# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:30:50 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: {3-[(2S,3R)-2-carboxypyrrolidin-3-yl]propyl}(trihydroxido)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NCC[C@H]1CCC[B-](O)(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
 VUV  VUV  "3-[(2~{S},3~{R})-2-carboxypyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide"
  ligand  31  15  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VUV
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
 VUV  C4   C  CR15   0  -0.177  15.9907  7.0456  24.7834
 VUV  C5   C  C      0   0.394  17.2627  7.7495  24.2775
 VUV  C6   C  CH2    0  -0.277  13.6916  6.8208  24.2350
 VUV  C7   C  CH2    0  -0.471  14.2980  5.4362  24.4992
 VUV  O4   O  O      0  -0.600  17.1215  8.6888  23.4673
 VUV  O3   O  OC    -1  -0.611  18.3383  7.2935  24.7147
 VUV  N    N  NR15   0  -0.618  14.7642  7.7835  24.5011
 VUV  C3   C  CR15   0  -0.258  15.7834  5.6341  24.1898
 VUV  C2   C  CH2    0  -0.407  16.0738  5.5222  22.6917
 VUV  C1   C  CH2    0  -0.446  15.9929  4.0942  22.1554
 VUV  C    C  CH2    0  -0.661  16.1634  3.9722  20.6397
 VUV  B    B  B     -1   0.476  16.2195  2.4316  20.0279
 VUV  O2   O  OB     0  -0.749  17.4479  1.7340  20.5112
 VUV  O1   O  OB     0  -0.752  14.9895  1.6743  20.3589
 VUV  O    O  OB     0  -0.734  16.2689  2.4309  18.5538
 VUV  H1   H  HCR5   0   0.198  16.0984  6.9224  25.8703
 VUV  H2   H  HCH2   0   0.202  12.8212  6.9959  24.8749
 VUV  H3   H  HCH2   0   0.204  13.3384  6.8953  23.2018
 VUV  H4   H  HCH2   0   0.231  13.8229  4.6549  23.9039
 VUV  H5   H  HCH2   0   0.224  14.1696  5.1612  25.5495
 VUV  H7   H  HNR5   0   0.330  14.9415  8.3628  23.6912
 VUV  H9   H  HCR5   0   0.208  16.4017  4.9029  24.7202
 VUV  H10  H  HCH2   0   0.210  17.0789  5.8987  22.4785
 VUV  H11  H  HCH2   0   0.198  15.3874  6.1612  22.1242
 VUV  H12  H  HCH2   0   0.186  15.0336  3.6520  22.4513
 VUV  H13  H  HCH2   0   0.179  16.7558  3.4986  22.6753
 VUV  H14  H  HCH2   0   0.148  17.0775  4.5181  20.3579
 VUV  H15  H  HCH2   0   0.149  15.3452  4.5372  20.1687
 VUV  H16  H  H      0   0.404  17.5946  1.9596  21.4324
 VUV  H17  H  H      0   0.410  14.6219  1.9981  21.1825
 VUV  H8   H  H      0   0.408  17.0446  2.9250  18.2814

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
 VUV  O   B    single  1.475  0.020  1.475
 VUV  O1  B    single  1.482  0.020  1.482
 VUV  B   C    single  1.659  0.020  1.659
 VUV  B   O2   single  1.493  0.020  1.493
 VUV  C   C1   single  1.530  0.020  1.530
 VUV  C1  C2   single  1.528  0.020  1.528
 VUV  C2  C3   single  1.530  0.020  1.530
 VUV  O4  C5   deloc   1.248  0.020  1.248
 VUV  C5  O3   deloc   1.247  0.020  1.247
 VUV  C5  C4   single  1.539  0.020  1.539
 VUV  C3  C7   single  1.530  0.020  1.530
 VUV  C3  C4   single  1.545  0.020  1.545
 VUV  C6  N    single  1.466  0.020  1.466
 VUV  C6  C7   single  1.534  0.020  1.534
 VUV  N   C4   single  1.459  0.020  1.459
 VUV  C4  H1   single  0.970  0.020  1.090
 VUV  C6  H2   single  0.970  0.020  1.090
 VUV  C6  H3   single  0.970  0.020  1.090
 VUV  C7  H4   single  0.970  0.020  1.090
 VUV  C7  H5   single  0.970  0.020  1.090
 VUV  N   H7   single  0.890  0.020  1.040
 VUV  C3  H9   single  0.970  0.020  1.090
 VUV  C2  H10  single  0.970  0.020  1.090
 VUV  C2  H11  single  0.970  0.020  1.090
 VUV  C1  H12  single  0.970  0.020  1.090
 VUV  C1  H13  single  0.970  0.020  1.090
 VUV  C   H14  single  0.970  0.020  1.090
 VUV  C   H15  single  0.970  0.020  1.090
 VUV  O2  H16  single  0.850  0.020  0.980
 VUV  O1  H17  single  0.850  0.020  0.980
