# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 22:39:17 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: {3-[(1R,5S,8R)-5-carboxy-2,6-diazabicyclo[3.2.1]octan-8-yl]propyl}(trihydroxido)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@]12CCN[C@@H](CN1)[C@H]2CCC[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
 VV4  VV4  "3-[(1~{R},5~{S},8~{R})-5-carboxy-2,6-diazabicyclo[3.2.1]octan-8-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide"
  ligand  37  18  .  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_VV4
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
 VV4  C1   C  CT     0  -0.044  -12.3510  7.0287  26.7158
 VV4  C2   C  CH2    0  -0.396  -12.3252  6.9232  28.2495
 VV4  C3   C  CH2    0  -0.295  -13.6009  6.2711  28.7705
 VV4  O4   O  OB     0  -0.734  -11.6601  2.2203  20.6579
 VV4  C7   C  CH2    0  -0.406  -12.1591  5.4411  24.6709
 VV4  C8   C  CH2    0  -0.449  -12.2364  4.0017  24.1649
 VV4  C9   C  CH2    0  -0.655  -11.9071  3.8280  22.6812
 VV4  C    C  C      0   0.411  -11.1274  7.8022  26.1794
 VV4  O1   O  O      0  -0.598  -11.3319  8.6835  25.3182
 VV4  C6   C  CH1    0  -0.205  -12.4294  5.5833  26.1678
 VV4  C5   C  CH1    0  -0.136  -13.8731  5.2811  26.5709
 VV4  C4   C  CH2    0  -0.307  -14.5946  6.5612  26.1095
 VV4  N1   N  NH1    0  -0.616  -13.6215  7.6423  26.3042
 VV4  N    N  NH1    0  -0.590  -13.9161  5.0639  28.0147
 VV4  B    B  B     -1   0.475  -11.9401  2.2739  22.1030
 VV4  O3   O  OB     0  -0.750  -13.2958  1.6872  22.2249
 VV4  O2   O  OB     0  -0.750  -10.9076  1.4486  22.7969
 VV4  H1   H  HCH2   0   0.206  -11.4517  6.3470  28.5599
 VV4  H2   H  HCH2   0   0.213  -12.2310  7.9160  28.6991
 VV4  H3   H  HCH2   0   0.191  -14.4113  7.0129  28.7344
 VV4  H4   H  HCH2   0   0.220  -13.4806  6.0036  29.8239
 VV4  H5   H  H      0   0.409  -10.8094  2.6367  20.5066
 VV4  H6   H  HCH2   0   0.209  -11.1530  5.8163  24.4579
 VV4  H7   H  HCH2   0   0.198  -12.8401  6.0676  24.0849
 VV4  H8   H  HCH2   0   0.187  -13.2381  3.6030  24.3648
 VV4  H9   H  HCH2   0   0.178  -11.5565  3.3961  24.7795
 VV4  H10  H  HCH2   0   0.146  -10.9187  4.2801  22.5015
 VV4  H11  H  HCH2   0   0.148  -12.6091  4.4514  22.1083
 VV4  H13  H  HCH1   0   0.205  -11.7432  4.9181  26.7024
 VV4  H14  H  HCH1   0   0.230  -14.2810  4.3910  26.0875
 VV4  H15  H  HCH2   0   0.206  -15.5098  6.7238  26.6904
 VV4  H16  H  HCH2   0   0.218  -14.9026  6.4736  25.0628
 VV4  H17  H  HNH1   0   0.333  -13.4484  8.1373  25.4397
 VV4  H19  H  HNH1   0   0.339  -14.8421  4.7487  28.2766
 VV4  H21  H  H      0   0.408  -13.6489  1.8858  23.0938
 VV4  H22  H  H      0   0.405  -10.8118  1.7494  23.7028
 VV4  O    O  OC    -1  -0.602  -10.0199  7.4570  26.6374

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
 VV4  O4  B    single  1.473  0.020  1.473
 VV4  O3  B    single  1.482  0.020  1.482
 VV4  B   C9   single  1.658  0.020  1.658
