# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 14:17:57 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: {3-[(3aR,4S,5S,6aR)-5-azaniumyl-5-carboxyoctahydrocyclopenta[c]pyrrol-2-ium-4-yl]propyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@]1(C[C@H]2C[NH2+]C[C@H]2[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
 QR1  QR1  {3-[(3aR,4S,5S,6aR)-5-azaniumyl-5-carboxyoctahydrocyclopenta[c]pyrrol-2-ium-4-yl]propyl}(trihydroxy)borate(1-)  ligand  42  19  .  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_QR1
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
 QR1  O1   O  O      0  -0.585  17.0334  8.8243  23.2719
 QR1  C1   C  C      0   0.479  17.0230  7.9622  24.1752
 QR1  O    O  OC    -1  -0.546  17.9777  7.4961  24.8054
 QR1  C    C  CT     0  -0.029  15.6164  7.3888  24.5242
 QR1  N    N  NT3    1  -0.826  14.6376  8.2948  23.8533
 QR1  C7   C  CH2    0  -0.443  15.3568  7.2793  26.0234
 QR1  C4   C  CR15   0  -0.251  15.9919  5.9502  26.4430
 QR1  C5   C  CH2    0  -0.331  15.1557  5.1390  27.4278
 QR1  N1   N  N      1  -0.643  14.3702  4.2125  26.5612
 QR1  C6   C  CH2    0  -0.330  15.3042  3.8109  25.4690
 QR1  C3   C  CR15   0  -0.254  16.0709  5.0907  25.1476
 QR1  C2   C  CH1    0  -0.241  15.4462  5.9396  24.0284
 QR1  C8   C  CH2    0  -0.400  15.9679  5.6492  22.6254
 QR1  C9   C  CH2    0  -0.440  15.7371  4.2144  22.1604
 QR1  C10  C  CH2    0  -0.676  16.1414  3.9528  20.7110
 QR1  B    B  B     -1   0.488  15.9936  2.3745  20.2225
 QR1  O4   O  OB     0  -0.740  14.6183  1.8635  20.3530
 QR1  O3   O  OB     0  -0.748  16.8801  1.5085  21.0546
 QR1  O2   O  OB     0  -0.739  16.2880  2.2540  18.7760
 QR1  H2   H  HNT3   0   0.459  13.8476  7.8113  23.4273
 QR1  H3   H  HNT3   0   0.462  14.2567  9.0018  24.4828
 QR1  H4   H  HNT3   0   0.451  15.1954  8.7922  23.1341
 QR1  H5   H  HCH2   0   0.275  15.7445  8.1272  26.5887
 QR1  H6   H  HCH2   0   0.259  14.2745  7.2498  26.1910
 QR1  H7   H  HCR5   0   0.291  16.9820  6.1173  26.8579
 QR1  H8   H  HCH2   0   0.307  15.7747  4.5152  28.0692
 QR1  H9   H  HCH2   0   0.306  14.4780  5.7231  28.0457
 QR1  H10  H  H      0   0.468  13.5480  4.6826  26.1775
 QR1  H11  H  H      0   0.475  14.0129  3.4089  27.0795
 QR1  H12  H  HCH2   0   0.307  14.7325  3.3907  24.6459
 QR1  H13  H  HCH2   0   0.307  15.9534  3.0417  25.8830
 QR1  H14  H  HCR5   0   0.286  17.1034  4.8453  24.9030
 QR1  H15  H  HCH1   0   0.255  14.3621  5.7453  24.0273
 QR1  H16  H  HCH2   0   0.217  17.0407  5.8612  22.5790
 QR1  H17  H  HCH2   0   0.217  15.4873  6.3312  21.9151
 QR1  H18  H  HCH2   0   0.188  14.6772  3.9622  22.2956
 QR1  H19  H  HCH2   0   0.196  16.2924  3.5338  22.8154
 QR1  H20  H  HCH2   0   0.150  17.1780  4.3063  20.5807
 QR1  H21  H  HCH2   0   0.155  15.5413  4.6112  20.0662
 QR1  H22  H  H      0   0.409  14.3737  1.8734  21.2802
