# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:27:11 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-[(3~{S})-6-[[2-(4-methyl-3-oxidanylidene-piperazin-1-yl)-2-oxidanylidene-ethyl]carbamoyl]-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1=O)C(=O)CNC(=O)c2ccc3[C@H](CC(O)=O)OB(O)c3c2
#
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
 S0Q  S0Q  '2-[(3~{S})-6-[[2-(4-methyl-3-oxidanylidene-piperazin-1-yl)-2-oxidanylidene-ethyl]carbamoyl]-1-oxidanyl-3~{H}-2,1-benzoxaborol-3-yl]ethanoic acid'  ligand  47  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S0Q
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
 S0Q  C1   C  CH2    0  -0.443   9.1173  -0.5941  -16.4870
 S0Q  N1   N  NT     0  -0.469  11.4495  -0.2988  -17.1876
 S0Q  C2   C  C      0   0.550  10.2714   0.3091  -16.9289
 S0Q  N2   N  NT     0  -0.455  13.8517  -0.9679  -15.9885
 S0Q  O2   O  O      0  -0.475  10.1164   1.5126  -17.0363
 S0Q  C3   C  CH2    0  -0.396  12.6129   0.4689  -17.5601
 S0Q  O3   O  O      0  -0.481   2.6398   4.5235  -18.1749
 S0Q  C4   C  C      0   0.530  13.8785   0.0938  -16.8091
 S0Q  O4   O  O      0  -0.602  -0.0867   1.7692  -15.3781
 S0Q  C5   C  CH2    0  -0.257  12.7076  -1.8519  -15.8412
 S0Q  O5   O  OC    -1  -0.602   1.3539   3.2008  -14.4522
 S0Q  C7   C  CH3    0  -0.519  15.0325  -1.2735  -15.2037
 S0Q  C9   C  CR16   0  -0.294   5.2568   1.3028  -16.0288
 S0Q  C10  C  CR16   0  -0.277   4.1176   2.0720  -15.8422
 S0Q  C11  C  CR56   0  -0.011   3.7242   2.9318  -16.8585
 S0Q  C12  C  CR56   0  -0.075   4.4603   3.0209  -18.0388
 S0Q  C15  C  C      0   0.420   0.7931   2.6476  -15.4211
 S0Q  C16  C  CR16   0  -0.377   5.5890   2.2380  -18.2230
 S0Q  C13  C  CR15   0   0.053   2.5284   3.8483  -16.9136
 S0Q  B    B  B      0   0.491   3.7217   4.0891  -18.8863
 S0Q  C8   C  CR6    0  -0.021   6.0005   1.3755  -17.2113
 S0Q  O    O  O      0  -0.476   7.5529   0.2215  -18.5810
 S0Q  N    N  NH1    0  -0.636   7.8927   0.1362  -16.3575
 S0Q  C6   C  CH2    0  -0.361  11.7468  -1.7005  -16.9989
 S0Q  H1   H  HCH2   0   0.284   8.9808  -1.4108  -17.1966
 S0Q  H2   H  HCH2   0   0.304   9.3533  -1.0476  -15.5224
 S0Q  H3   H  HCH2   0   0.294  12.4308   1.5269  -17.3817
 S0Q  H4   H  HCH2   0   0.282  12.8214   0.3558  -18.6298
 S0Q  H5   H  HCH2   0   0.250  12.1942  -1.6502  -14.8960
 S0Q  H6   H  HCH2   0   0.260  13.0641  -2.8829  -15.8081
 S0Q  H8   H  HCH3   0   0.250  14.7648  -1.9944  -14.4350
 S0Q  H9   H  HCH3   0   0.244  15.8249  -1.7053  -15.8172
 S0Q  H10  H  HCH3   0   0.248  15.4218  -0.3837  -14.7124
 S0Q  H11  H  HCR6   0   0.259   5.5463   0.6164  -15.2423
 S0Q  H12  H  HCR6   0   0.256   3.5554   1.9976  -14.9220
 S0Q  H13  H  HCH2   0   0.247   0.4123   3.8281  -17.1657
 S0Q  H14  H  HCH2   0   0.227   1.1715   2.2949  -17.5357
 S0Q  H15  H  HCR6   0   0.255   6.1580   2.2993  -19.1424
