# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:02:42 2021
#   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  43  19  .  2022-08-10  2022-11-17
;
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  -0.414  16.9506  8.9380  23.2860
 QR1  C1   C  C      0   0.598  16.8851  8.0387  24.0814
 QR1  O    O  OH1    0  -0.566  17.9084  7.4912  24.6960
 QR1  C    C  CT     0  -0.088  15.5708  7.3842  24.4868
 QR1  N    N  NT3    1  -0.788  14.4964  8.2059  23.8691
 QR1  C7   C  CH2    0  -0.437  15.3794  7.2839  26.0015
 QR1  C4   C  CH1    0  -0.263  16.0665  5.9755  26.4125
 QR1  C5   C  CH2    0  -0.332  15.2764  5.1543  27.4257
 QR1  N1   N  NT2    1  -0.641  14.4746  4.2244  26.5824
 QR1  C6   C  CH2    0  -0.333  15.3867  3.8176  25.4772
 QR1  C3   C  CH1    0  -0.267  16.1326  5.1023  25.1260
 QR1  C2   C  CH1    0  -0.232  15.4633  5.9205  24.0087
 QR1  C8   C  CH2    0  -0.413  15.9816  5.6466  22.6016
 QR1  C9   C  CH2    0  -0.462  15.7647  4.2102  22.1343
 QR1  C10  C  CH2    0  -0.665  16.2119  3.9614  20.6946
 QR1  B    B  B     -1   0.459  16.0070  2.4229  20.1171
 QR1  O4   O  OB     0  -0.753  14.5740  2.0677  20.0344
 QR1  O3   O  OB     0  -0.752  16.7723  1.4486  20.9443
 QR1  O2   O  OB     0  -0.739  16.4922  2.3004  18.7362
 QR1  H1   H  HOH1   0   0.504  18.7424  7.9014  24.4154
 QR1  H2   H  HNT3   0   0.480  13.5718  7.8540  24.1218
 QR1  H3   H  HNT3   0   0.484  14.5273  9.1834  24.1663
 QR1  H4   H  HNT3   0   0.476  14.5419  8.2106  22.8482
 QR1  H5   H  HCH2   0   0.307  15.7565  8.1507  26.5439
 QR1  H6   H  HCH2   0   0.282  14.3052  7.2323  26.2044
 QR1  H7   H  HCH1   0   0.313  17.0588  6.1717  26.8102
 QR1  H8   H  HCH2   0   0.318  15.9292  4.5370  28.0383
 QR1  H9   H  HCH2   0   0.316  14.6160  5.7286  28.0703
 QR1  H10  H  HNT2   0   0.467  13.6427  4.6891  26.2157
 QR1  H11  H  HNT2   0   0.483  14.1287  3.4230  27.1103
 QR1  H12  H  HCH2   0   0.312  14.8047  3.3798  24.6700
 QR1  H13  H  HCH2   0   0.320  16.0550  3.0629  25.8855
 QR1  H14  H  HCH1   0   0.308  17.1613  4.8634  24.8587
 QR1  H15  H  HCH1   0   0.278  14.3868  5.6935  24.0176
 QR1  H16  H  HCH2   0   0.233  17.0520  5.8703  22.5461
 QR1  H17  H  HCH2   0   0.231  15.4848  6.3157  21.8905
 QR1  H18  H  HCH2   0   0.200  14.7015  3.9614  22.2503
 QR1  H19  H  HCH2   0   0.201  16.3063  3.5373  22.8102
 QR1  H20  H  HCH2   0   0.164  17.2703  4.2542  20.6210
 QR1  H21  H  HCH2   0   0.164  15.6773  4.6751  20.0511
 QR1  H22  H  H      0   0.416  14.0923  2.4729  20.7574
 QR1  H23  H  H      0   0.412  16.6494  1.6405  21.8765
 QR1  H24  H  H      0   0.419  17.4001  2.6080  18.6972

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  1.469  0.020  1.469
 QR1  O4   B    single  1.479  0.020  1.479
 QR1  B    C10  single  1.656  0.020  1.656
 QR1  B    O3   single  1.490  0.020  1.490
 QR1  C10  C9   single  1.528  0.020  1.528
 QR1  C9   C8   single  1.526  0.020  1.526
 QR1  C8   C2   single  1.524  0.020  1.524
 QR1  O1   C1   double  1.202  0.020  1.202
 QR1  C1   O    single  1.313  0.020  1.313
 QR1  C1   C    single  1.523  0.020  1.523
 QR1  N    C    single  1.487  0.020  1.487
 QR1  C2   C    single  1.544  0.020  1.544
 QR1  C2   C3   single  1.538  0.020  1.538
 QR1  C    C7   single  1.530  0.020  1.530
 QR1  C3   C6   single  1.527  0.020  1.527
 QR1  C3   C4   single  1.556  0.020  1.556
 QR1  C6   N1   single  1.490  0.020  1.490
 QR1  C7   C4   single  1.534  0.020  1.534
 QR1  C4   C5   single  1.525  0.020  1.525
