# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:55:43 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 2-[(3~{S})-1-oxidanyl-5-phenylmethoxy-3~{H}-2,1-benzoxaborol-3-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB1O[C@@H](CC(O)=O)c2cc(OCc3ccccc3)ccc12
#
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
 S1K  S1K  '2-[(3~{S})-1-oxidanyl-5-phenylmethoxy-3~{H}-2,1-benzoxaborol-3-yl]ethanoic acid'  ligand  36  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_S1K
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
 S1K  C12  C  CR16   0  -0.288   6.6774  -2.9713  -14.7976
 S1K  C13  C  C1     0  -0.329   6.7876   1.2819  -18.0354
 S1K  C14  C  C1     0  -0.328   6.3437   2.3295  -18.8161
 S1K  C15  C  CR5    0  -0.124   5.1619   2.9908  -18.4834
 S1K  O    O  O      0  -0.605  -0.3637   3.1352  -17.6520
 S1K  C    C  C      0   0.412   0.6497   3.4443  -16.9973
 S1K  O5   O  OC    -1  -0.605   0.7396   4.3343  -16.1281
 S1K  C2   C  CR15   0   0.024   3.2076   3.4053  -17.1883
 S1K  O4   O  O      0  -0.483   3.2483   4.3682  -18.2458
 S1K  B    B  B      0   0.480   4.3461   4.1779  -19.0443
 S1K  C3   C  CR5    0   0.037   4.4476   2.5718  -17.3676
 S1K  C5   C  C      0   0.385   6.0575   0.8761  -16.9059
 S1K  C4   C  C1     0  -0.438   4.8697   1.5198  -16.5651
 S1K  O1   O  O2     0  -0.465   6.5900  -0.1479  -16.2144
 S1K  C6   C  CH2    0  -0.272   5.9499  -0.5780  -15.0186
 S1K  C7   C  CR6    0   0.103   6.8127  -1.6415  -14.4095
 S1K  C11  C  CR16   0  -0.241   7.4985  -3.9506  -14.2558
 S1K  C10  C  CR16   0  -0.259   8.4645  -3.6066  -13.3186
 S1K  C9   C  CR16   0  -0.239   8.6060  -2.2821  -12.9261
 S1K  C8   C  CR16   0  -0.293   7.7841  -1.3054  -13.4717
 S1K  H1   H  HCR6   0   0.253   5.9204  -3.2435  -15.5237
 S1K  H2   H  H      0   0.257   7.7061   0.7620  -18.2782
 S1K  H3   H  H      0   0.251   6.9240   2.6301  -19.6802
 S1K  H5   H  HCH2   0   0.221   1.8621   2.0856  -18.2155
 S1K  H6   H  HCH2   0   0.238   1.9692   1.8268  -16.4869
 S1K  H7   H  HCR5   0   0.242   3.2402   3.9433  -16.2357
 S1K  H9   H  H      0   0.275   4.2875   1.2198  -15.7030
 S1K  H10  H  HCH2   0   0.243   5.8358   0.2614  -14.3248
 S1K  H11  H  HCH2   0   0.242   4.9517  -0.9691  -15.2418
 S1K  H12  H  HCR6   0   0.256   7.3824  -4.9822  -14.5622
 S1K  H13  H  HCR6   0   0.257   9.1031  -4.3699  -12.8927
 S1K  H14  H  HCR6   0   0.256   9.3550  -2.0096  -12.1938
 S1K  H15  H  HCR6   0   0.253   7.8944  -0.2729  -13.1613
 S1K  H8   H  HOH1   0   0.485   3.9738   5.6295  -20.3019
 S1K  C1   C  CH2    0  -0.590   1.9209   2.6067  -17.2560
 S1K  O2   O  OH1    0  -0.614   4.6211   4.9376  -20.1299

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
 S1K  B    C15  single    1.546  0.020  1.546
 S1K  B    O4   single    1.371  0.020  1.371
 S1K  C14  C15  aromatic  1.394  0.020  1.394
 S1K  C14  C13  aromatic  1.380  0.020  1.380
 S1K  C15  C3   aromatic  1.390  0.020  1.390
 S1K  C13  C5   aromatic  1.405  0.020  1.405
