# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 14:21:06 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-[(3~{S},4~{R})-4-azanyl-4-carboxy-pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1(CNC[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
 HE8  HE8  3-[(3~{S},4~{R})-4-azanyl-4-carboxy-pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide  ligand  33  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HE8
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
 HE8  C11  C  CH2    0  -0.307  -1.2491   1.9628  -0.0063
 HE8  C13  C  C      0   0.408  -2.6657  -1.5260  -0.0165
 HE8  O14  O  OC    -1  -0.618  -2.6208  -2.3275   0.9422
 HE8  O15  O  O      0  -0.607  -2.7375  -1.8331  -1.2235
 HE8  B6   B  B     -1   0.443   3.9895  -0.0548  -0.0709
 HE8  C1   C  CT     0  -0.035  -2.6137  -0.0248   0.3427
 HE8  C2   C  CH1    0  -0.227  -1.1655   0.5051   0.5364
 HE8  C3   C  CH2    0  -0.416  -0.0551  -0.2882  -0.1472
 HE8  C4   C  CH2    0  -0.406   1.3425   0.2164   0.2022
 HE8  C5   C  CH2    0  -0.666   2.4737  -0.5472  -0.4787
 HE8  C9   C  CH2    0  -0.310  -3.1393   0.9138  -0.7463
 HE8  N10  N  NH1    0  -0.584  -2.6291   2.2346  -0.4023
 HE8  N12  N  NH2    0  -0.801  -3.3478   0.2910   1.5726
 HE8  O16  O  OB     0  -0.751   4.2159   1.3771  -0.3675
 HE8  O7   O  OB     0  -0.750   4.2420  -0.1485   1.3840
 HE8  O8   O  OB     0  -0.752   4.9219  -0.9243  -0.8415
 HE8  H1   H  HCH2   0   0.224  -0.9024   2.7095   0.7090
 HE8  H2   H  HCH2   0   0.208  -0.6061   2.0500  -0.8892
 HE8  H4   H  HCH1   0   0.209  -0.9497   0.5171   1.6109
 HE8  H5   H  HCH2   0   0.202  -0.1178  -1.3414   0.1436
 HE8  H6   H  HCH2   0   0.192  -0.1922  -0.2631  -1.2347
 HE8  H7   H  HCH2   0   0.188   1.4267   1.2805  -0.0473
 HE8  H8   H  HCH2   0   0.177   1.4666   0.1637   1.2907
 HE8  H9   H  HCH2   0   0.152   2.3240  -0.4760  -1.5677
 HE8  H10  H  HCH2   0   0.152   2.3422  -1.6180  -0.2563
 HE8  H11  H  HCH2   0   0.219  -2.7448   0.6126  -1.7187
 HE8  H12  H  HCH2   0   0.220  -4.2304   0.9199  -0.8214
 HE8  H13  H  HNH1   0   0.333  -3.1297   2.5250   0.4300
 HE8  H15  H  HNH2   0   0.327  -4.3194   0.0217   1.4532
 HE8  H16  H  HNH2   0   0.329  -3.0015  -0.3204   2.3033
 HE8  H18  H  H      0   0.416   3.8362   1.5743  -1.2260
 HE8  H19  H  H      0   0.416   3.9028  -0.9888   1.6981
 HE8  H14  H  H      0   0.418   5.8254  -0.6729  -0.6280

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
 HE8  O8   B6   single  1.490  0.020  1.490
 HE8  O16  B6   single  1.480  0.020  1.480
 HE8  B6   O7   single  1.480  0.020  1.480
 HE8  B6   C5   single  1.645  0.020  1.645
 HE8  C5   C4   single  1.525  0.020  1.525
 HE8  C4   C3   single  1.526  0.020  1.526
 HE8  C3   C2   single  1.526  0.020  1.526
 HE8  C2   C1   single  1.554  0.020  1.554
 HE8  C2   C11  single  1.558  0.020  1.558
 HE8  N12  C1   single  1.467  0.020  1.467
 HE8  O15  C13  deloc   1.248  0.020  1.248
 HE8  C1   C13  single  1.544  0.020  1.544
 HE8  C1   C9   single  1.531  0.020  1.531
 HE8  C13  O14  deloc   1.250  0.020  1.250
 HE8  C11  N10  single  1.461  0.020  1.461
 HE8  C9   N10  single  1.457  0.020  1.457
 HE8  C11  H1   single  0.970  0.020  1.090
 HE8  C11  H2   single  0.970  0.020  1.090
 HE8  C2   H4   single  0.970  0.020  1.090