 VV4  B   O2   single  1.493  0.020  1.493
 VV4  C9  C8   single  1.530  0.020  1.530
 VV4  C8  C7   single  1.528  0.020  1.528
 VV4  C7  C6   single  1.528  0.020  1.528
 VV4  O1  C    deloc   1.249  0.020  1.249
 VV4  C   O    deloc   1.247  0.020  1.247
 VV4  C   C1   single  1.544  0.020  1.544
 VV4  C4  N1   single  1.468  0.020  1.468
 VV4  C4  C5   single  1.540  0.020  1.540
 VV4  N1  C1   single  1.470  0.020  1.470
 VV4  C6  C1   single  1.548  0.020  1.548
 VV4  C6  C5   single  1.529  0.020  1.529
 VV4  C1  C2   single  1.538  0.020  1.538
 VV4  C5  N    single  1.461  0.020  1.461
 VV4  N   C3   single  1.459  0.020  1.459
 VV4  C2  C3   single  1.524  0.020  1.524
 VV4  C2  H1   single  0.970  0.020  1.090
 VV4  C2  H2   single  0.970  0.020  1.090
 VV4  C3  H3   single  0.970  0.020  1.090
 VV4  C3  H4   single  0.970  0.020  1.090
 VV4  O4  H5   single  0.850  0.020  0.980
 VV4  C7  H6   single  0.970  0.020  1.090
 VV4  C7  H7   single  0.970  0.020  1.090
 VV4  C8  H8   single  0.970  0.020  1.090
 VV4  C8  H9   single  0.970  0.020  1.090
 VV4  C9  H10  single  0.970  0.020  1.090
 VV4  C9  H11  single  0.970  0.020  1.090
 VV4  C6  H13  single  0.970  0.020  1.090
 VV4  C5  H14  single  0.970  0.020  1.090
 VV4  C4  H15  single  0.970  0.020  1.090
 VV4  C4  H16  single  0.970  0.020  1.090
 VV4  N1  H17  single  0.890  0.020  1.040
 VV4  N   H19  single  0.890  0.020  1.040
 VV4  O3  H21  single  0.850  0.020  0.980
 VV4  O2  H22  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
 VV4  N1   C1  C6   104.30  3.000
 VV4  C6   C1  C    112.64  3.000
 VV4  N1   C1  C    112.25  3.000
 VV4  C6   C1  C2   106.85  3.000
 VV4  N1   C1  C2   108.82  3.000
 VV4  C    C1  C2   111.57  3.000
 VV4  H2   C2  H1   107.05  3.000
 VV4  H2   C2  C3   108.65  3.000
 VV4  H1   C2  C3   110.29  3.000
 VV4  H2   C2  C1   110.43  3.000
 VV4  H1   C2  C1   109.47  3.000
 VV4  C3   C2  C1   110.87  3.000
 VV4  H4   C3  H3   106.13  3.000
 VV4  H4   C3  N    108.69  3.000
 VV4  H3   C3  N    112.47  3.000
 VV4  H4   C3  C2   109.98  3.000
 VV4  H3   C3  C2   108.49  3.000
 VV4  N    C3  C2   110.96  3.000
 VV4  H5   O4  B    107.90  3.000
 VV4  H7   C7  H6   105.74  3.000
 VV4  H7   C7  C6   111.16  3.000
 VV4  H6   C7  C6   108.74  3.000
 VV4  H7   C7  C8   109.28  3.000
 VV4  H6   C7  C8   107.76  3.000
 VV4  C6   C7  C8   113.78  3.000
 VV4  H9   C8  H8   105.24  3.000
 VV4  H9   C8  C9   110.29  3.000
 VV4  H8   C8  C9   109.41  3.000
 VV4  H9   C8  C7   107.63  3.000
 VV4  H8   C8  C7   109.17  3.000
 VV4  C9   C8  C7   114.67  3.000
 VV4  H11  C9  H10  104.78  3.000
 VV4  H11  C9  B    109.68  3.000
 VV4  H10  C9  B    110.22  3.000
 VV4  H11  C9  C8   107.66  3.000
 VV4  H10  C9  C8   107.74  3.000
 VV4  B    C9  C8   116.12  3.000
 VV4  O1   C   O    126.43  3.000
 VV4  O    C   C1   115.95  3.000
 VV4  O1   C   C1   117.60  3.000
 VV4  H13  C6  C5   110.05  3.000
