# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 13:32:46 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: methyl (2~{R})-2-[(1-oxidanyl-3~{H}-2,1-benzoxaborol-6-yl)carbonylamino]-2-phenyl-ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](NC(=O)c1ccc2COB(O)c2c1)c3ccccc3
#
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
 S0Z  S0Z  'methyl (2~{R})-2-[(1-oxidanyl-3~{H}-2,1-benzoxaborol-6-yl)carbonylamino]-2-phenyl-ethanoate'  ligand  40  24  .  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_S0Z
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
 S0Z  C15  C  CR16  0  -0.264   3.7600   1.8219  -16.0617
 S0Z  C14  C  CR56  0  -0.033   3.5335   2.8672  -16.9432
 S0Z  C13  C  CH2   0  -0.178   2.4055   3.8556  -16.9551
 S0Z  C12  C  CR56  0  -0.071   4.3990   3.1193  -18.0048
 S0Z  C11  C  CR16  0  -0.371   5.5115   2.3150  -18.1989
 S0Z  C16  C  CR16  0  -0.306   4.8817   1.0309  -16.2560
 S0Z  O5   O  O     0  -0.471   7.4104   0.2531  -18.6881
 S0Z  C10  C  CR6   0  -0.016   5.7651   1.2703  -17.3142
 S0Z  O4   O  O     0  -0.467   2.6312   4.6965  -18.0783
 S0Z  B    B  B     0   0.516   3.7808   4.3425  -18.7368
 S0Z  N    N  NH1   0  -0.667   7.5011  -0.1843  -16.4812
 S0Z  C2   C  CH1   0  -0.256   8.5761  -1.1333  -16.6205
 S0Z  C    C  C     0   0.593   9.3385  -1.3500  -15.3230
 S0Z  O1   O  O2    0  -0.449   8.6154  -1.0865  -14.2513
 S0Z  C1   C  CH3   0  -0.421   9.2130  -1.3135  -12.9705
 S0Z  O    O  O     0  -0.427  10.4641  -1.7712  -15.3026
 S0Z  C3   C  CR6   0   0.121   8.0998  -2.4952  -17.0960
 S0Z  C8   C  CR16  0  -0.300   8.7867  -3.1620  -18.1022
 S0Z  C7   C  CR16  0  -0.240   8.3690  -4.4176  -18.5240
 S0Z  C6   C  CR16  0  -0.261   7.2620  -5.0154  -17.9381
 S0Z  C5   C  CR16  0  -0.238   6.5739  -4.3517  -16.9298
 S0Z  C4   C  CR16  0  -0.287   6.9912  -3.0974  -16.5086
 S0Z  H1   H  HCR6  0   0.261   3.0810   1.6122  -15.2448
 S0Z  H2   H  HCH2  0   0.255   2.3812   4.4578  -16.0428
 S0Z  H3   H  HCH2  0   0.255   1.4330   3.3652  -17.0505
 S0Z  H4   H  HCR6  0   0.260   6.1874   2.4953  -19.0255
 S0Z  H5   H  HCR6  0   0.264   5.0424   0.1978  -15.5825
 S0Z  H7   H  HNH1  0   0.416   7.1295  -0.0002  -15.5637
 S0Z  H8   H  HCH1  0   0.312   9.3017  -0.7471  -17.3400
 S0Z  H9   H  HCH3  0   0.257   8.4605  -1.0357  -12.2393
 S0Z  H10  H  HCH3  0   0.246   9.4771  -2.3624  -12.8428
 S0Z  H11  H  HCH3  0   0.246  10.0992  -0.6951  -12.8358
 S0Z  H12  H  HCR6  0   0.256   9.6479  -2.6959  -18.5659
 S0Z  H13  H  HCR6  0   0.258   8.9066  -4.9259  -19.3139
 S0Z  H14  H  HCR6  0   0.258   6.9337  -5.9927  -18.2671
 S0Z  H15  H  HCR6  0   0.258   5.7093  -4.8121  -16.4695
 S0Z  H16  H  HCR6  0   0.257   6.4407  -2.5888  -15.7258
 S0Z  O2   O  OH1   0  -0.606   4.2560   4.9759  -19.8271
 S0Z  H6   H  HOH1  0   0.490   3.7238   5.7201  -20.1288
 S0Z  C9   C  C     0   0.552   6.9560   0.4051  -17.5644

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
 S0Z  O5   C9   double    1.222  0.020  1.222
 S0Z  B    C12  single    1.554  0.020  1.554
 S0Z  B    O4   single    1.371  0.020  1.371
 S0Z  C7   C8   aromatic  1.389  0.020  1.389
 S0Z  C7   C6   aromatic  1.388  0.020  1.388
 S0Z  C11  C12  aromatic  1.386  0.020  1.386
 S0Z  C11  C10  aromatic  1.392  0.020  1.392
 S0Z  C8   C3   aromatic  1.389  0.020  1.389
 S0Z  C12  C14  aromatic  1.393  0.020  1.393
