# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 01:09:54 2022
#   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  37  21  .  2022-03-29  2022-03-29
;
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   0.499  14.3086  -4.3726   -9.8464
 WXM  C02  C  C      0   0.401  17.3709  -5.4875   -7.0737
 WXM  C04  C  CH2    0  -0.582  16.6624  -6.5720   -7.9064
 WXM  C05  C  CH1    0   0.083  15.3342  -6.1412   -8.5051
 WXM  C06  C  CH2    0  -0.444  14.6264  -7.3180   -9.1992
 WXM  C07  C  CH2    0  -0.439  13.5855  -6.8402  -10.2193
 WXM  C08  C  CH1    0  -0.253  13.0582  -5.4602   -9.8215
 WXM  C12  C  CH2    0  -0.660   9.7911  -4.8035  -11.6792
 WXM  C13  C  CR5    0  -0.113   8.4971  -4.3501  -11.0946
 WXM  C14  C  CR15   0  -0.243   7.2714  -4.9359  -11.1880
 WXM  C15  C  CR15   0  -0.180   6.2600  -4.2401  -10.4676
 WXM  C16  C  CR15   0  -0.471   6.7374  -3.1368   -9.8318
 WXM  N09  N  NH1    0  -0.644  11.9882  -5.0099  -10.6951
 WXM  O01  O  O      0  -0.619  18.6082  -5.3868   -7.2121
 WXM  O03  O  OC    -1  -0.617  16.6585  -4.8142   -6.2985
 WXM  O11  O  O      0  -0.505  10.2794  -6.1900   -9.7893
 WXM  O19  O  OB     0  -0.745  14.4747  -3.9293  -11.2331
 WXM  O20  O  OB     0  -0.725  14.0503  -3.1776   -9.0192
 WXM  O21  O  OC2    0  -0.565  15.5363  -5.0801   -9.3935
 WXM  S17  S  S2     0   0.203   8.4178  -2.9345  -10.1118
 WXM  H1   H  HCH2   0   0.204  16.4817  -7.4359   -7.2532
 WXM  H2   H  HCH2   0   0.185  17.3216  -6.9296   -8.7043
 WXM  H3   H  HCH1   0   0.146  14.6970  -5.8264   -7.6614
 WXM  H4   H  HCH2   0   0.198  14.1501  -7.9378   -8.4324
 WXM  H5   H  HCH2   0   0.199  15.3610  -7.9623   -9.6943
 WXM  H6   H  HCH2   0   0.197  12.7811  -7.5781  -10.3056
 WXM  H7   H  HCH2   0   0.196  14.0408  -6.7733  -11.2123
 WXM  H8   H  HCH1   0   0.179  12.6344  -5.5425   -8.8120
 WXM  H9   H  HCH2   0   0.288   9.5800  -5.5873  -12.4114
 WXM  H10  H  HCH2   0   0.272  10.2785  -3.9931  -12.2260
 WXM  H11  H  HCR5   0   0.258   7.0969  -5.8388  -11.7573
 WXM  H12  H  HCR5   0   0.261   5.2254  -4.5498  -10.4261
 WXM  H13  H  HCR5   0   0.290   6.1947  -2.4309   -9.2221
 WXM  H14  H  HNH1   0   0.384  12.2494  -4.3535  -11.4148
 WXM  H16  H  H      0   0.428  15.0364  -3.1511  -11.2574
 WXM  H17  H  H      0   0.411  14.1232  -3.4165   -8.0918
 WXM  C10  C  C      0   0.523  10.7171  -5.4030  -10.6222

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    1.465  0.020  1.465
 WXM  C12  C13  single    1.491  0.020  1.491
 WXM  C12  C10  single    1.528  0.020  1.528
 WXM  C14  C13  aromatic  1.362  0.020  1.362
 WXM  C14  C15  aromatic  1.423  0.020  1.423
 WXM  C13  S17  aromatic  1.725  0.020  1.725
 WXM  N09  C10  single    1.332  0.020  1.332
