3.000
 QR4  H21  C9   C5   111.28  3.000
 QR4  C10  C9   C5   105.45  3.000
 QR4  H1   C10  N1   107.44  3.000
 QR4  H1   C10  C2   112.06  3.000
 QR4  N1   C10  C2   101.74  3.000
 QR4  H1   C10  C9   113.72  3.000
 QR4  N1   C10  C9   113.67  3.000
 QR4  C2   C10  C9   107.65  3.000
 QR4  H    C2   C1   111.01  3.000
 QR4  H    C2   C10  109.02  3.000
 QR4  C1   C2   C10  106.24  3.000
 QR4  H    C2   C3   107.50  3.000
 QR4  C1   C2   C3   118.77  3.000
 QR4  C10  C2   C3   103.77  3.000
 QR4  H6   C1   H7   106.93  3.000
 QR4  H6   C1   C    110.09  3.000
 QR4  H7   C1   C    111.33  3.000
 QR4  H6   C1   C2   111.14  3.000
 QR4  H7   C1   C2   112.33  3.000
 QR4  C    C1   C2   105.07  3.000
 QR4  H2   N1   H3   111.22  3.000
 QR4  H2   N1   C    106.98  3.000
 QR4  H3   N1   C    113.56  3.000
 QR4  H2   N1   C10  104.89  3.000
 QR4  H3   N1   C10  113.73  3.000
 QR4  C    N1   C10  105.83  3.000
 QR4  H5   C    H4   109.00  3.000
 QR4  H5   C    N1   108.11  3.000
 QR4  H4   C    N1   109.47  3.000
 QR4  H5   C    C1   111.82  3.000
 QR4  H4   C    C1   114.39  3.000
 QR4  N1   C    C1   103.76  3.000
 QR4  H13  C6   H12  106.53  3.000
 QR4  H13  C6   C7   108.74  3.000
 QR4  H12  C6   C7   108.83  3.000
 QR4  H13  C6   C5   109.86  3.000
 QR4  H12  C6   C5   109.85  3.000
 QR4  C7   C6   C5   112.83  3.000
 QR4  H14  C7   H15  105.62  3.000
 QR4  H14  C7   C8   109.45  3.000
 QR4  H15  C7   C8   109.69  3.000
 QR4  H14  C7   C6   108.96  3.000
 QR4  H15  C7   C6   108.49  3.000
 QR4  C8   C7   C6   114.27  3.000
 QR4  H17  C8   H16  104.62  3.000
 QR4  H17  C8   B    110.43  3.000
 QR4  H16  C8   B    110.76  3.000
 QR4  H17  C8   C7   108.18  3.000
 QR4  H16  C8   C7   107.85  3.000
 QR4  B    C8   C7   114.49  3.000
 QR4  O2   B    O3   112.40  3.000
 QR4  O3   B    O4   107.73  3.000
 QR4  O2   B    O4   104.19  3.000
 QR4  O3   B    C8   109.43  3.000
 QR4  O4   B    C8   112.76  3.000
 QR4  O2   B    C8   110.27  3.000
 QR4  H20  O4   B    108.83  3.000
 QR4  H19  O3   B    108.80  3.000
 QR4  H18  O2   B    108.69  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
 QR4  Var_01  C1  C   N1  C10  -39.15  30.0  1
 QR4  Var_02  N1  C   C1  C2    20.19  30.0  1
 QR4  Var_03  C8  C7  C6  C5   177.75  30.0  1
 QR4  Var_04  B   C8  C7  C6   176.73  30.0  1
 QR4  Var_05  O2  B   C8  C7   174.02  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
 QR4  chir_01  C3   C5  C4   C2  positiv
 QR4  chir_02  C5   C6  C3   C9  positiv
 QR4  chir_03  C10  N1  C2   C9  negativ
 QR4  chir_04  C2   C3  C10  C1  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
 QR4  plan-1  O   0.020
 QR4  plan-1  C4  0.020
 QR4  plan-1  O1  0.020
 QR4  plan-1  C3  0.020