 S0Z  O4   C13  single    1.421  0.020  1.421
 S0Z  C6   C5   aromatic  1.390  0.020  1.390
 S0Z  C9   C10  single    1.493  0.020  1.493
 S0Z  C9   N    single    1.348  0.020  1.348
 S0Z  C10  C16  aromatic  1.399  0.020  1.399
 S0Z  C14  C13  single    1.500  0.020  1.500
 S0Z  C14  C15  aromatic  1.386  0.020  1.386
 S0Z  C3   C2   single    1.519  0.020  1.519
 S0Z  C3   C4   aromatic  1.392  0.020  1.392
 S0Z  C2   N    single    1.441  0.020  1.441
 S0Z  C2   C    single    1.520  0.020  1.520
 S0Z  C16  C15  aromatic  1.386  0.020  1.386
 S0Z  C5   C4   aromatic  1.387  0.020  1.387
 S0Z  C    O    double    1.202  0.020  1.202
 S0Z  C    O1   single    1.319  0.020  1.319
 S0Z  O1   C1   single    1.432  0.020  1.432
 S0Z  C15  H1   single    0.930  0.020  1.080
 S0Z  C13  H2   single    0.970  0.020  1.090
 S0Z  C13  H3   single    0.970  0.020  1.090
 S0Z  C11  H4   single    0.930  0.020  1.080
 S0Z  C16  H5   single    0.930  0.020  1.080
 S0Z  N    H7   single    0.860  0.020  1.020
 S0Z  C2   H8   single    0.970  0.020  1.090
 S0Z  C1   H9   single    0.970  0.020  1.090
 S0Z  C1   H10  single    0.970  0.020  1.090
 S0Z  C1   H11  single    0.970  0.020  1.090
 S0Z  C8   H12  single    0.930  0.020  1.080
 S0Z  C7   H13  single    0.930  0.020  1.080
 S0Z  C6   H14  single    0.930  0.020  1.080
 S0Z  C5   H15  single    0.930  0.020  1.080
 S0Z  C4   H16  single    0.930  0.020  1.080
 S0Z  B    O2   single    1.348  0.020  1.348
 S0Z  O2   H6   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
 S0Z  H1   C15  C16  120.18  3.000
 S0Z  H1   C15  C14  121.56  3.000
 S0Z  C16  C15  C14  118.25  3.000
 S0Z  C12  C14  C13  110.00  3.000
 S0Z  C13  C14  C15  128.68  3.000
 S0Z  C12  C14  C15  121.32  3.000
 S0Z  H3   C13  H2   107.47  3.000
 S0Z  H3   C13  O4   109.74  3.000
 S0Z  H2   C13  O4   109.69  3.000
 S0Z  H3   C13  C14  111.97  3.000
 S0Z  H2   C13  C14  111.90  3.000
 S0Z  O4   C13  C14  106.07  3.000
 S0Z  B    C12  C11  135.24  3.000
 S0Z  C11  C12  C14  120.02  3.000
 S0Z  B    C12  C14  104.73  3.000
 S0Z  H4   C11  C10  119.75  3.000
 S0Z  H4   C11  C12  120.74  3.000
 S0Z  C10  C11  C12  119.50  3.000
 S0Z  H5   C16  C10  120.54  3.000
 S0Z  H5   C16  C15  118.14  3.000
 S0Z  C10  C16  C15  121.29  3.000
 S0Z  C9   C10  C16  122.09  3.000
 S0Z  C16  C10  C11  119.60  3.000
 S0Z  C9   C10  C11  118.27  3.000
 S0Z  B    O4   C13  111.10  3.000
 S0Z  O2   B    O4   124.25  3.000
 S0Z  O2   B    C12  127.65  3.000
 S0Z  O4   B    C12  108.09  3.000
 S0Z  H7   N    C2   118.94  3.000
 S0Z  H7   N    C9   120.19  3.000
 S0Z  C2   N    C9   120.79  3.000
 S0Z  H8   C2   C3   108.61  3.000
 S0Z  H8   C2   C    106.22  3.000
 S0Z  C3   C2   C    107.25  3.000
 S0Z  H8   C2   N    109.06  3.000
 S0Z  C    C2   N    112.68  3.000
 S0Z  C3   C2   N    112.76  3.000
 S0Z  O    C    O1   124.71  3.000
 S0Z  O1   C    C2   112.95  3.000
 S0Z  O    C    C2   122.28  3.000
 S0Z  C1   O1   C    117.79  3.000
 S0Z  H11  C1   H10  109.57  3.000
 S0Z  H11  C1   H9   109.61  3.000
 S0Z  H10  C1   H9   109.62  3.000
 S0Z  H11  C1   O1   111.12  3.000
 S0Z  H10  C1   O1   111.03  3.000
 S0Z  H9   C1   O1   105.82  3.000
 S0Z  C4   C3   C8   119.47  3.000
 S0Z  C4   C3   C2   120.38  3.000
 S0Z  C8   C3   C2   120.14  3.000
 S0Z  H12  C8   C7   119.87  3.000
 S0Z  H12  C8   C3   119.77  3.000