 QR1  H23  H  H      0   0.404  17.6567  2.0119  21.3070
 QR1  H24  H  H      0   0.408  16.9902  2.8685  18.5550

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
 QR1  O2   B    single  1.481  0.020  1.481
 QR1  O4   B    single  1.473  0.020  1.473
 QR1  B    C10  single  1.659  0.020  1.659
 QR1  B    O3   single  1.493  0.020  1.493
 QR1  C10  C9   single  1.527  0.020  1.527
 QR1  C9   C8   single  1.526  0.020  1.526
 QR1  C8   C2   single  1.525  0.020  1.525
 QR1  O1   C1   deloc   1.249  0.020  1.249
 QR1  C1   O    deloc   1.235  0.020  1.235
 QR1  C1   C    single  1.559  0.020  1.559
 QR1  N    C    single  1.493  0.020  1.493
 QR1  C2   C    single  1.541  0.020  1.541
 QR1  C2   C3   single  1.537  0.020  1.537
 QR1  C    C7   single  1.525  0.020  1.525
 QR1  C3   C6   single  1.526  0.020  1.526
 QR1  C3   C4   single  1.557  0.020  1.557
 QR1  C6   N1   single  1.492  0.020  1.492
 QR1  C7   C4   single  1.532  0.020  1.532
 QR1  C4   C5   single  1.525  0.020  1.525
 QR1  N1   C5   single  1.492  0.020  1.492
 QR1  N    H2   single  0.890  0.020  1.040
 QR1  N    H3   single  0.890  0.020  1.040
 QR1  N    H4   single  0.890  0.020  1.040
 QR1  C7   H5   single  0.970  0.020  1.090
 QR1  C7   H6   single  0.970  0.020  1.090
 QR1  C4   H7   single  0.970  0.020  1.090
 QR1  C5   H8   single  0.970  0.020  1.090
 QR1  C5   H9   single  0.970  0.020  1.090
 QR1  N1   H10  single  0.890  0.020  1.040
 QR1  N1   H11  single  0.890  0.020  1.040
 QR1  C6   H12  single  0.970  0.020  1.090
 QR1  C6   H13  single  0.970  0.020  1.090
 QR1  C3   H14  single  0.970  0.020  1.090
 QR1  C2   H15  single  0.970  0.020  1.090
 QR1  C8   H16  single  0.970  0.020  1.090
 QR1  C8   H17  single  0.970  0.020  1.090
 QR1  C9   H18  single  0.970  0.020  1.090
 QR1  C9   H19  single  0.970  0.020  1.090
 QR1  C10  H20  single  0.970  0.020  1.090
 QR1  C10  H21  single  0.970  0.020  1.090
 QR1  O4   H22  single  0.850  0.020  0.980
 QR1  O3   H23  single  0.850  0.020  0.980
 QR1  O2   H24  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
 QR1  C    C1   O    116.39  3.000
 QR1  C    C1   O1   115.06  3.000
 QR1  O    C1   O1   128.55  3.000
 QR1  C2   C    C7   103.29  3.000
 QR1  C7   C    N    111.94  3.000
 QR1  C2   C    N    110.71  3.000
 QR1  C7   C    C1   113.58  3.000
 QR1  C2   C    C1   111.94  3.000
 QR1  N    C    C1   105.53  3.000
 QR1  H4   N    H3   107.23  3.000
 QR1  H4   N    H2   110.76  3.000
 QR1  H3   N    H2   107.28  3.000
 QR1  H4   N    C    104.48  3.000
 QR1  H3   N    C    112.83  3.000
 QR1  H2   N    C    114.08  3.000
 QR1  H6   C7   H5   107.03  3.000
 QR1  H6   C7   C4   110.14  3.000
 QR1  H5   C7   C4   112.67  3.000
 QR1  H6   C7   C    108.68  3.000
 QR1  H5   C7   C    113.15  3.000
 QR1  C4   C7   C    105.13  3.000
