# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:57:01 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: 2-[(3~{R},6~{S})-2,2-bis(oxidanyl)-3-(2-thiophen-2-ylethanoylamino)-1-oxa-2-boranuidacyclohex-6-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CC[C@H](NC(=O)Cc2sccc2)[B-](O)(O)O1
#
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
 WXM  WXM  '2-[(3~{R},6~{S})-2,2-bis(oxidanyl)-3-(2-thiophen-2-ylethanoylamino)-1-oxa-2-boranuidacyclohex-6-yl]ethanoic acid'  ligand  38  21  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WXM
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
 WXM  B18  B  B     -1   0.504  14.2344  -4.3678   -9.5571
 WXM  C02  C  C      0   0.541  17.3067  -5.6138   -7.1174
 WXM  C04  C  CH2    0  -0.582  16.6197  -6.7171   -7.8715
 WXM  C05  C  CR16   0   0.072  15.2630  -6.2392   -8.3826
 WXM  C06  C  C      0  -0.454  14.5196  -7.3655   -9.1163
 WXM  C07  C  C      0  -0.442  13.4953  -6.8046  -10.1102
 WXM  C08  C  CR16   0  -0.261  12.9773  -5.4459   -9.6332
 WXM  C12  C  CH2    0  -0.670   9.8121  -4.6808  -11.6126
 WXM  C13  C  CR5    0  -0.109   8.4421  -4.3526  -11.1285
 WXM  C14  C  CR15   0  -0.246   7.2723  -4.9950  -11.3979
 WXM  C15  C  CR15   0  -0.182   6.1503  -4.4195  -10.7373
 WXM  C16  C  CR15   0  -0.473   6.4891  -3.3481   -9.9713
 WXM  N09  N  NH1    0  -0.646  11.9412  -4.9262  -10.5087
 WXM  O01  O  O      0  -0.459  16.8409  -5.0625   -6.1490
 WXM  O03  O  OH1    0  -0.592  18.4971  -5.2987   -7.6184
 WXM  O11  O  O      0  -0.509  10.1980  -6.1698   -9.7725
 WXM  O19  O  OB     0  -0.745  14.4018  -3.7755  -10.8806
 WXM  O20  O  OB     0  -0.729  14.0055  -3.2727   -8.6008
 WXM  O21  O  O      0  -0.565  15.4653  -5.1336   -9.2037
 WXM  S17  S  S2     0   0.202   8.1738  -3.0316  -10.0530
 WXM  H1   H  HCH2   0   0.269  16.4817  -7.5612   -7.1899
 WXM  H2   H  HCH2   0   0.248  17.2331  -7.0640   -8.7050
 WXM  H3   H  HCR6   0   0.174  14.6681  -5.9697   -7.4935
 WXM  H4   H  H      0   0.212  14.0241  -7.9979   -8.3735
 WXM  H5   H  H      0   0.214  15.2307  -8.0108   -9.6426
 WXM  H6   H  H      0   0.208  12.6841  -7.5267  -10.2449
 WXM  H7   H  H      0   0.203  13.9602  -6.6825  -11.0930
 WXM  H8   H  HCR6   0   0.186  12.5229  -5.5906   -8.6440
 WXM  H9   H  HCH2   0   0.292   9.7222  -5.4003  -12.4311
 WXM  H10  H  HCH2   0   0.275  10.3036  -3.7987  -12.0284
 WXM  H11  H  HCR5   0   0.260   7.2148  -5.8548  -12.0514
 WXM  H12  H  HCR5   0   0.264   5.1389  -4.7884  -10.8311
 WXM  H13  H  HCR5   0   0.292   5.8444  -2.7263   -9.3699
 WXM  H14  H  HNH1   0   0.387  12.2330  -4.2239  -11.1711
 WXM  H15  H  HOH1   0   0.474  18.8943  -4.5863   -7.0949
 WXM  H16  H  H      0   0.436  14.9174  -2.9675  -10.8202
 WXM  H17  H  H      0   0.418  13.9903  -3.6183   -7.7049
 WXM  C10  C  C      0   0.532  10.6723  -5.3318  -10.5314

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
 WXM  O19  B18  single    1.460  0.020  1.460
