# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 02:48:46 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: {3-[(2S,3R,4R)-4-amino-2-carboxypyrrolidin-3-yl]propyl}(trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CN[C@@H]([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
 XFG  XFG  "3-[(2~{S},3~{R},4~{R})-4-azanyl-2-carboxy-pyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boron"
  ligand  33  16  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XFG
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
 XFG  N1   N  NH1    0  -0.613  13.1936  6.7288  23.9861
 XFG  C4   C  CH1    0  -0.262  14.2298  4.5815  23.8028
 XFG  C5   C  CH2    0  -0.410  14.5518  4.4326  22.3137
 XFG  C6   C  CH2    0  -0.448  14.4811  2.9947  21.8021
 XFG  C7   C  CH2    0  -0.656  14.8032  2.8355  20.3149
 XFG  O    O  OC    -1  -0.610  16.7592  6.2771  24.3539
 XFG  O1   O  O      0  -0.599  15.5806  7.5998  22.9955
 XFG  C2   C  CH1    0  -0.198  14.4129  6.0143  24.3470
 XFG  C1   C  CH2    0  -0.282  12.1297  5.7418  23.7856
 XFG  C    C  CH1    0  -0.122  12.7349  4.3597  24.0935
 XFG  N    N  NH2    0  -0.795  12.4168  3.9545  25.4587
 XFG  B    B  B     -1   0.476  14.7798  1.2864  19.7235
 XFG  O4   O  OB     0  -0.750  15.8184  0.4634  20.4109
 XFG  O3   O  OB     0  -0.749  13.4279  0.6901  19.8408
 XFG  O2   O  OB     0  -0.734  15.0572  1.2443  18.2769
 XFG  H1   H  HNH1   0   0.331  13.3875  7.2267  23.1274
 XFG  H3   H  HCH1   0   0.209  14.8434  3.8686  24.3648
 XFG  H4   H  HCH2   0   0.210  15.5637  4.8004  22.1187
 XFG  H5   H  HCH2   0   0.199  13.8843  5.0626  21.7142
 XFG  H6   H  HCH2   0   0.188  13.4847  2.5850  22.0067
 XFG  H7   H  HCH2   0   0.178  15.1705  2.3927  22.4096
 XFG  H8   H  HCH2   0   0.146  15.7862  3.2986  20.1339
 XFG  H9   H  HCH2   0   0.149  14.0926  3.4592  19.7528
 XFG  H11  H  HCH1   0   0.199  14.4852  5.9459  25.4418
 XFG  H12  H  HCH2   0   0.203  11.2743  5.9217  24.4450
 XFG  H13  H  HCH2   0   0.216  11.7496  5.7760  22.7614
 XFG  H14  H  HCH1   0   0.230  12.3081  3.6008  23.4329
 XFG  H15  H  HNH2   0   0.337  12.8913  3.0837  25.6669
 XFG  H16  H  HNH2   0   0.337  12.7912  4.6292  26.1172
 XFG  H18  H  H      0   0.405  15.9212  0.7679  21.3147
 XFG  H19  H  H      0   0.408  13.0748  0.8739  20.7131
 XFG  H20  H  H      0   0.409  15.9031  1.6709  18.1262
 XFG  C3   C  C      0   0.398  15.6982  6.7029  23.8557

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
 XFG  O2  B    single  1.474  0.020  1.474
 XFG  O3  B    single  1.482  0.020  1.482
 XFG  B   C7   single  1.658  0.020  1.658
 XFG  B   O4   single  1.493  0.020  1.493
 XFG  C7  C6   single  1.530  0.020  1.530
 XFG  C6  C5   single  1.528  0.020  1.528
 XFG  C5  C4   single  1.531  0.020  1.531
 XFG  O1  C3   deloc   1.248  0.020  1.248
 XFG  C3  O    deloc   1.247  0.020  1.247
 XFG  C3  C2   single  1.539  0.020  1.539
 XFG  N1  C1   single  1.465  0.020  1.465
 XFG  N1  C2   single  1.459  0.020  1.459
 XFG  C1  C    single  1.540  0.020  1.540
 XFG  C4  C    single  1.539  0.020  1.539
 XFG  C4  C2   single  1.544  0.020  1.544
 XFG  C   N    single  1.459  0.020  1.459
 XFG  N1  H1   single  0.890  0.020  1.040
 XFG  C4  H3   single  0.970  0.020  1.090
 XFG  C5  H4   single  0.970  0.020  1.090
 XFG  C5  H5   single  0.970  0.020  1.090
 XFG  C6  H6   single  0.970  0.020  1.090
 XFG  C6  H7   single  0.970  0.020  1.090
 XFG  C7  H8   single  0.970  0.020  1.090
 XFG  C7  H9   single  0.970  0.020  1.090
 XFG  C2  H11  single  0.970  0.020  1.090
 XFG  C1  H12  single  0.970  0.020  1.090
 XFG  C1  H13  single  0.970  0.020  1.090
 XFG  C   H14  single  0.970  0.020  1.090
 XFG  N   H15  single  0.890  0.020  1.040