 VV4  H13  C6  C7   108.12  3.000
 VV4  C5   C6  C7   114.01  3.000
 VV4  H13  C6  C1   111.27  3.000
 VV4  C5   C6  C1    97.99  3.000
 VV4  C7   C6  C1   115.14  3.000
 VV4  H14  C5  N    107.78  3.000
 VV4  H14  C5  C4   111.71  3.000
 VV4  N    C5  C4   113.95  3.000
 VV4  H14  C5  C6   113.40  3.000
 VV4  N    C5  C6   108.53  3.000
 VV4  C4   C5  C6   101.48  3.000
 VV4  H16  C4  H15  106.48  3.000
 VV4  H16  C4  N1   111.87  3.000
 VV4  H15  C4  N1   111.97  3.000
 VV4  H16  C4  C5   110.60  3.000
 VV4  H15  C4  C5   110.83  3.000
 VV4  N1   C4  C5   105.18  3.000
 VV4  H17  N1  C4   111.14  3.000
 VV4  H17  N1  C1   107.21  3.000
 VV4  C4   N1  C1   107.63  3.000
 VV4  H19  N   C5   109.20  3.000
 VV4  H19  N   C3   108.73  3.000
 VV4  C5   N   C3   112.50  3.000
 VV4  O2   B   O3   112.06  3.000
 VV4  O2   B   C9   110.01  3.000
 VV4  O3   B   C9   111.13  3.000
 VV4  O2   B   O4   107.73  3.000
 VV4  C9   B   O4   111.86  3.000
 VV4  O3   B   O4   103.89  3.000
 VV4  H21  O3  B    109.23  3.000
 VV4  H22  O2  B    109.55  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
 VV4  Var_01  C5   C4  N1  C1     5.75  30.0  3
 VV4  Var_02  N    C3  C2  C1    47.37  30.0  1
 VV4  Var_03  C5   N   C3  C2   -49.27  30.0  1
 VV4  Var_04  H15  C4  N1  C1   126.20  30.0  3
 VV4  Var_05  H16  C4  N1  C1  -114.36  30.0  3
 VV4  Var_06  H3   C3  C2  C1   -76.67  30.0  1
 VV4  Var_07  H4   C3  C2  C1   167.66  30.0  1
 VV4  Var_08  H19  N   C3  C2  -170.36  30.0  1
 VV4  Var_09  H17  N1  C4  C5   122.86  30.0  3
 VV4  Var_10  H3   C3  N   C5    72.46  30.0  1
 VV4  Var_11  H4   C3  N   C5  -170.33  30.0  1
 VV4  Var_12  H1   C2  C3  N    -74.05  30.0  1
 VV4  Var_13  H2   C2  C3  N    168.89  30.0  1
 VV4  Var_14  C6   C7  C8  C9  -177.37  30.0  3
 VV4  Var_15  H8   C8  C7  C6    59.49  30.0  1
 VV4  Var_16  H9   C8  C7  C6   -54.25  30.0  1
 VV4  Var_17  C8   C9  B   O4   177.83  30.0  3
 VV4  Var_18  B    C9  C8  C7   178.41  30.0  1
 VV4  Var_19  O3   B   C9  C8    62.21  30.0  2
 VV4  Var_20  O2   B   C9  C8   -62.48  30.0  2
 VV4  Var_21  H10  C9  B   O4   -59.33  30.0  3
 VV4  Var_22  H11  C9  B   O4    55.54  30.0  3
 VV4  Var_23  H10  C9  C8  C7    54.28  30.0  1
 VV4  Var_24  H11  C9  C8  C7   -58.23  30.0  1
 VV4  Var_25  H6   C7  C8  C9   -56.72  30.0  3
 VV4  Var_26  H7   C7  C8  C9    57.73  30.0  3
 VV4  Var_27  H8   C8  C9  B    -58.57  30.0  3
 VV4  Var_28  H9   C8  C9  B     56.74  30.0  3
 VV4  Var_29  H10  C9  B   O3  -174.94  30.0  3
 VV4  Var_30  H11  C9  B   O3   -60.08  30.0  3
 VV4  Var_31  H10  C9  B   O2    60.36  30.0  3
 VV4  Var_32  H11  C9  B   O2   175.23  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
 VV4  chir_01  C1  N1  C6  C2  positiv
 VV4  chir_02  C6  C7  C1  C5  negativ
 VV4  chir_03  C5  N   C6  C4  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
 VV4  plan-1  C1  0.020
 VV4  plan-1  C   0.020
 VV4  plan-1  O1  0.020
 VV4  plan-1  O   0.020

