# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 23:39:59 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: {3-[(1S,2S,5R)-2-carboxy-6-thia-3-azabicyclo[3.2.0]heptan-1-yl]propyl}(trihydroxido)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1NC[C@@H]2SC[C@]12CCC[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
 VUY  VUY  "3-[(1~{S},2~{S},5~{R})-2-carboxy-6-thia-3-azabicyclo[3.2.0]heptan-1-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boranuide"
  ligand  33  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VUY
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
 VUY  C4   C  CH2    0  -0.515  14.9059  3.6691  24.9164
 VUY  C5   C  CR5    0  -0.054  14.4267  4.6522  23.8355
 VUY  C6   C  CH2    0  -0.410  14.9818  4.4355  22.4319
 VUY  C7   C  CH2    0  -0.430  14.7030  3.0833  21.7791
 VUY  C8   C  CH2    0  -0.674  15.3475  2.9288  20.4016
 VUY  O    O  OC    -1  -0.606  16.8736  6.4636  24.3840
 VUY  O1   O  O      0  -0.596  15.7054  7.6871  22.9264
 VUY  C1   C  CR15   0  -0.185  14.5389  6.1325  24.3124
 VUY  S    S  S2     0  -0.062  13.2083  3.5046  25.5887
 VUY  C3   C  CR15   0  -0.357  12.9110  4.4152  24.0149
 VUY  C2   C  CH2    0  -0.272  12.2499  5.8000  24.1045
 VUY  N    N  NR15   0  -0.585  13.3081  6.7797  23.8997
 VUY  B    B  B     -1   0.488  15.0454  1.4863  19.6435
 VUY  O4   O  OB     0  -0.750  15.5326  0.3604  20.4954
 VUY  O3   O  OB     0  -0.741  13.6107  1.2694  19.3848
 VUY  O2   O  OB     0  -0.740  15.6582  1.4728  18.2952
 VUY  H1   H  HCH2   0   0.261  15.2735  2.7184  24.5325
 VUY  H2   H  HCH2   0   0.256  15.6327  4.0757  25.6181
 VUY  H3   H  HCH2   0   0.210  16.0670  4.5812  22.4692
 VUY  H4   H  HCH2   0   0.205  14.5943  5.2221  21.7746
 VUY  H5   H  HCH2   0   0.185  13.6201  2.9407  21.6871
 VUY  H6   H  HCH2   0   0.186  15.0530  2.2773  22.4334
 VUY  H7   H  HCH2   0   0.147  16.4313  3.0957  20.5193
 VUY  H8   H  HCH2   0   0.151  15.0075  3.7629  19.7701
 VUY  H10  H  HCR5   0   0.216  14.5573  6.1199  25.4106
 VUY  H11  H  HCR5   0   0.270  12.4413  3.7651  23.2767
 VUY  H12  H  HCH2   0   0.216  11.7892  5.9358  25.0868
 VUY  H13  H  HCH2   0   0.233  11.4617  5.9270  23.3606
 VUY  H14  H  HNR5   0   0.333  13.3853  7.0172  22.9183
 VUY  H16  H  H      0   0.405  16.2757  0.6688  21.0177
 VUY  H17  H  H      0   0.409  13.1537  1.2058  20.2256
 VUY  H15  H  H      0   0.407  16.5041  1.9224  18.3391
 VUY  C    C  C      0   0.402  15.8191  6.8362  23.8296

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
 VUY  O2  B    single  1.481  0.020  1.481
 VUY  O3  B    single  1.474  0.020  1.474
 VUY  B   O4   single  1.494  0.020  1.494
 VUY  B   C8   single  1.657  0.020  1.657
 VUY  C8  C7   single  1.529  0.020  1.529
 VUY  C7  C6   single  1.527  0.020  1.527
 VUY  C6  C5   single  1.525  0.020  1.525
 VUY  O1  C    deloc   1.246  0.020  1.246
 VUY  C   O    deloc   1.248  0.020  1.248
 VUY  C   C1   single  1.539  0.020  1.539
 VUY  C5  C3   single  1.545  0.020  1.545
 VUY  C5  C1   single  1.559  0.020  1.559
 VUY  C5  C4   single  1.538  0.020  1.538
 VUY  N   C2   single  1.457  0.020  1.457
 VUY  N   C1   single  1.450  0.020  1.450
 VUY  C2  C3   single  1.537  0.020  1.537
 VUY  C3  S    single  1.842  0.020  1.842
 VUY  C4  S    single  1.833  0.020  1.833
 VUY  C4  H1   single  0.970  0.020  1.090
 VUY  C4  H2   single  0.970  0.020  1.090
 VUY  C6  H3   single  0.970  0.020  1.090
 VUY  C6  H4   single  0.970  0.020  1.090
 VUY  C7  H5   single  0.970  0.020  1.090
 VUY  C7  H6   single  0.970  0.020  1.090
 VUY  C8  H7   single  0.970  0.020  1.090
 VUY  C8  H8   single  0.970  0.020  1.090
 VUY  C1  H10  single  0.970  0.020  1.090
 VUY  C3  H11  single  0.970  0.020  1.090
 VUY  C2  H12  single  0.970  0.020  1.090
 VUY  C2  H13  single  0.970  0.020  1.090
 VUY  N   H14  single  0.890  0.020  1.040
 VUY  O4  H16  single  0.850  0.020  0.980