 HE8  C3   H5   single  0.970  0.020  1.090
 HE8  C3   H6   single  0.970  0.020  1.090
 HE8  C4   H7   single  0.970  0.020  1.090
 HE8  C4   H8   single  0.970  0.020  1.090
 HE8  C5   H9   single  0.970  0.020  1.090
 HE8  C5   H10  single  0.970  0.020  1.090
 HE8  C9   H11  single  0.970  0.020  1.090
 HE8  C9   H12  single  0.970  0.020  1.090
 HE8  N10  H13  single  0.890  0.020  1.040
 HE8  N12  H15  single  0.890  0.020  1.040
 HE8  N12  H16  single  0.890  0.020  1.040
 HE8  O16  H18  single  0.850  0.020  0.980
 HE8  O7   H19  single  0.850  0.020  0.980
 HE8  O8   H14  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
 HE8  H2   C11  H1   106.71  3.000
 HE8  H2   C11  N10  108.73  3.000
 HE8  H1   C11  N10  110.52  3.000
 HE8  H2   C11  C2   108.88  3.000
 HE8  H1   C11  C2   113.28  3.000
 HE8  N10  C11  C2   108.61  3.000
 HE8  C1   C13  O15  117.79  3.000
 HE8  C1   C13  O14  116.33  3.000
 HE8  O15  C13  O14  125.88  3.000
 HE8  O8   B6   O7   111.40  3.000
 HE8  O7   B6   O16  103.43  3.000
 HE8  O8   B6   O16  111.43  3.000
 HE8  O7   B6   C5   112.46  3.000
 HE8  O16  B6   C5   112.39  3.000
 HE8  O8   B6   C5   105.89  3.000
 HE8  N12  C1   C9   107.02  3.000
 HE8  C9   C1   C2   101.51  3.000
 HE8  N12  C1   C2   106.77  3.000
 HE8  C9   C1   C13  114.77  3.000
 HE8  N12  C1   C13  112.79  3.000
 HE8  C2   C1   C13  113.06  3.000
 HE8  H4   C2   C3   107.55  3.000
 HE8  H4   C2   C1   108.02  3.000
 HE8  C3   C2   C1   116.42  3.000
 HE8  H4   C2   C11  109.99  3.000
 HE8  C1   C2   C11  103.04  3.000
 HE8  C3   C2   C11  111.68  3.000
 HE8  H6   C3   H5   106.17  3.000
 HE8  H6   C3   C4   109.51  3.000
 HE8  H5   C3   C4   108.05  3.000
 HE8  H6   C3   C2   109.96  3.000
 HE8  H5   C3   C2   109.85  3.000
 HE8  C4   C3   C2   113.07  3.000
 HE8  H8   C4   H7   105.30  3.000
 HE8  H8   C4   C5   109.57  3.000
 HE8  H7   C4   C5   109.11  3.000
 HE8  H8   C4   C3   108.35  3.000
 HE8  H7   C4   C3   109.83  3.000
 HE8  C5   C4   C3   114.29  3.000
 HE8  H10  C5   H9   104.25  3.000
 HE8  H10  C5   C4   107.94  3.000
 HE8  H9   C5   C4   107.95  3.000
 HE8  H10  C5   B6   110.54  3.000
 HE8  H9   C5   B6   110.54  3.000
 HE8  C4   C5   B6   115.02  3.000
 HE8  H12  C9   H11  107.51  3.000
 HE8  H12  C9   N10  111.13  3.000
 HE8  H11  C9   N10  109.50  3.000
 HE8  H12  C9   C1   113.26  3.000
 HE8  H11  C9   C1   109.91  3.000
 HE8  N10  C9   C1   105.52  3.000
 HE8  H13  N10  C9   106.30  3.000
 HE8  H13  N10  C11  107.29  3.000
 HE8  C9   N10  C11  103.07  3.000
 HE8  H16  N12  H15  104.58  3.000
 HE8  H16  N12  C1   107.67  3.000
 HE8  H15  N12  C1   108.86  3.000
 HE8  H18  O16  B6   108.53  3.000
 HE8  H19  O7   B6   108.49  3.000
 HE8  H14  O8   B6   108.70  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
 HE8  Var_01  C1  C9   N10  C11    42.53  30.0  1
 HE8  Var_02  C9  N10  C11  C2    -27.43  30.0  1
 HE8  Var_03  C5  C4   C3   C2   -179.35  30.0  1
 HE8  Var_04  C3  C4   C5   B6   -177.80  30.0  3
 HE8  Var_05  O8  B6   C5   C4   -179.99  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
 HE8  chir_01  C1  C2  C13  C9   positiv
 HE8  chir_02  C2  C3  C1   C11  positiv

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
 HE8  plan-1  C13  0.020
 HE8  plan-1  O14  0.020
 HE8  plan-1  O15  0.020
 HE8  plan-1  C1   0.020