 S0Q  H16  H  HCR5   0   0.248   2.5837   4.6002  -16.1219
 S0Q  H18  H  HNH1   0   0.408   7.7084   0.5778  -15.4719
 S0Q  H19  H  HCH2   0   0.291  10.8529  -2.2849  -16.8039
 S0Q  H20  H  HCH2   0   0.273  12.1929  -2.0933  -17.9173
 S0Q  H17  H  HOH1   0   0.488   3.4755   5.2206  -20.4652
 S0Q  O1   O  O      0  -0.502  14.8828   0.7722  -16.9790
 S0Q  C    C  C      0   0.533   7.2123   0.5377  -17.4508
 S0Q  C14  C  CH2    0  -0.608   1.1904   3.1320  -16.8318
 S0Q  O6   O  OH1    0  -0.610   4.0622   4.5435  -20.1116

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
 S0Q  O    C    double    1.222  0.020  1.222
 S0Q  B    C12  single    1.551  0.020  1.551
 S0Q  B    O3   single    1.366  0.020  1.366
 S0Q  O1   C4   double    1.224  0.020  1.224
 S0Q  C16  C12  aromatic  1.386  0.020  1.386
 S0Q  C16  C8   aromatic  1.392  0.020  1.392
 S0Q  C12  C11  aromatic  1.394  0.020  1.394
 S0Q  O3   C13  single    1.435  0.020  1.435
 S0Q  C    C8   single    1.493  0.020  1.493
 S0Q  C    N    single    1.349  0.020  1.349
 S0Q  C3   C4   single    1.519  0.020  1.519
 S0Q  C3   N1   single    1.443  0.020  1.443
 S0Q  C8   C9   aromatic  1.399  0.020  1.399
 S0Q  C4   N2   single    1.342  0.020  1.342
 S0Q  C11  C13  single    1.508  0.020  1.508
 S0Q  C11  C10  aromatic  1.388  0.020  1.388
 S0Q  N1   C2   single    1.351  0.020  1.351
 S0Q  N1   C6   single    1.445  0.020  1.445
 S0Q  C14  C13  single    1.520  0.020  1.520
 S0Q  C14  C15  single    1.544  0.020  1.544
 S0Q  O2   C2   double    1.218  0.020  1.218
 S0Q  C2   C1   single    1.531  0.020  1.531
 S0Q  C1   N    single    1.432  0.020  1.432
 S0Q  C6   C5   single    1.512  0.020  1.512
 S0Q  C9   C10  aromatic  1.387  0.020  1.387
 S0Q  N2   C5   single    1.453  0.020  1.453
 S0Q  N2   C7   single    1.450  0.020  1.450
 S0Q  O4   C15  deloc     1.244  0.020  1.244
 S0Q  C15  O5   deloc     1.249  0.020  1.249
 S0Q  C1   H1   single    0.970  0.020  1.090
 S0Q  C1   H2   single    0.970  0.020  1.090
 S0Q  C3   H3   single    0.970  0.020  1.090
 S0Q  C3   H4   single    0.970  0.020  1.090
 S0Q  C5   H5   single    0.970  0.020  1.090
 S0Q  C5   H6   single    0.970  0.020  1.090
 S0Q  C7   H8   single    0.970  0.020  1.090
 S0Q  C7   H9   single    0.970  0.020  1.090
 S0Q  C7   H10  single    0.970  0.020  1.090
 S0Q  C9   H11  single    0.930  0.020  1.080
 S0Q  C10  H12  single    0.930  0.020  1.080
 S0Q  C14  H13  single    0.970  0.020  1.090
 S0Q  C14  H14  single    0.970  0.020  1.090
 S0Q  C16  H15  single    0.930  0.020  1.080
 S0Q  C13  H16  single    0.970  0.020  1.090
 S0Q  N    H18  single    0.860  0.020  1.020
 S0Q  C6   H19  single    0.970  0.020  1.090
 S0Q  C6   H20  single    0.970  0.020  1.090
 S0Q  B    O6   single    1.350  0.020  1.350
 S0Q  O6   H17  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
 S0Q  H2   C1   H1   106.91  3.000