 QR1  N1   C5   single  1.489  0.020  1.489
 QR1  O    H1   single  0.850  0.020  0.980
 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    111.63  3.000
 QR1  C    C1   O1   122.98  3.000
 QR1  O    C1   O1   125.38  3.000
 QR1  H1   O    C1   110.97  3.000
 QR1  C2   C    C7   103.64  3.000
 QR1  C7   C    N    110.92  3.000
 QR1  C2   C    N    110.18  3.000
 QR1  C7   C    C1   113.55  3.000
 QR1  C2   C    C1   112.65  3.000
 QR1  N    C    C1   105.99  3.000
 QR1  H4   N    H3   106.54  3.000
 QR1  H4   N    H2   106.81  3.000
 QR1  H3   N    H2   106.56  3.000
 QR1  H4   N    C    112.66  3.000
 QR1  H3   N    C    112.70  3.000
 QR1  H2   N    C    111.16  3.000
 QR1  H6   C7   H5   106.55  3.000
 QR1  H6   C7   C4   110.47  3.000
 QR1  H5   C7   C4   112.95  3.000
 QR1  H6   C7   C    108.03  3.000
 QR1  H5   C7   C    113.41  3.000
 QR1  C4   C7   C    105.37  3.000
 QR1  H7   C4   C3   111.41  3.000
 QR1  H7   C4   C5   109.10  3.000
 QR1  C3   C4   C5   105.61  3.000
 QR1  H7   C4   C7   110.67  3.000
 QR1  C5   C4   C7   113.91  3.000
 QR1  C3   C4   C7   106.02  3.000
 QR1  H9   C5   H8   109.30  3.000
 QR1  H9   C5   N1   109.79  3.000
 QR1  H8   C5   N1   106.72  3.000
 QR1  H9   C5   C4   115.11  3.000
 QR1  H8   C5   C4   111.65  3.000
 QR1  N1   C5   C4   103.83  3.000
 QR1  H11  N1   H10  105.49  3.000
 QR1  H11  N1   C6   112.16  3.000
 QR1  H10  N1   C6   110.90  3.000
 QR1  H11  N1   C5   112.34  3.000
 QR1  H10  N1   C5   110.96  3.000
 QR1  C6   N1   C5   105.13  3.000
 QR1  H13  C6   H12  109.16  3.000
 QR1  H13  C6   C3   111.72  3.000
 QR1  H12  C6   C3   115.45  3.000
 QR1  H13  C6   N1   106.69  3.000
 QR1  H12  C6   N1   109.46  3.000
 QR1  C3   C6   N1   103.89  3.000
 QR1  H14  C3   C2   110.45  3.000
 QR1  H14  C3   C6   109.47  3.000
 QR1  C2   C3   C6   113.71  3.000
 QR1  H14  C3   C4   111.47  3.000
 QR1  C6   C3   C4   105.14  3.000
 QR1  C2   C3   C4   106.48  3.000
 QR1  H15  C2   C8   107.64  3.000
 QR1  H15  C2   C3   108.07  3.000
 QR1  C8   C2   C3   115.28  3.000
 QR1  H15  C2   C    105.15  3.000
 QR1  C3   C2   C    104.43  3.000
 QR1  C8   C2   C    115.63  3.000
 QR1  H17  C8   H16  106.60  3.000
 QR1  H17  C8   C9   108.16  3.000
 QR1  H16  C8   C9   108.41  3.000
 QR1  H17  C8   C2   109.58  3.000
 QR1  H16  C8   C2   110.03  3.000
 QR1  C9   C8   C2   113.79  3.000
 QR1  H19  C9   H18  105.90  3.000
 QR1  H19  C9   C10  109.65  3.000
 QR1  H18  C9   C10  110.25  3.000
 QR1  H19  C9   C8   108.58  3.000
 QR1  H18  C9   C8   108.58  3.000
 QR1  C10  C9   C8   113.59  3.000
 QR1  H21  C10  H20  104.82  3.000
 QR1  H21  C10  B    109.80  3.000
 QR1  H20  C10  B    110.04  3.000
 QR1  H21  C10  C9   107.66  3.000
 QR1  H20  C10  C9   107.53  3.000
 QR1  B    C10  C9   116.34  3.000
 QR1  O2   B    O3   107.32  3.000
 QR1  O3   B    O4   111.82  3.000
 QR1  O2   B    O4   104.33  3.000
 QR1  O3   B    C10  110.52  3.000
 QR1  O4   B    C10  111.26  3.000
 QR1  O2   B    C10  111.38  3.000
 QR1  H22  O4   B    110.08  3.000
 QR1  H23  O3   B    110.05  3.000
 QR1  H24  O2   B    108.91  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  CONST_01  H1   O    C1   C    180.00   0.0  0
 QR1  Var_01    C6   N1   C5   C4    39.28  30.0  1
 QR1  Var_02    C3   C6   N1   C5   -39.72  30.0  1
 QR1  Var_03    C10  C9   C8   C2   176.64  30.0  1
 QR1  Var_04    B    C10  C9   C8   180.00  30.0  1
 QR1  Var_05    O2   B    C10  C9  -179.04  30.0  2

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
 QR1  plan-1  H1  0.020

