# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:08:56 2021
#   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  43  19  .  2022-03-23  2022-11-17
;
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  -0.395  15.7468  7.8879  23.5110
 QR4  C4   C  C      0   0.592  15.4868  6.9565  24.2218
 QR4  O1   O  OH1    0  -0.591  16.3578  6.2876  24.9494
 QR4  C3   C  CT     0  -0.080  14.0869  6.3782  24.3685
 QR4  N    N  NT3    1  -0.793  13.1777  7.3114  23.6536
 QR4  C5   C  CH1    0  -0.231  13.9897  4.9627  23.7469
 QR4  C9   C  CH2    0  -0.471  14.4222  4.0196  24.8760
 QR4  C10  C  CH1    0  -0.085  13.9971  4.7229  26.1631
 QR4  C2   C  CH1    0  -0.256  13.6146  6.1722  25.8214
 QR4  C1   C  CH2    0  -0.472  14.1809  7.0627  26.9417
 QR4  N1   N  NT2    1  -0.657  15.0677  4.8595  27.1949
 QR4  C    C  CH2    0  -0.325  14.7387  6.0864  27.9745
 QR4  C6   C  CH2    0  -0.423  14.7230  4.7668  22.4273
 QR4  C7   C  CH2    0  -0.454  14.4781  3.3926  21.8076
 QR4  C8   C  CH2    0  -0.667  15.1351  3.2153  20.4397
 QR4  B    B  B     -1   0.458  14.9093  1.7489  19.7040
 QR4  O4   O  OB     0  -0.754  13.4758  1.5021  19.4340
 QR4  O3   O  OB     0  -0.753  15.5140  0.6599  20.5212
 QR4  O2   O  OB     0  -0.738  15.5381  1.7058  18.3777
 QR4  H10  H  HOH1   0   0.511  17.2581  6.6363  24.8397
 QR4  H8   H  HNT3   0   0.485  13.1576  8.2455  24.0683
 QR4  H23  H  HNT3   0   0.478  13.4366  7.4386  22.6726
 QR4  H9   H  HNT3   0   0.484  12.2159  6.9665  23.6609
 QR4  H11  H  HCH1   0   0.293  12.9200  4.7953  23.5714
 QR4  H21  H  HCH2   0   0.296  13.9413  3.0488  24.7792
 QR4  H22  H  HCH2   0   0.274  15.4987  3.8399  24.8488
 QR4  H1   H  HCH1   0   0.346  13.1736  4.2159  26.6608
 QR4  H    H  HCH1   0   0.335  12.5256  6.2405  25.8133
 QR4  H7   H  HCH2   0   0.281  14.9536  7.7479  26.5979
 QR4  H6   H  HCH2   0   0.303  13.4014  7.6725  27.3913
 QR4  H3   H  HNT2   0   0.481  15.1210  4.0340  27.7915
 QR4  H2   H  HNT2   0   0.467  15.9857  4.9545  26.7575
 QR4  H4   H  HCH2   0   0.316  15.6299  6.4346  28.4885
 QR4  H5   H  HCH2   0   0.310  13.9885  5.8053  28.7095
 QR4  H12  H  HCH2   0   0.231  15.8003  4.9021  22.5686
 QR4  H13  H  HCH2   0   0.230  14.4050  5.5274  21.7054
 QR4  H15  H  HCH2   0   0.198  13.3938  3.2378  21.7363
 QR4  H14  H  HCH2   0   0.205  14.8415  2.6275  22.5038
 QR4  H16  H  HCH2   0   0.162  16.2096  3.4208  20.5583
 QR4  H17  H  HCH2   0   0.162  14.7650  4.0193  19.7871
 QR4  H20  H  H      0   0.416  12.9460  1.8355  20.1601
 QR4  H19  H  H      0   0.412  15.3236  0.8027  21.4510
 QR4  H18  H  H      0   0.419  16.4637  1.9414  18.4664

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  1.468  0.020  1.468
 QR4  O4   B    single  1.479  0.020  1.479
 QR4  B    O3   single  1.490  0.020  1.490
 QR4  B    C8   single  1.656  0.020  1.656
 QR4  C8   C7   single  1.528  0.020  1.528
 QR4  C7   C6   single  1.527  0.020  1.527
 QR4  C6   C5   single  1.522  0.020  1.522
 QR4  O    C4   double  1.200  0.020  1.200
 QR4  N    C3   single  1.486  0.020  1.486
 QR4  C5   C3   single  1.549  0.020  1.549
 QR4  C5   C9   single  1.533  0.020  1.533
 QR4  C4   C3   single  1.522  0.020  1.522
 QR4  C4   O1   single  1.317  0.020  1.317
 QR4  C3   C2   single  1.542  0.020  1.542
 QR4  C9   C10  single  1.527  0.020  1.527
 QR4  C2   C10  single  1.537  0.020  1.537
 QR4  C2   C1   single  1.539  0.020  1.539
 QR4  C10  N1   single  1.493  0.020  1.493
 QR4  C1   C    single  1.527  0.020  1.527
 QR4  N1   C    single  1.490  0.020  1.490
