# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:12:52 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: 1,3,3-trimethyl-4-[(1-oxidanyl-3~{H}-2,1-benzoxaborol-6-yl)carbonyl]piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(C(=O)c2ccc3COB(O)c3c2)C(C)(C)C1=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
 S1B  S1B  1,3,3-trimethyl-4-[(1-oxidanyl-3~{H}-2,1-benzoxaborol-6-yl)carbonyl]piperazin-2-one  ligand  41  22  .  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_S1B
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
 S1B  C1   C  CH2   0  -0.256   -6.5944  -0.6276  14.6870
 S1B  C2   C  CH2   0  -0.372   -7.0779   0.3915  15.6788
 S1B  C3   C  CT    0  -0.003   -8.0702  -1.2926  17.1508
 S1B  C4   C  CH3   0  -0.668   -7.5486  -2.3578  18.1269
 S1B  C5   C  C     0   0.570   -8.2406  -2.0599  15.8167
 S1B  C6   C  CH3   0  -0.637   -9.4364  -0.7613  17.5904
 S1B  C8   C  CR6   0  -0.062   -5.4574   1.4062  17.8028
 S1B  C9   C  CR16  0  -0.366   -5.5260   2.7135  18.2677
 S1B  C10  C  CR56  0  -0.080   -4.4474   3.5628  18.0632
 S1B  C11  C  CR56  0  -0.034   -3.2977   3.0908  17.4350
 S1B  C12  C  CR16  0  -0.269   -3.2038   1.7808  16.9898
 S1B  C13  C  CR16  0  -0.263   -4.2976   0.9483  17.1705
 S1B  C14  C  CH2   0  -0.179   -2.2747   4.1846  17.3454
 S1B  O1   O  O     0  -0.467   -2.8710   5.3287  17.9410
 S1B  O4   O  O     0  -0.463   -6.9589   0.3044  19.2297
 S1B  N1   N  NT    0  -0.485   -7.1045  -0.1926  17.0064
 S1B  O    O  O     0  -0.491   -9.0946  -2.9339  15.7616
 S1B  N    N  NT    0  -0.457   -7.3977  -1.8272  14.7959
 S1B  C    C  CH3   0  -0.525   -7.4319  -2.6864  13.6302
 S1B  B    B  B     0   0.514   -4.1409   5.0520  18.3783
 S1B  H1   H  HCH2  0   0.249   -5.5352  -0.8545  14.8402
 S1B  H2   H  HCH2  0   0.258   -6.7021  -0.2255  13.6771
 S1B  H3   H  HCH2  0   0.295   -6.4433   1.2717  15.6520
 S1B  H4   H  HCH2  0   0.272   -8.0870   0.7242  15.4089
 S1B  H5   H  HCH3  0   0.258   -7.4888  -1.9740  19.1401
 S1B  H6   H  HCH3  0   0.246   -8.2249  -3.2099  18.1323
 S1B  H7   H  HCH3  0   0.238   -6.5594  -2.7084  17.8276
 S1B  H8   H  HCH3  0   0.245   -9.3626  -0.3084  18.5763
 S1B  H9   H  HCH3  0   0.236   -9.8144  -0.0097  16.8948
 S1B  H10  H  HCH3  0   0.240  -10.1648  -1.5675  17.6433
 S1B  H11  H  HCR6  0   0.260   -6.4214   3.0654  18.7664
 S1B  H12  H  HCR6  0   0.258   -2.3081   1.4076  16.5092
 S1B  H13  H  HCR6  0   0.268   -4.2480  -0.0768  16.8235
 S1B  H15  H  HCH3  0   0.253   -7.6258  -3.7174  13.9125
 S1B  H16  H  HCH3  0   0.241   -8.1937  -2.3697  12.9141
 S1B  H17  H  HCH3  0   0.250   -6.4619  -2.6435  13.1377
 S1B  O2   O  OH1   0  -0.607   -4.9484   5.9557  18.9688
 S1B  H19  H  HCH2  0   0.253   -1.3543   3.9286  17.8772
 S1B  H18  H  HCH2  0   0.253   -2.0042   4.4084  16.3098
 S1B  H14  H  HOH1  0   0.489   -4.5644   6.8328  19.0756
 S1B  C7   C  C     0   0.537   -6.5891   0.4646  18.0781

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
 S1B  C    N    single    1.449  0.020  1.449
 S1B  C1   N    single    1.448  0.020  1.448
 S1B  C1   C2   single    1.502  0.020  1.502
 S1B  N    C5   single    1.344  0.020  1.344
 S1B  C2   N1   single    1.451  0.020  1.451
 S1B  C5   O    double    1.223  0.020  1.223