 XFG  N   H16  single  0.890  0.020  1.040
 XFG  O4  H18  single  0.850  0.020  0.980
 XFG  O3  H19  single  0.850  0.020  0.980
 XFG  O2  H20  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
 XFG  H1   N1  C1   110.78  3.000
 XFG  H1   N1  C2   106.91  3.000
 XFG  C1   N1  C2   108.11  3.000
 XFG  H3   C4  C    110.69  3.000
 XFG  H3   C4  C2   110.90  3.000
 XFG  C    C4  C2   100.51  3.000
 XFG  H3   C4  C5   108.54  3.000
 XFG  C2   C4  C5   114.10  3.000
 XFG  C    C4  C5   111.97  3.000
 XFG  H5   C5  H4   105.81  3.000
 XFG  H5   C5  C6   109.24  3.000
 XFG  H4   C5  C6   107.42  3.000
 XFG  H5   C5  C4   110.37  3.000
 XFG  H4   C5  C4   109.59  3.000
 XFG  C6   C5  C4   114.05  3.000
 XFG  H7   C6  H6   105.21  3.000
 XFG  H7   C6  C7   110.39  3.000
 XFG  H6   C6  C7   109.49  3.000
 XFG  H7   C6  C5   107.55  3.000
 XFG  H6   C6  C5   109.34  3.000
 XFG  C7   C6  C5   114.43  3.000
 XFG  H9   C7  H8   104.72  3.000
 XFG  H9   C7  B    109.78  3.000
 XFG  H8   C7  B    110.28  3.000
 XFG  H9   C7  C6   107.56  3.000
 XFG  H8   C7  C6   107.69  3.000
 XFG  B    C7  C6   116.16  3.000
 XFG  H11  C2  C3   106.91  3.000
 XFG  H11  C2  C4   107.53  3.000
 XFG  C3   C2  C4   113.70  3.000
 XFG  H11  C2  N1   109.38  3.000
 XFG  C4   C2  N1   105.56  3.000
 XFG  C3   C2  N1   113.58  3.000
 XFG  H13  C1  H12  106.70  3.000
 XFG  H13  C1  C    110.62  3.000
 XFG  H12  C1  C    109.52  3.000
 XFG  H13  C1  N1   111.08  3.000
 XFG  H12  C1  N1   111.97  3.000
 XFG  C    C1  N1   106.98  3.000
 XFG  H14  C   N    106.72  3.000
 XFG  H14  C   C1   110.42  3.000
 XFG  N    C   C1   110.52  3.000
 XFG  H14  C   C4   111.42  3.000
 XFG  N    C   C4   115.37  3.000
 XFG  C1   C   C4   102.39  3.000
 XFG  H16  N   H15  105.39  3.000
 XFG  H16  N   C    110.01  3.000
 XFG  H15  N   C    109.19  3.000
 XFG  O2   B   O3   103.76  3.000
 XFG  O3   B   O4   112.11  3.000
 XFG  O2   B   O4   107.78  3.000
 XFG  O4   B   C7   109.94  3.000
 XFG  O3   B   C7   111.13  3.000
 XFG  O2   B   C7   111.97  3.000
 XFG  H18  O4  B    109.48  3.000
 XFG  H19  O3  B    109.32  3.000
 XFG  H20  O2  B    107.91  3.000
 XFG  C2   C3  O1   117.57  3.000
 XFG  C2   C3  O    115.48  3.000
 XFG  O1   C3  O    126.93  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
 XFG  Var_01  C    C1  N1  C2     2.10  30.0  1
 XFG  Var_02  H12  C1  N1  C2   122.09  30.0  1
 XFG  Var_03  H13  C1  N1  C2  -118.72  30.0  1
 XFG  Var_04  H1   N1  C1  C    118.94  30.0  1
 XFG  Var_05  C7   C6  C5  C4  -179.92  30.0  1
 XFG  Var_06  H6   C6  C5  C4    56.85  30.0  1
 XFG  Var_07  H7   C6  C5  C4   -56.90  30.0  1
 XFG  Var_08  B    C7  C6  C5   178.38  30.0  1
 XFG  Var_09  O2   B   C7  C6   178.07  30.0  3
 XFG  Var_10  O3   B   C7  C6    62.55  30.0  3
 XFG  Var_11  O4   B   C7  C6   -62.16  30.0  3
 XFG  Var_12  H8   C7  C6  C5    54.18  30.0  1
 XFG  Var_13  H9   C7  C6  C5   -58.19  30.0  1
 XFG  Var_14  H4   C5  C6  C7   -58.27  30.0  3
 XFG  Var_15  H5   C5  C6  C7    56.06  30.0  3
 XFG  Var_16  H6   C6  C7  B    -58.47  30.0  3
 XFG  Var_17  H7   C6  C7  B     56.90  30.0  3
 XFG  Var_18  H8   C7  B   O4    60.69  30.0  3
 XFG  Var_19  H9   C7  B   O4   175.58  30.0  3
 XFG  Var_20  H8   C7  B   O3  -174.61  30.0  3
 XFG  Var_21  H9   C7  B   O3   -59.72  30.0  3
 XFG  Var_22  H8   C7  B   O2   -59.08  30.0  3
 XFG  Var_23  H9   C7  B   O2    55.81  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
 XFG  chir_01  C4  C5  C   C2  positiv
 XFG  chir_02  C2  N1  C4  C3  negativ
 XFG  chir_03  C   N   C4  C1  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
 XFG  plan-1  O   0.020
 XFG  plan-1  O1  0.020
 XFG  plan-1  C2  0.020
 XFG  plan-1  C3  0.020