 QR4  O1   H10  single  0.850  0.020  0.980
 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   111.22  3.000
 QR4  O1   C4   O    125.31  3.000
 QR4  C3   C4   O    123.46  3.000
 QR4  H10  O1   C4   111.59  3.000
 QR4  C2   C3   C5   103.70  3.000
 QR4  C2   C3   N    110.48  3.000
 QR4  C5   C3   N    110.02  3.000
 QR4  C2   C3   C4   115.06  3.000
 QR4  C5   C3   C4   111.49  3.000
 QR4  N    C3   C4   106.13  3.000
 QR4  H9   N    H23  106.68  3.000
 QR4  H9   N    H8   106.68  3.000
 QR4  H23  N    H8   106.29  3.000
 QR4  H9   N    C3   111.13  3.000
 QR4  H23  N    C3   112.63  3.000
 QR4  H8   N    C3   113.00  3.000
 QR4  H11  C5   C6   108.15  3.000
 QR4  H11  C5   C9   107.40  3.000
 QR4  C6   C5   C9   115.04  3.000
 QR4  H11  C5   C3   105.36  3.000
 QR4  C9   C5   C3   104.41  3.000
 QR4  C6   C5   C3   115.80  3.000
 QR4  H22  C9   H21  106.67  3.000
 QR4  H22  C9   C10  111.80  3.000
 QR4  H21  C9   C10  111.29  3.000
 QR4  H22  C9   C5   111.16  3.000
 QR4  H21  C9   C5   111.02  3.000
 QR4  C10  C9   C5   105.00  3.000
 QR4  H1   C10  N1   105.62  3.000
 QR4  H1   C10  C2   110.66  3.000
 QR4  N1   C10  C2   104.23  3.000
 QR4  H1   C10  C9   112.44  3.000
 QR4  N1   C10  C9   115.15  3.000
 QR4  C2   C10  C9   108.43  3.000
 QR4  H    C2   C1   109.66  3.000
 QR4  H    C2   C10  108.00  3.000
 QR4  C1   C2   C10  106.98  3.000
 QR4  H    C2   C3   106.88  3.000
 QR4  C1   C2   C3   119.73  3.000
 QR4  C10  C2   C3   105.03  3.000
 QR4  H6   C1   H7   106.65  3.000
 QR4  H6   C1   C    109.93  3.000
 QR4  H7   C1   C    110.91  3.000
 QR4  H6   C1   C2   111.21  3.000
 QR4  H7   C1   C2   113.30  3.000
 QR4  C    C1   C2   104.89  3.000
 QR4  H2   N1   H3   106.20  3.000
 QR4  H2   N1   C    110.23  3.000
 QR4  H3   N1   C    111.83  3.000
 QR4  H2   N1   C10  110.92  3.000
 QR4  H3   N1   C10  111.57  3.000
 QR4  C    N1   C10  106.17  3.000
 QR4  H5   C    H4   109.22  3.000
 QR4  H5   C    N1   107.05  3.000
 QR4  H4   C    N1   109.29  3.000
 QR4  H5   C    C1   111.75  3.000
 QR4  H4   C    C1   114.52  3.000
 QR4  N1   C    C1   104.66  3.000
 QR4  H13  C6   H12  106.55  3.000
 QR4  H13  C6   C7   108.10  3.000
 QR4  H12  C6   C7   108.74  3.000
 QR4  H13  C6   C5   110.00  3.000
 QR4  H12  C6   C5   110.26  3.000
 QR4  C7   C6   C5   112.97  3.000
 QR4  H14  C7   H15  105.67  3.000
 QR4  H14  C7   C8   110.18  3.000
 QR4  H15  C7   C8   110.51  3.000
 QR4  H14  C7   C6   108.49  3.000
 QR4  H15  C7   C6   108.16  3.000
 QR4  C8   C7   C6   113.50  3.000
 QR4  H17  C8   H16  104.83  3.000
 QR4  H17  C8   B    109.75  3.000
 QR4  H16  C8   B    110.27  3.000
 QR4  H17  C8   C7   107.57  3.000
 QR4  H16  C8   C7   107.56  3.000
 QR4  B    C8   C7   116.23  3.000
 QR4  O2   B    O3   107.47  3.000
 QR4  O3   B    O4   111.81  3.000
 QR4  O2   B    O4   104.19  3.000
 QR4  O3   B    C8   110.38  3.000
 QR4  O4   B    C8   111.15  3.000
 QR4  O2   B    C8   111.65  3.000
 QR4  H20  O4   B    109.83  3.000
 QR4  H19  O3   B    110.00  3.000
 QR4  H18  O2   B    108.81  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  CONST_01  H10  O1  C4  C3    180.00   0.0  0
 QR4  Var_01    C1   C   N1  C10   -37.06  30.0  1
 QR4  Var_02    N1   C   C1  C2     25.93  30.0  1
 QR4  Var_03    C8   C7  C6  C5    176.28  30.0  1
 QR4  Var_04    B    C8  C7  C6   -179.87  30.0  1
 QR4  Var_05    O2   B   C8  C7    177.83  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
 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
 QR4  plan-1  H10  0.020