 S1B  C5   C3   single    1.548  0.020  1.548
 S1B  C12  C13  aromatic  1.386  0.020  1.386
 S1B  C12  C11  aromatic  1.387  0.020  1.387
 S1B  C13  C8   aromatic  1.398  0.020  1.398
 S1B  N1   C3   single    1.471  0.020  1.471
 S1B  N1   C7   single    1.359  0.020  1.359
 S1B  C3   C6   single    1.530  0.020  1.530
 S1B  C3   C4   single    1.536  0.020  1.536
 S1B  C14  C11  single    1.500  0.020  1.500
 S1B  C14  O1   single    1.421  0.020  1.421
 S1B  C11  C10  aromatic  1.393  0.020  1.393
 S1B  C8   C7   single    1.498  0.020  1.498
 S1B  C8   C9   aromatic  1.389  0.020  1.389
 S1B  C7   O4   double    1.220  0.020  1.220
 S1B  C10  C9   aromatic  1.388  0.020  1.388
 S1B  C10  B    single    1.553  0.020  1.553
 S1B  O1   B    single    1.371  0.020  1.371
 S1B  C1   H1   single    0.970  0.020  1.090
 S1B  C1   H2   single    0.970  0.020  1.090
 S1B  C2   H3   single    0.970  0.020  1.090
 S1B  C2   H4   single    0.970  0.020  1.090
 S1B  C4   H5   single    0.970  0.020  1.090
 S1B  C4   H6   single    0.970  0.020  1.090
 S1B  C4   H7   single    0.970  0.020  1.090
 S1B  C6   H8   single    0.970  0.020  1.090
 S1B  C6   H9   single    0.970  0.020  1.090
 S1B  C6   H10  single    0.970  0.020  1.090
 S1B  C9   H11  single    0.930  0.020  1.080
 S1B  C12  H12  single    0.930  0.020  1.080
 S1B  C13  H13  single    0.930  0.020  1.080
 S1B  C    H15  single    0.970  0.020  1.090
 S1B  C    H16  single    0.970  0.020  1.090
 S1B  C    H17  single    0.970  0.020  1.090
 S1B  B    O2   single    1.348  0.020  1.348
 S1B  C14  H19  single    0.970  0.020  1.090
 S1B  C14  H18  single    0.970  0.020  1.090
 S1B  O2   H14  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
 S1B  H2   C1   H1   107.53  3.000
 S1B  H2   C1   N    108.65  3.000
 S1B  H1   C1   N    110.78  3.000
 S1B  H2   C1   C2   109.21  3.000
 S1B  H1   C1   C2   111.10  3.000
 S1B  N    C1   C2   109.51  3.000
 S1B  H4   C2   H3   106.62  3.000
 S1B  H4   C2   N1   109.31  3.000
 S1B  H3   C2   N1   111.09  3.000
 S1B  H4   C2   C1   109.85  3.000
 S1B  H3   C2   C1   110.22  3.000
 S1B  N1   C2   C1   109.69  3.000
 S1B  N1   C3   C6   110.77  3.000
 S1B  C6   C3   C5   108.74  3.000
 S1B  N1   C3   C5   110.99  3.000
 S1B  C6   C3   C4   111.18  3.000
 S1B  N1   C3   C4   110.98  3.000
 S1B  C5   C3   C4   103.96  3.000
 S1B  H7   C4   H6   108.25  3.000
 S1B  H7   C4   H5   108.65  3.000
 S1B  H6   C4   H5   107.86  3.000
 S1B  H7   C4   C3   110.87  3.000
 S1B  H6   C4   C3   109.58  3.000
 S1B  H5   C4   C3   111.52  3.000
 S1B  N    C5   O    121.82  3.000
 S1B  O    C5   C3   118.02  3.000
 S1B  N    C5   C3   119.97  3.000
 S1B  H10  C6   H9   108.02  3.000
 S1B  H10  C6   H8   108.06  3.000
 S1B  H9   C6   H8   108.33  3.000
 S1B  H10  C6   C3   110.76  3.000
 S1B  H9   C6   C3   111.41  3.000
 S1B  H8   C6   C3   110.15  3.000
 S1B  C13  C8   C9   120.03  3.000
 S1B  C9   C8   C7   119.52  3.000
 S1B  C13  C8   C7   120.27  3.000
 S1B  H11  C9   C10  120.75  3.000
 S1B  H11  C9   C8   120.03  3.000
 S1B  C10  C9   C8   119.22  3.000
 S1B  B    C10  C11  104.69  3.000
 S1B  B    C10  C9   135.26  3.000
 S1B  C11  C10  C9   120.04  3.000
 S1B  C14  C11  C12  128.56  3.000
 S1B  C14  C11  C10  110.05  3.000
 S1B  C12  C11  C10  121.39  3.000