 VUY  O3  H17  single  0.850  0.020  0.980
 VUY  O2  H15  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
 VUY  H2   C4  H1   109.13  3.000
 VUY  H2   C4  S    114.53  3.000
 VUY  H1   C4  S    111.32  3.000
 VUY  H2   C4  C5   114.97  3.000
 VUY  H1   C4  C5   114.55  3.000
 VUY  S    C4  C5    91.52  3.000
 VUY  C3   C5  C1   100.41  3.000
 VUY  C1   C5  C6   112.97  3.000
 VUY  C3   C5  C6   116.26  3.000
 VUY  C1   C5  C4   111.69  3.000
 VUY  C3   C5  C4    97.24  3.000
 VUY  C6   C5  C4   116.28  3.000
 VUY  H4   C6  H3   105.97  3.000
 VUY  H4   C6  C7   108.34  3.000
 VUY  H3   C6  C7   108.25  3.000
 VUY  H4   C6  C5   108.74  3.000
 VUY  H3   C6  C5   108.08  3.000
 VUY  C7   C6  C5   116.93  3.000
 VUY  H6   C7  H5   105.66  3.000
 VUY  H6   C7  C8   109.22  3.000
 VUY  H5   C7  C8   109.13  3.000
 VUY  H6   C7  C6   109.74  3.000
 VUY  H5   C7  C6   109.36  3.000
 VUY  C8   C7  C6   113.44  3.000
 VUY  H8   C8  H7   104.49  3.000
 VUY  H8   C8  B    109.94  3.000
 VUY  H7   C8  B    111.08  3.000
 VUY  H8   C8  C7   108.08  3.000
 VUY  H7   C8  C7   107.63  3.000
 VUY  B    C8  C7   115.05  3.000
 VUY  H10  C1  N    107.69  3.000
 VUY  H10  C1  C    107.76  3.000
 VUY  N    C1  C    114.37  3.000
 VUY  H10  C1  C5   107.22  3.000
 VUY  N    C1  C5   105.99  3.000
 VUY  C    C1  C5   113.46  3.000
 VUY  C3   S   C4    77.98  3.000
 VUY  H11  C3  C2   113.04  3.000
 VUY  H11  C3  S    110.69  3.000
 VUY  C2   C3  S    117.70  3.000
 VUY  H11  C3  C5   115.83  3.000
 VUY  S    C3  C5    90.96  3.000
 VUY  C2   C3  C5   106.89  3.000
 VUY  H13  C2  H12  107.07  3.000
 VUY  H13  C2  N    110.52  3.000
 VUY  H12  C2  N    110.42  3.000
 VUY  H13  C2  C3   112.08  3.000
 VUY  H12  C2  C3   110.21  3.000
 VUY  N    C2  C3   106.58  3.000
 VUY  H14  N   C2   110.45  3.000
 VUY  H14  N   C1   108.40  3.000
 VUY  C2   N   C1   106.04  3.000
 VUY  O2   B   O3   103.98  3.000
 VUY  O3   B   O4   107.86  3.000
 VUY  O2   B   O4   112.18  3.000
 VUY  O4   B   C8   109.62  3.000
 VUY  O3   B   C8   112.69  3.000
 VUY  O2   B   C8   110.42  3.000
 VUY  H16  O4  B    108.71  3.000
 VUY  H17  O3  B    108.65  3.000
 VUY  H15  O2  B    108.60  3.000
 VUY  C1   C   O1   117.64  3.000
 VUY  C1   C   O    115.28  3.000
 VUY  O1   C   O    127.07  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
 VUY  Var_01  C3   S   C4  C5    10.55  30.0  1
 VUY  Var_02  C3   C2  N   C1   -25.82  30.0  1
 VUY  Var_03  H12  C2  N   C1    93.88  30.0  1
 VUY  Var_04  H13  C2  N   C1  -147.83  30.0  1
 VUY  Var_05  H14  N   C2  C3    91.43  30.0  1
 VUY  Var_06  H1   C4  S   C3  -106.61  30.0  1
 VUY  Var_07  H2   C4  S   C3   129.00  30.0  1
 VUY  Var_08  C8   C7  C6  C5  -177.42  30.0  1
 VUY  Var_09  H5   C7  C6  C5    60.52  30.0  1
 VUY  Var_10  H6   C7  C6  C5   -54.96  30.0  1
 VUY  Var_11  B    C8  C7  C6  -178.85  30.0  1
 VUY  Var_12  O2   B   C8  C7   177.15  30.0  3
 VUY  Var_13  O3   B   C8  C7    61.35  30.0  3
 VUY  Var_14  O4   B   C8  C7   -58.78  30.0  3
 VUY  Var_15  H7   C8  C7  C6    56.74  30.0  1
 VUY  Var_16  H8   C8  C7  C6   -55.59  30.0  1
 VUY  Var_17  H3   C6  C7  C8   -55.14  30.0  3
 VUY  Var_18  H4   C6  C7  C8    59.35  30.0  3
 VUY  Var_19  H5   C7  C8  B    -56.66  30.0  3
 VUY  Var_20  H6   C7  C8  B     58.40  30.0  3
 VUY  Var_21  H7   C8  B   O4    63.80  30.0  3
 VUY  Var_22  H8   C8  B   O4   178.96  30.0  3
 VUY  Var_23  H7   C8  B   O3  -176.07  30.0  3
 VUY  Var_24  H8   C8  B   O3   -60.91  30.0  3
 VUY  Var_25  H7   C8  B   O2   -60.28  30.0  3
 VUY  Var_26  H8   C8  B   O2    54.88  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
 VUY  chir_01  C5  C3  C1  C4  negativ
 VUY  chir_02  C1  N   C5  C   negativ
 VUY  chir_03  C3  S   C2  C5  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
 VUY  plan-1  O   0.020
 VUY  plan-1  O1  0.020
 VUY  plan-1  C1  0.020
 VUY  plan-1  C   0.020