 QR1  H7   C4   C3   110.89  3.000
 QR1  H7   C4   C5   109.57  3.000
 QR1  C3   C4   C5   105.75  3.000
 QR1  H7   C4   C7   110.42  3.000
 QR1  C5   C4   C7   114.27  3.000
 QR1  C3   C4   C7   105.79  3.000
 QR1  H9   C5   H8   109.12  3.000
 QR1  H9   C5   N1   109.60  3.000
 QR1  H8   C5   N1   106.61  3.000
 QR1  H9   C5   C4   115.02  3.000
 QR1  H8   C5   C4   111.94  3.000
 QR1  N1   C5   C4   104.12  3.000
 QR1  H11  N1   H10  105.74  3.000
 QR1  H11  N1   C6   112.26  3.000
 QR1  H10  N1   C6   110.65  3.000
 QR1  H11  N1   C5   112.22  3.000
 QR1  H10  N1   C5   110.86  3.000
 QR1  C6   N1   C5   105.23  3.000
 QR1  H13  C6   H12  109.18  3.000
 QR1  H13  C6   C3   111.90  3.000
 QR1  H12  C6   C3   115.41  3.000
 QR1  H13  C6   N1   106.57  3.000
 QR1  H12  C6   N1   109.22  3.000
 QR1  C3   C6   N1   104.06  3.000
 QR1  H14  C3   C2   110.25  3.000
 QR1  H14  C3   C6   109.55  3.000
 QR1  C2   C3   C6   114.34  3.000
 QR1  H14  C3   C4   111.06  3.000
 QR1  C6   C3   C4   105.20  3.000
 QR1  C2   C3   C4   106.28  3.000
 QR1  H15  C2   C8   107.59  3.000
 QR1  H15  C2   C3   107.66  3.000
 QR1  C8   C2   C3   115.19  3.000
 QR1  H15  C2   C    105.96  3.000
 QR1  C3   C2   C    103.90  3.000
 QR1  C8   C2   C    115.93  3.000
 QR1  H17  C8   H16  106.37  3.000
 QR1  H17  C8   C9   108.75  3.000
 QR1  H16  C8   C9   108.51  3.000
 QR1  H17  C8   C2   109.14  3.000
 QR1  H16  C8   C2   109.72  3.000
 QR1  C9   C8   C2   114.07  3.000
 QR1  H19  C9   H18  105.83  3.000
 QR1  H19  C9   C10  109.07  3.000
 QR1  H18  C9   C10  109.46  3.000
 QR1  H19  C9   C8   108.98  3.000
 QR1  H18  C9   C8   108.94  3.000
 QR1  C10  C9   C8   114.22  3.000
 QR1  H21  C10  H20  104.58  3.000
 QR1  H21  C10  B    110.39  3.000
 QR1  H20  C10  B    110.73  3.000
 QR1  H21  C10  C9   108.02  3.000
 QR1  H20  C10  C9   107.82  3.000
 QR1  B    C10  C9   114.76  3.000
 QR1  O2   B    O3   112.28  3.000
 QR1  O3   B    O4   107.69  3.000
 QR1  O2   B    O4   104.12  3.000
 QR1  O3   B    C10  109.57  3.000
 QR1  O4   B    C10  112.78  3.000
 QR1  O2   B    C10  110.32  3.000
 QR1  H22  O4   B    108.68  3.000
 QR1  H23  O3   B    108.85  3.000
 QR1  H24  O2   B    108.57  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
 QR1  Var_01  C6   N1   C5   C4   38.08  30.0  1
 QR1  Var_02  C3   C6   N1   C5  -39.07  30.0  1
 QR1  Var_03  C10  C9   C8   C2  174.67  30.0  1
 QR1  Var_04  B    C10  C9   C8  176.02  30.0  1
 QR1  Var_05  O2   B    C10  C9  174.73  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
 QR1  chir_01  C   N   C2  C7  positiv
 QR1  chir_02  C4  C5  C7  C3  positiv
 QR1  chir_03  C3  C4  C6  C2  negativ
 QR1  chir_04  C2  C3  C   C8  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
 QR1  plan-1  O1  0.020
 QR1  plan-1  C1  0.020
 QR1  plan-1  O   0.020
 QR1  plan-1  C   0.020