 S1K  O4   C2   single    1.431  0.020  1.431
 S1K  O    C    deloc     1.245  0.020  1.245
 S1K  C3   C2   single    1.505  0.020  1.505
 S1K  C3   C4   aromatic  1.389  0.020  1.389
 S1K  C1   C2   single    1.516  0.020  1.516
 S1K  C1   C    single    1.544  0.020  1.544
 S1K  C5   C4   aromatic  1.393  0.020  1.393
 S1K  C5   O1   single    1.345  0.020  1.345
 S1K  C    O5   deloc     1.247  0.020  1.247
 S1K  O1   C6   single    1.423  0.020  1.423
 S1K  C6   C7   single    1.499  0.020  1.499
 S1K  C7   C12  aromatic  1.392  0.020  1.392
 S1K  C7   C8   aromatic  1.392  0.020  1.392
 S1K  C12  C11  aromatic  1.388  0.020  1.388
 S1K  C11  C10  aromatic  1.389  0.020  1.389
 S1K  C8   C9   aromatic  1.388  0.020  1.388
 S1K  C10  C9   aromatic  1.389  0.020  1.389
 S1K  C12  H1   single    0.930  0.020  1.080
 S1K  C13  H2   single    0.930  0.020  1.080
 S1K  C14  H3   single    0.930  0.020  1.080
 S1K  C1   H5   single    0.970  0.020  1.090
 S1K  C1   H6   single    0.970  0.020  1.090
 S1K  C2   H7   single    0.970  0.020  1.090
 S1K  C4   H9   single    0.930  0.020  1.080
 S1K  C6   H10  single    0.970  0.020  1.090
 S1K  C6   H11  single    0.970  0.020  1.090
 S1K  C11  H12  single    0.930  0.020  1.080
 S1K  C10  H13  single    0.930  0.020  1.080
 S1K  C9   H14  single    0.930  0.020  1.080
 S1K  C8   H15  single    0.930  0.020  1.080
 S1K  B    O2   single    1.353  0.020  1.353
 S1K  O2   H8   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
 S1K  H1   C12  C11  119.83  3.000
 S1K  H1   C12  C7   119.65  3.000
 S1K  C11  C12  C7   120.52  3.000
 S1K  H2   C13  C5   118.84  3.000
 S1K  H2   C13  C14  120.69  3.000
 S1K  C5   C13  C14  120.47  3.000
 S1K  H3   C14  C15  120.84  3.000
 S1K  H3   C14  C13  119.31  3.000
 S1K  C15  C14  C13  119.85  3.000
 S1K  C3   C15  B    104.57  3.000
 S1K  C3   C15  C14  118.96  3.000
 S1K  B    C15  C14  136.46  3.000
 S1K  C1   C    O5   116.39  3.000
 S1K  O5   C    O    127.02  3.000
 S1K  C1   C    O    116.56  3.000
 S1K  H7   C2   C3   110.57  3.000
 S1K  H7   C2   O4   108.16  3.000
 S1K  C3   C2   O4   105.14  3.000
 S1K  H7   C2   C1   108.85  3.000
 S1K  C3   C2   C1   113.72  3.000
 S1K  O4   C2   C1   110.23  3.000
 S1K  B    O4   C2   111.10  3.000
 S1K  O2   B    O4   123.51  3.000
 S1K  O2   B    C15  127.95  3.000
 S1K  O4   B    C15  108.54  3.000
 S1K  C4   C3   C2   126.95  3.000
 S1K  C4   C3   C15  122.42  3.000
 S1K  C2   C3   C15  110.62  3.000
 S1K  O1   C5   C4   124.28  3.000
 S1K  O1   C5   C13  115.30  3.000
 S1K  C4   C5   C13  120.41  3.000
 S1K  H9   C4   C5   121.68  3.000
 S1K  H9   C4   C3   120.43  3.000
 S1K  C5   C4   C3   117.89  3.000
 S1K  C6   O1   C5   118.95  3.000
 S1K  H11  C6   H10  107.93  3.000
 S1K  H11  C6   C7   110.74  3.000
 S1K  H10  C6   C7   110.27  3.000
 S1K  H11  C6   O1   110.28  3.000
 S1K  H10  C6   O1   110.35  3.000
 S1K  C7   C6   O1   107.28  3.000
 S1K  C8   C7   C6   120.29  3.000
 S1K  C8   C7   C12  119.11  3.000
 S1K  C6   C7   C12  120.58  3.000