 S1B  H12  C12  C13  120.23  3.000
 S1B  H12  C12  C11  121.60  3.000
 S1B  C13  C12  C11  118.17  3.000
 S1B  H13  C13  C12  119.36  3.000
 S1B  H13  C13  C8   119.52  3.000
 S1B  C12  C13  C8   121.12  3.000
 S1B  H18  C14  H19  107.48  3.000
 S1B  H18  C14  O1   109.63  3.000
 S1B  H19  C14  O1   109.75  3.000
 S1B  H18  C14  C11  111.99  3.000
 S1B  H19  C14  C11  111.98  3.000
 S1B  O1   C14  C11  106.01  3.000
 S1B  B    O1   C14  111.09  3.000
 S1B  C7   N1   C3   122.23  3.000
 S1B  C7   N1   C2   121.34  3.000
 S1B  C3   N1   C2   113.77  3.000
 S1B  C    N    C5   119.59  3.000
 S1B  C5   N    C1   123.26  3.000
 S1B  C    N    C1   116.36  3.000
 S1B  H17  C    H16  108.26  3.000
 S1B  H17  C    H15  108.30  3.000
 S1B  H16  C    H15  108.72  3.000
 S1B  H17  C    N    108.64  3.000
 S1B  H16  C    N    111.84  3.000
 S1B  H15  C    N    110.98  3.000
 S1B  O2   B    O1   123.99  3.000
 S1B  O2   B    C10  127.85  3.000
 S1B  O1   B    C10  108.15  3.000
 S1B  H14  O2   B    114.84  3.000
 S1B  N1   C7   O4   124.47  3.000
 S1B  O4   C7   C8   119.02  3.000
 S1B  N1   C7   C8   116.47  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
 S1B  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 S1B  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 S1B  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 S1B  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 S1B  CONST_05  C13  C12  C11  C10     0.00   0.0  0
 S1B  CONST_06  C13  C8   C9   C10     0.00   0.0  0
 S1B  CONST_08  C12  C13  C8   C7    180.00   0.0  0
 S1B  CONST_09  C10  C9   C8   C7    180.00   0.0  0
 S1B  CONST_11  C8   C7   N1   C3    180.00   0.0  0
 S1B  CONST_12  O    C5   N    C1    180.00   0.0  0
 S1B  CONST_13  C    N    C5   C3    180.00   0.0  0
 S1B  CONST_14  H12  C12  C13  C8    180.00   0.0  0
 S1B  CONST_15  H13  C13  C8   C9    180.00   0.0  0
 S1B  CONST_16  H11  C9   C10  C11   180.00   0.0  0
 S1B  CONST_18  O4   C7   N1   C3      0.00   0.0  0
 S1B  CONST_19  C    N    C5   O       0.00   0.0  0
 S1B  Var_01    C3   N1   C2   C1    -64.79  30.0  1
 S1B  Var_02    C5   N    C1   C2    -12.65  30.0  1
 S1B  Var_03    C5   C3   N1   C2     31.14  30.0  1
 S1B  Var_04    O1   B    C10  C9    179.24  30.0  1
 S1B  Var_05    O1   C14  C11  C10    -0.34  30.0  1
 S1B  Var_06    N    C1   C2   N1     53.72  30.0  1
 S1B  Var_07    N    C5   C3   N1     10.70  30.0  1
 S1B  Var_08    N1   C7   C8   C9    128.11  30.0  2
 S1B  Var_09    H15  C    N    C1    153.07  30.0  3
 S1B  Var_10    H8   C6   C3   C5    174.09  30.0  3
 S1B  Var_11    H5   C4   C3   C5   -173.69  30.0  3

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
 S1B  plan-1  C2   0.020
 S1B  plan-1  C3   0.020
 S1B  plan-1  C8   0.020
 S1B  plan-1  O4   0.020
 S1B  plan-1  N1   0.020
 S1B  plan-1  C7   0.020
 S1B  plan-2  C8   0.020
 S1B  plan-2  C9   0.020
 S1B  plan-2  C10  0.020
 S1B  plan-2  C11  0.020
 S1B  plan-2  C12  0.020
 S1B  plan-2  C13  0.020
 S1B  plan-2  C14  0.020
 S1B  plan-2  B    0.020
 S1B  plan-2  H11  0.020
 S1B  plan-2  H12  0.020
 S1B  plan-2  H13  0.020
 S1B  plan-2  C7   0.020
 S1B  plan-3  C1   0.020
 S1B  plan-3  C3   0.020
 S1B  plan-3  C5   0.020
 S1B  plan-3  O    0.020
 S1B  plan-3  N    0.020
 S1B  plan-3  C    0.020