 VUV  O   H8   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
 VUV  H1   C4  C3   106.89  3.000
 VUV  H1   C4  N    109.29  3.000
 VUV  C3   C4  N    105.95  3.000
 VUV  H1   C4  C5   107.17  3.000
 VUV  N    C4  C5   113.57  3.000
 VUV  C3   C4  C5   113.73  3.000
 VUV  O3   C5  O4   126.87  3.000
 VUV  O3   C5  C4   115.48  3.000
 VUV  O4   C5  C4   117.64  3.000
 VUV  H3   C6  H2   106.53  3.000
 VUV  H3   C6  N    111.27  3.000
 VUV  H2   C6  N    111.77  3.000
 VUV  H3   C6  C7   110.58  3.000
 VUV  H2   C6  C7   110.98  3.000
 VUV  N    C6  C7   105.80  3.000
 VUV  H5   C7  H4   107.03  3.000
 VUV  H5   C7  C3   109.93  3.000
 VUV  H4   C7  C3   113.89  3.000
 VUV  H5   C7  C6   110.24  3.000
 VUV  H4   C7  C6   112.34  3.000
 VUV  C3   C7  C6   103.42  3.000
 VUV  H7   N   C6   111.05  3.000
 VUV  H7   N   C4   107.30  3.000
 VUV  C6   N   C4   108.55  3.000
 VUV  H9   C3  C2   108.56  3.000
 VUV  H9   C3  C7   111.35  3.000
 VUV  C2   C3  C7   111.89  3.000
 VUV  H9   C3  C4   110.38  3.000
 VUV  C7   C3  C4    99.83  3.000
 VUV  C2   C3  C4   114.67  3.000
 VUV  H11  C2  H10  105.89  3.000
 VUV  H11  C2  C1   109.28  3.000
 VUV  H10  C2  C1   107.58  3.000
 VUV  H11  C2  C3   110.20  3.000
 VUV  H10  C2  C3   109.87  3.000
 VUV  C1   C2  C3   113.70  3.000
 VUV  H13  C1  H12  105.14  3.000
 VUV  H13  C1  C    110.37  3.000
 VUV  H12  C1  C    109.42  3.000
 VUV  H13  C1  C2   107.69  3.000
 VUV  H12  C1  C2   109.18  3.000
 VUV  C    C1  C2   114.60  3.000
 VUV  H15  C   H14  104.66  3.000
 VUV  H15  C   B    110.13  3.000
 VUV  H14  C   B    109.75  3.000
 VUV  H15  C   C1   107.47  3.000
 VUV  H14  C   C1   107.85  3.000
 VUV  B    C   C1   116.31  3.000
 VUV  O    B   O1   104.52  3.000
 VUV  O1   B   O2   111.83  3.000
 VUV  O    B   O2   107.20  3.000
 VUV  O2   B   C    110.02  3.000
 VUV  O1   B   C    111.36  3.000
 VUV  O    B   C    111.73  3.000
 VUV  H16  O2  B    109.06  3.000
 VUV  H17  O1  B    109.74  3.000
 VUV  H8   O   B    108.09  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
 VUV  Var_01  C7   C6  N   C4     5.17  30.0  1
 VUV  Var_02  C3   C7  C6  N    -28.58  30.0  1
 VUV  Var_03  H2   C6  N   C4   126.07  30.0  1
 VUV  Var_04  H3   C6  N   C4  -114.97  30.0  1
 VUV  Var_05  H7   N   C6  C7   122.89  30.0  1
 VUV  Var_06  H4   C7  C6  N   -151.83  30.0  1
 VUV  Var_07  H5   C7  C6  N     88.90  30.0  1
 VUV  Var_08  H2   C6  C7  C3  -149.99  30.0  1
 VUV  Var_09  H3   C6  C7  C3    92.01  30.0  1
 VUV  Var_10  C    C1  C2  C3   175.11  30.0  1
 VUV  Var_11  H12  C1  C2  C3    51.98  30.0  1
 VUV  Var_12  H13  C1  C2  C3   -61.67  30.0  1
 VUV  Var_13  B    C   C1  C2   174.68  30.0  1
 VUV  Var_14  O    B   C   C1   175.11  30.0  3
 VUV  Var_15  O1   B   C   C1    58.64  30.0  3
 VUV  Var_16  O2   B   C   C1   -65.93  30.0  3
 VUV  Var_17  H14  C   C1  C2    50.96  30.0  1
 VUV  Var_18  H15  C   C1  C2   -61.39  30.0  1
 VUV  Var_19  H10  C2  C1  C    -62.99  30.0  3
 VUV  Var_20  H11  C2  C1  C     51.53  30.0  3
 VUV  Var_21  H12  C1  C   B    -62.32  30.0  3
 VUV  Var_22  H13  C1  C   B     52.91  30.0  3
 VUV  Var_23  H14  C   B   O2    56.80  30.0  3
 VUV  Var_24  H15  C   B   O2   171.52  30.0  3
 VUV  Var_25  H14  C   B   O1  -178.63  30.0  3
 VUV  Var_26  H15  C   B   O1   -63.91  30.0  3
 VUV  Var_27  H14  C   B   O    -62.15  30.0  3
 VUV  Var_28  H15  C   B   O     52.56  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
 VUV  chir_01  C4  C5  C3  N   positiv
 VUV  chir_02  C3  C4  C7  C2  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
 VUV  plan-1  C4  0.020
 VUV  plan-1  C5  0.020
 VUV  plan-1  O4  0.020
 VUV  plan-1  O3  0.020