 S1K  H12  C11  C10  120.10  3.000
 S1K  H12  C11  C12  119.90  3.000
 S1K  C10  C11  C12  120.00  3.000
 S1K  H13  C10  C9   120.08  3.000
 S1K  H13  C10  C11  120.07  3.000
 S1K  C9   C10  C11  119.85  3.000
 S1K  H14  C9   C8   119.90  3.000
 S1K  H14  C9   C10  120.12  3.000
 S1K  C8   C9   C10  119.98  3.000
 S1K  H15  C8   C9   119.83  3.000
 S1K  H15  C8   C7   119.62  3.000
 S1K  C9   C8   C7   120.55  3.000
 S1K  H6   C1   H5   106.20  3.000
 S1K  H6   C1   C2   107.82  3.000
 S1K  H5   C1   C2   109.62  3.000
 S1K  H6   C1   C    107.73  3.000
 S1K  H5   C1   C    111.18  3.000
 S1K  C2   C1   C    113.92  3.000
 S1K  H8   O2   B    114.20  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
 S1K  CONST_01  C9   C8   C7   C12     0.00   0.0  0
 S1K  CONST_02  C9   C10  C11  C12     0.00   0.0  0
 S1K  CONST_03  C3   C15  C14  C13     0.00   0.0  0
 S1K  CONST_04  C3   C4   C5   C13     0.00   0.0  0
 S1K  CONST_05  C4   C3   C15  C14     0.00   0.0  0
 S1K  CONST_06  C4   C5   C13  C14     0.00   0.0  0
 S1K  CONST_07  C5   C13  C14  C15     0.00   0.0  0
 S1K  CONST_08  C5   C4   C3   C15     0.00   0.0  0
 S1K  CONST_09  C10  C11  C12  C7      0.00   0.0  0
 S1K  CONST_10  C10  C9   C8   C7      0.00   0.0  0
 S1K  CONST_11  C8   C7   C12  C11     0.00   0.0  0
 S1K  CONST_12  C8   C9   C10  C11     0.00   0.0  0
 S1K  CONST_13  O1   C5   C13  C14   180.00   0.0  0
 S1K  CONST_14  O1   C5   C4   C3    180.00   0.0  0
 S1K  CONST_15  C11  C12  C7   C6    180.00   0.0  0
 S1K  CONST_16  C9   C8   C7   C6    180.00   0.0  0
 S1K  CONST_17  H15  C8   C7   C12   180.00   0.0  0
 S1K  CONST_18  H13  C10  C11  C12   180.00   0.0  0
 S1K  CONST_19  H9   C4   C5   C13   180.00   0.0  0
 S1K  CONST_20  H2   C13  C14  C15   180.00   0.0  0
 S1K  CONST_21  H3   C14  C15  B       0.00   0.0  0
 S1K  CONST_22  H12  C11  C12  C7    180.00   0.0  0
 S1K  CONST_23  H14  C9   C8   C7    180.00   0.0  0
 S1K  CONST_24  H1   C12  C11  C10   180.00   0.0  0
 S1K  Var_01    O4   B    C15  C14  -179.21  30.0  1
 S1K  Var_02    O1   C6   C7   C12   -86.30  30.0  2
 S1K  Var_03    C7   C6   O1   C5   -175.44  30.0  3
 S1K  Var_04    C2   C1   C    O     144.25  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
 S1K  chir_01  C2  O4  C3  C1  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
 S1K  plan-1  C12  0.020
 S1K  plan-1  C6   0.020
 S1K  plan-1  C7   0.020
 S1K  plan-1  C11  0.020
 S1K  plan-1  C10  0.020
 S1K  plan-1  C9   0.020
 S1K  plan-1  C8   0.020
 S1K  plan-1  H1   0.020
 S1K  plan-1  H12  0.020
 S1K  plan-1  H13  0.020
 S1K  plan-1  H14  0.020
 S1K  plan-1  H15  0.020
 S1K  plan-2  C13  0.020
 S1K  plan-2  C14  0.020
 S1K  plan-2  C15  0.020
 S1K  plan-2  C2   0.020
 S1K  plan-2  B    0.020
 S1K  plan-2  C3   0.020
 S1K  plan-2  C5   0.020
 S1K  plan-2  C4   0.020
 S1K  plan-2  O1   0.020
 S1K  plan-2  H2   0.020
 S1K  plan-2  H3   0.020
 S1K  plan-2  H9   0.020
 S1K  plan-3  O    0.020
 S1K  plan-3  C    0.020
 S1K  plan-3  O5   0.020
 S1K  plan-3  C1   0.020