 S0Z  C7   C8   C3   120.36  3.000
 S0Z  H13  C7   C6   120.14  3.000
 S0Z  H13  C7   C8   119.80  3.000
 S0Z  C6   C7   C8   120.07  3.000
 S0Z  H14  C6   C5   120.11  3.000
 S0Z  H14  C6   C7   120.17  3.000
 S0Z  C5   C6   C7   119.71  3.000
 S0Z  H15  C5   C4   119.72  3.000
 S0Z  H15  C5   C6   120.07  3.000
 S0Z  C4   C5   C6   120.21  3.000
 S0Z  H16  C4   C5   119.39  3.000
 S0Z  H16  C4   C3   120.42  3.000
 S0Z  C5   C4   C3   120.18  3.000
 S0Z  H6   O2   B    114.94  3.000
 S0Z  N    C9   C10  116.18  3.000
 S0Z  N    C9   O5   122.29  3.000
 S0Z  C10  C9   O5   121.53  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
 S0Z  CONST_01  C11  C12  C14  C15     0.00   0.0  0
 S0Z  CONST_02  C11  C10  C16  C15     0.00   0.0  0
 S0Z  CONST_03  C10  C11  C12  C14     0.00   0.0  0
 S0Z  CONST_04  C10  C16  C15  C14     0.00   0.0  0
 S0Z  CONST_05  C16  C10  C11  C12     0.00   0.0  0
 S0Z  CONST_06  C16  C15  C14  C12     0.00   0.0  0
 S0Z  CONST_07  C6   C7   C8   C3      0.00   0.0  0
 S0Z  CONST_08  C6   C5   C4   C3      0.00   0.0  0
 S0Z  CONST_09  C5   C6   C7   C8      0.00   0.0  0
 S0Z  CONST_10  C5   C4   C3   C8      0.00   0.0  0
 S0Z  CONST_11  C4   C3   C8   C7      0.00   0.0  0
 S0Z  CONST_12  C4   C5   C6   C7      0.00   0.0  0
 S0Z  CONST_13  C9   C10  C16  C15   180.00   0.0  0
 S0Z  CONST_14  C9   C10  C11  C12   180.00   0.0  0
 S0Z  CONST_15  C7   C8   C3   C2    180.00   0.0  0
 S0Z  CONST_16  C5   C4   C3   C2    180.00   0.0  0
 S0Z  CONST_17  H4   C11  C12  C14   180.00   0.0  0
 S0Z  CONST_18  H5   C16  C15  C14   180.00   0.0  0
 S0Z  CONST_19  H1   C15  C14  C13     0.00   0.0  0
 S0Z  CONST_20  H13  C7   C8   C3    180.00   0.0  0
 S0Z  CONST_21  H15  C5   C4   C3    180.00   0.0  0
 S0Z  CONST_22  H14  C6   C7   C8    180.00   0.0  0
 S0Z  CONST_23  H16  C4   C3   C8    180.00   0.0  0
 S0Z  CONST_24  H12  C8   C7   C6    180.00   0.0  0
 S0Z  CONST_25  C2   N    C9   C10   180.00   0.0  0
 S0Z  CONST_26  H7   N    C9   C10     0.00   0.0  0
 S0Z  CONST_27  C2   N    C9   O5      0.00   0.0  0
 S0Z  Var_01    O4   C13  C14  C15  -178.83  30.0  1
 S0Z  Var_02    O4   B    C12  C14    -0.51  30.0  1
 S0Z  Var_03    C12  B    O4   C13     0.93  30.0  1
 S0Z  Var_04    O5   C9   C10  C11   -26.64  30.0  2
 S0Z  Var_05    O    C    O1   C1      0.21  30.0  1
 S0Z  Var_06    H9   C1   O1   C     179.90  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
 S0Z  chir_01  C2  C3  N  C  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
 S0Z  plan-1  C2   0.020
 S0Z  plan-1  C3   0.020
 S0Z  plan-1  C8   0.020
 S0Z  plan-1  C7   0.020
 S0Z  plan-1  C6   0.020
 S0Z  plan-1  C5   0.020
 S0Z  plan-1  C4   0.020
 S0Z  plan-1  H12  0.020
 S0Z  plan-1  H13  0.020
 S0Z  plan-1  H14  0.020
 S0Z  plan-1  H15  0.020
 S0Z  plan-1  H16  0.020
 S0Z  plan-2  C15  0.020
 S0Z  plan-2  C14  0.020
 S0Z  plan-2  C13  0.020
 S0Z  plan-2  C12  0.020
 S0Z  plan-2  C11  0.020
 S0Z  plan-2  C16  0.020
 S0Z  plan-2  C10  0.020
 S0Z  plan-2  B    0.020
 S0Z  plan-2  H1   0.020
 S0Z  plan-2  H4   0.020
 S0Z  plan-2  H5   0.020
 S0Z  plan-2  C9   0.020
 S0Z  plan-3  O5   0.020
 S0Z  plan-3  C10  0.020
 S0Z  plan-3  N    0.020
 S0Z  plan-3  C2   0.020
 S0Z  plan-3  H7   0.020
 S0Z  plan-3  C9   0.020
 S0Z  plan-4  C2   0.020
 S0Z  plan-4  C    0.020
 S0Z  plan-4  O1   0.020
 S0Z  plan-4  O    0.020