 WXM  C12  C13  single    1.490  0.020  1.490
 WXM  C12  C10  single    1.527  0.020  1.527
 WXM  C14  C13  aromatic  1.362  0.020  1.362
 WXM  C14  C15  aromatic  1.424  0.020  1.424
 WXM  C13  S17  aromatic  1.724  0.020  1.724
 WXM  N09  C10  single    1.332  0.020  1.332
 WXM  N09  C08  single    1.453  0.020  1.453
 WXM  C10  O11  double    1.226  0.020  1.226
 WXM  C15  C16  aromatic  1.360  0.020  1.360
 WXM  B18  C08  single    1.658  0.020  1.658
 WXM  B18  O20  single    1.472  0.020  1.472
 WXM  B18  O21  single    1.492  0.020  1.492
 WXM  C07  C08  single    1.530  0.020  1.530
 WXM  C07  C06  single    1.533  0.020  1.533
 WXM  S17  C16  aromatic  1.716  0.020  1.716
 WXM  C06  C05  single    1.536  0.020  1.536
 WXM  O21  C05  single    1.392  0.020  1.392
 WXM  C05  C04  single    1.526  0.020  1.526
 WXM  C04  C02  single    1.503  0.020  1.503
 WXM  C02  O01  double    1.208  0.020  1.208
 WXM  C02  O03  single    1.329  0.020  1.329
 WXM  C04  H1   single    0.970  0.020  1.090
 WXM  C04  H2   single    0.970  0.020  1.090
 WXM  C05  H3   single    0.970  0.020  1.090
 WXM  C06  H4   single    0.970  0.020  1.090
 WXM  C06  H5   single    0.970  0.020  1.090
 WXM  C07  H6   single    0.970  0.020  1.090
 WXM  C07  H7   single    0.970  0.020  1.090
 WXM  C08  H8   single    0.970  0.020  1.090
 WXM  C12  H9   single    0.970  0.020  1.090
 WXM  C12  H10  single    0.970  0.020  1.090
 WXM  C14  H11  single    0.930  0.020  1.080
 WXM  C15  H12  single    0.930  0.020  1.080
 WXM  C16  H13  single    0.930  0.020  1.080
 WXM  N09  H14  single    0.860  0.020  1.020
 WXM  O03  H15  single    0.850  0.020  0.980
 WXM  O19  H16  single    0.850  0.020  0.980
 WXM  O20  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
 WXM  O21  B18  O20  110.87  3.000
 WXM  O21  B18  O19  109.17  3.000
 WXM  O20  B18  O19  107.76  3.000
 WXM  O21  B18  C08  107.62  3.000
 WXM  O20  B18  C08  113.32  3.000
 WXM  O19  B18  C08  108.01  3.000
 WXM  O03  C02  O01  122.64  3.000
 WXM  O03  C02  C04  113.22  3.000
 WXM  O01  C02  C04  124.14  3.000
 WXM  H2   C04  H1   107.55  3.000
 WXM  H2   C04  C05  110.08  3.000
 WXM  H1   C04  C05  109.77  3.000
 WXM  H2   C04  C02  111.08  3.000
 WXM  H1   C04  C02  108.15  3.000
 WXM  C05  C04  C02  110.15  3.000
 WXM  H3   C05  O21  111.08  3.000
 WXM  H3   C05  C06  107.64  3.000
 WXM  O21  C05  C06  111.78  3.000
 WXM  H3   C05  C04  106.61  3.000
 WXM  O21  C05  C04  108.48  3.000
 WXM  C06  C05  C04  111.13  3.000
 WXM  H5   C06  H4   106.25  3.000
 WXM  H5   C06  C07  109.75  3.000
 WXM  H4   C06  C07  110.42  3.000
 WXM  H5   C06  C05  110.32  3.000
 WXM  H4   C06  C05  108.58  3.000
 WXM  C07  C06  C05  111.39  3.000
 WXM  H7   C07  H6   106.15  3.000
 WXM  H7   C07  C08  108.94  3.000
 WXM  H6   C07  C08  111.92  3.000
 WXM  H7   C07  C06  109.83  3.000
 WXM  H6   C07  C06  109.49  3.000
 WXM  C08  C07  C06  110.42  3.000
 WXM  H8   C08  N09  107.15  3.000