 S0Q  H2   C1   N    108.48  3.000
 S0Q  H1   C1   N    109.51  3.000
 S0Q  H2   C1   C2   109.70  3.000
 S0Q  H1   C1   C2   110.39  3.000
 S0Q  N    C1   C2   111.72  3.000
 S0Q  C6   N1   C3   112.58  3.000
 S0Q  C6   N1   C2   126.22  3.000
 S0Q  C3   N1   C2   120.88  3.000
 S0Q  O2   C2   N1   122.60  3.000
 S0Q  O2   C2   C1   120.83  3.000
 S0Q  N1   C2   C1   116.58  3.000
 S0Q  C7   N2   C5   117.25  3.000
 S0Q  C7   N2   C4   118.77  3.000
 S0Q  C5   N2   C4   123.97  3.000
 S0Q  H4   C3   H3   106.99  3.000
 S0Q  H4   C3   C4   107.38  3.000
 S0Q  H3   C3   C4   107.36  3.000
 S0Q  H4   C3   N1   110.52  3.000
 S0Q  H3   C3   N1   109.88  3.000
 S0Q  C4   C3   N1   114.39  3.000
 S0Q  B    O3   C13  111.70  3.000
 S0Q  C3   C4   N2   118.76  3.000
 S0Q  N2   C4   O1   122.67  3.000
 S0Q  C3   C4   O1   118.57  3.000
 S0Q  H6   C5   H5   107.52  3.000
 S0Q  H6   C5   C6   108.99  3.000
 S0Q  H5   C5   C6   110.17  3.000
 S0Q  H6   C5   N2   108.69  3.000
 S0Q  H5   C5   N2   110.16  3.000
 S0Q  C6   C5   N2   111.21  3.000
 S0Q  H10  C7   H9   108.51  3.000
 S0Q  H10  C7   H8   108.12  3.000
 S0Q  H9   C7   H8   108.30  3.000
 S0Q  H10  C7   N2   111.29  3.000
 S0Q  H9   C7   N2   111.74  3.000
 S0Q  H8   C7   N2   108.77  3.000
 S0Q  H11  C9   C8   120.31  3.000
 S0Q  H11  C9   C10  118.24  3.000
 S0Q  C8   C9   C10  121.44  3.000
 S0Q  H12  C10  C11  121.23  3.000
 S0Q  H12  C10  C9   120.24  3.000
 S0Q  C11  C10  C9   118.53  3.000
 S0Q  C13  C11  C12  110.43  3.000
 S0Q  C13  C11  C10  128.90  3.000
 S0Q  C12  C11  C10  120.66  3.000
 S0Q  B    C12  C16  134.78  3.000
 S0Q  C16  C12  C11  120.43  3.000
 S0Q  B    C12  C11  104.79  3.000
 S0Q  C14  C15  O5   117.03  3.000
 S0Q  O5   C15  O4   127.14  3.000
 S0Q  C14  C15  O4   115.80  3.000
 S0Q  H15  C16  C8   119.80  3.000
 S0Q  H15  C16  C12  120.58  3.000
 S0Q  C8   C16  C12  119.62  3.000
 S0Q  H16  C13  C14  109.25  3.000
 S0Q  H16  C13  C11  110.58  3.000
 S0Q  C14  C13  C11  114.19  3.000
 S0Q  H16  C13  O3   108.00  3.000
 S0Q  C14  C13  O3   109.72  3.000
 S0Q  C11  C13  O3   104.87  3.000
 S0Q  O6   B    C12  127.41  3.000
 S0Q  O6   B    O3   124.42  3.000
 S0Q  C12  B    O3   108.16  3.000
 S0Q  C    C8   C16  118.12  3.000
 S0Q  C    C8   C9   122.56  3.000
 S0Q  C16  C8   C9   119.31  3.000
 S0Q  H18  N    C    119.35  3.000
 S0Q  H18  N    C1   117.39  3.000
 S0Q  C    N    C1   120.66  3.000
 S0Q  H20  C6   H19  107.05  3.000
 S0Q  H20  C6   C5   110.34  3.000
 S0Q  H19  C6   C5   109.38  3.000
 S0Q  H20  C6   N1   108.82  3.000
 S0Q  H19  C6   N1   112.10  3.000
 S0Q  C5   C6   N1   109.13  3.000
 S0Q  N    C    O    122.14  3.000
 S0Q  N    C    C8   116.52  3.000
 S0Q  O    C    C8   121.33  3.000
 S0Q  H14  C14  H13  106.12  3.000
 S0Q  H14  C14  C13  109.95  3.000
 S0Q  H13  C14  C13  108.02  3.000
 S0Q  H14  C14  C15  110.09  3.000