 WXM  H8   C08  C07  107.69  3.000
 WXM  N09  C08  C07  111.79  3.000
 WXM  H8   C08  B18  110.98  3.000
 WXM  C07  C08  B18  109.57  3.000
 WXM  N09  C08  B18  109.63  3.000
 WXM  H10  C12  H9   106.47  3.000
 WXM  H10  C12  C13  111.08  3.000
 WXM  H9   C12  C13  108.22  3.000
 WXM  H10  C12  C10  111.12  3.000
 WXM  H9   C12  C10  107.20  3.000
 WXM  C13  C12  C10  112.44  3.000
 WXM  S17  C13  C14  110.56  3.000
 WXM  S17  C13  C12  120.97  3.000
 WXM  C14  C13  C12  128.45  3.000
 WXM  H11  C14  C15  124.05  3.000
 WXM  H11  C14  C13  122.71  3.000
 WXM  C15  C14  C13  113.24  3.000
 WXM  H12  C15  C16  123.44  3.000
 WXM  H12  C15  C14  124.01  3.000
 WXM  C16  C15  C14  112.55  3.000
 WXM  H13  C16  S17  120.46  3.000
 WXM  H13  C16  C15  128.25  3.000
 WXM  S17  C16  C15  111.29  3.000
 WXM  H14  N09  C10  118.45  3.000
 WXM  H14  N09  C08  116.01  3.000
 WXM  C10  N09  C08  125.50  3.000
 WXM  H15  O03  C02  109.74  3.000
 WXM  H16  O19  B18  110.24  3.000
 WXM  H17  O20  B18  109.93  3.000
 WXM  C05  O21  B18  115.31  3.000
 WXM  C16  S17  C13   92.36  3.000
 WXM  O11  C10  N09  124.47  3.000
 WXM  O11  C10  C12  120.77  3.000
 WXM  N09  C10  C12  114.75  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
 WXM  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 WXM  CONST_02  C15  C16  S17  C13     0.00   0.0  0
 WXM  CONST_03  C16  S17  C13  C14     0.00   0.0  0
 WXM  CONST_04  S17  C16  C15  C14     0.00   0.0  0
 WXM  CONST_05  S17  C13  C14  C15     0.00   0.0  0
 WXM  CONST_06  C15  C14  C13  C12   180.00   0.0  0
 WXM  CONST_07  C16  S17  C13  C12   180.00   0.0  0
 WXM  CONST_08  H12  C15  C14  C13   180.00   0.0  0
 WXM  CONST_09  H13  C16  S17  C13   180.00   0.0  0
 WXM  CONST_10  H11  C14  C15  C16   180.00   0.0  0
 WXM  CONST_11  C12  C10  N09  C08   180.00   0.0  0
 WXM  CONST_12  O11  C10  N09  C08     0.00   0.0  0
 WXM  CONST_13  H14  N09  C10  C12     0.00   0.0  0
 WXM  CONST_14  H15  O03  C02  C04   180.00   0.0  0
 WXM  Var_01    C08  C07  C06  C05   -29.00  30.0  1
 WXM  Var_02    C08  B18  O21  C05   -32.21  30.0  1
 WXM  Var_03    C14  C13  C12  C10  -104.85  30.0  2
 WXM  Var_04    O01  C02  C04  C05    58.10  30.0  3
 WXM  Var_05    N09  C10  C12  C13  -140.05  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
 WXM  chir_01  C05  C06  O21  C04  positiv
 WXM  chir_02  C08  N09  C07  B18  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
 WXM  plan-1  C12  0.020
 WXM  plan-1  C13  0.020
 WXM  plan-1  C14  0.020
 WXM  plan-1  C15  0.020
 WXM  plan-1  C16  0.020
 WXM  plan-1  S17  0.020
 WXM  plan-1  H11  0.020
 WXM  plan-1  H12  0.020
 WXM  plan-1  H13  0.020
 WXM  plan-2  C08  0.020
 WXM  plan-2  C12  0.020
 WXM  plan-2  N09  0.020
 WXM  plan-2  O11  0.020
 WXM  plan-2  H14  0.020
 WXM  plan-2  C10  0.020
 WXM  plan-3  C02  0.020
 WXM  plan-3  C04  0.020
 WXM  plan-3  O01  0.020
 WXM  plan-3  O03  0.020
 WXM  plan-3  H15  0.020