 S0Q  H13  C14  C15  107.15  3.000
 S0Q  C13  C14  C15  115.07  3.000
 S0Q  H17  O6   B    114.59  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
 S0Q  CONST_01  C12  C16  C8   C9      0.00   0.0  0
 S0Q  CONST_02  C12  C11  C10  C9      0.00   0.0  0
 S0Q  CONST_03  C16  C12  C11  C10     0.00   0.0  0
 S0Q  CONST_04  C16  C8   C9   C10     0.00   0.0  0
 S0Q  CONST_05  C8   C16  C12  C11     0.00   0.0  0
 S0Q  CONST_06  C8   C9   C10  C11     0.00   0.0  0
 S0Q  CONST_07  C5   N2   C4   C3      0.00   0.0  0
 S0Q  CONST_08  C    C8   C9   C10   180.00   0.0  0
 S0Q  CONST_09  C    C8   C16  C12   180.00   0.0  0
 S0Q  CONST_10  C5   N2   C4   O1    180.00   0.0  0
 S0Q  CONST_11  C7   N2   C4   C3    180.00   0.0  0
 S0Q  CONST_12  H15  C16  C8   C9    180.00   0.0  0
 S0Q  CONST_13  H11  C9   C10  C11   180.00   0.0  0
 S0Q  CONST_14  H12  C10  C11  C12   180.00   0.0  0
 S0Q  CONST_15  C3   N1   C2   C1    180.00   0.0  0
 S0Q  CONST_16  C6   N1   C2   C1      0.00   0.0  0
 S0Q  CONST_17  C3   N1   C2   O2      0.00   0.0  0
 S0Q  CONST_18  C6   N1   C2   O2    180.00   0.0  0
 S0Q  CONST_19  C7   N2   C4   O1      0.00   0.0  0
 S0Q  CONST_20  C8   C    N    C1    180.00   0.0  0
 S0Q  CONST_21  H18  N    C    C8      0.00   0.0  0
 S0Q  CONST_22  O    C    N    C1      0.00   0.0  0
 S0Q  Var_01    N2   C4   C3   N1      6.38  30.0  1
 S0Q  Var_02    N2   C5   C6   N1    -50.54  30.0  1
 S0Q  Var_03    C5   C6   N1   C3     63.64  30.0  1
 S0Q  Var_04    C16  C12  B    O3    179.72  30.0  1
 S0Q  Var_05    C6   N1   C3   C4    -41.07  30.0  1
 S0Q  Var_06    C6   C5   N2   C4     17.63  30.0  1
 S0Q  Var_07    O    C    C8   C9    152.18  30.0  2
 S0Q  Var_08    H8   C7   N2   C4    166.43  30.0  3
 S0Q  Var_09    N    C1   C2   N1   -174.77  30.0  3
 S0Q  Var_10    C13  C14  C15  O4   -161.39  30.0  2
 S0Q  Var_11    C    N    C1   C2     74.18  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
 S0Q  chir_01  C13  O3  C11  C14  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
 S0Q  plan-1  C1   0.020
 S0Q  plan-1  N1   0.020
 S0Q  plan-1  C2   0.020
 S0Q  plan-1  O2   0.020
 S0Q  plan-1  C3   0.020
 S0Q  plan-1  C6   0.020
 S0Q  plan-2  C9   0.020
 S0Q  plan-2  C10  0.020
 S0Q  plan-2  C11  0.020
 S0Q  plan-2  C12  0.020
 S0Q  plan-2  C16  0.020
 S0Q  plan-2  C13  0.020
 S0Q  plan-2  B    0.020
 S0Q  plan-2  C8   0.020
 S0Q  plan-2  H11  0.020
 S0Q  plan-2  H12  0.020
 S0Q  plan-2  H15  0.020
 S0Q  plan-2  C    0.020
 S0Q  plan-3  C1   0.020
 S0Q  plan-3  C8   0.020
 S0Q  plan-3  O    0.020
 S0Q  plan-3  N    0.020
 S0Q  plan-3  H18  0.020
 S0Q  plan-3  C    0.020
 S0Q  plan-4  N2   0.020
 S0Q  plan-4  C3   0.020
 S0Q  plan-4  C4   0.020
 S0Q  plan-4  C5   0.020
 S0Q  plan-4  C7   0.020
 S0Q  plan-4  O1   0.020
 S0Q  plan-5  O4   0.020
 S0Q  plan-5  O5   0.020
 S0Q  plan-5  C15  0.020
 S0Q  plan-5  C14  0.020