 WXM  N09  C08  single    1.453  0.020  1.453
 WXM  C10  O11  double    1.227  0.020  1.227
 WXM  C15  C16  aromatic  1.360  0.020  1.360
 WXM  B18  C08  single    1.657  0.020  1.657
 WXM  B18  O20  single    1.476  0.020  1.476
 WXM  B18  O21  single    1.488  0.020  1.488
 WXM  C07  C08  single    1.530  0.020  1.530
 WXM  C07  C06  single    1.534  0.020  1.534
 WXM  S17  C16  aromatic  1.715  0.020  1.715
 WXM  C06  C05  single    1.539  0.020  1.539
 WXM  O21  C05  single    1.399  0.020  1.399
 WXM  C05  C04  single    1.519  0.020  1.519
 WXM  C04  C02  single    1.540  0.020  1.540
 WXM  C02  O01  deloc     1.249  0.020  1.249
 WXM  C02  O03  deloc     1.250  0.020  1.250
 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  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  111.03  3.000
 WXM  O21  B18  O19  109.78  3.000
 WXM  O20  B18  O19  107.77  3.000
 WXM  O21  B18  C08  107.82  3.000
 WXM  O20  B18  C08  113.00  3.000
 WXM  O19  B18  C08  107.35  3.000
 WXM  O03  C02  O01  126.16  3.000
 WXM  O03  C02  C04  116.91  3.000
 WXM  O01  C02  C04  116.91  3.000
 WXM  H2   C04  H1   106.00  3.000
 WXM  H2   C04  C05  109.37  3.000
 WXM  H1   C04  C05  108.28  3.000
 WXM  H2   C04  C02  110.30  3.000
 WXM  H1   C04  C02  107.95  3.000
 WXM  C05  C04  C02  114.56  3.000
 WXM  H3   C05  O21  110.66  3.000
 WXM  H3   C05  C06  107.31  3.000
 WXM  O21  C05  C06  111.11  3.000
 WXM  H3   C05  C04  106.52  3.000
 WXM  O21  C05  C04  109.82  3.000
 WXM  C06  C05  C04  111.29  3.000
 WXM  H5   C06  H4   105.98  3.000
 WXM  H5   C06  C07  109.74  3.000
 WXM  H4   C06  C07  110.30  3.000
 WXM  H5   C06  C05  110.19  3.000
 WXM  H4   C06  C05  108.49  3.000
 WXM  C07  C06  C05  111.96  3.000
 WXM  H7   C07  H6   105.98  3.000
 WXM  H7   C07  C08  108.91  3.000
 WXM  H6   C07  C08  112.03  3.000
 WXM  H7   C07  C06  109.89  3.000
 WXM  H6   C07  C06  109.94  3.000
 WXM  C08  C07  C06  110.00  3.000
 WXM  H8   C08  N09  106.97  3.000
 WXM  H8   C08  C07  107.72  3.000
 WXM  N09  C08  C07  112.15  3.000
 WXM  H8   C08  B18  110.74  3.000
 WXM  C07  C08  B18  109.14  3.000
 WXM  N09  C08  B18  110.08  3.000
 WXM  H10  C12  H9   106.43  3.000
 WXM  H10  C12  C13  110.98  3.000
 WXM  H9   C12  C13  108.25  3.000
 WXM  H10  C12  C10  111.53  3.000
 WXM  H9   C12  C10  107.40  3.000
 WXM  C13  C12  C10  111.97  3.000
 WXM  S17  C13  C14  110.53  3.000
 WXM  S17  C13  C12  120.86  3.000
 WXM  C14  C13  C12  128.58  3.000
 WXM  H11  C14  C15  124.04  3.000
 WXM  H11  C14  C13  122.72  3.000
 WXM  C15  C14  C13  113.24  3.000
 WXM  H12  C15  C16  123.41  3.000
 WXM  H12  C15  C14  124.03  3.000
 WXM  C16  C15  C14  112.57  3.000
 WXM  H13  C16  S17  120.51  3.000
 WXM  H13  C16  C15  128.19  3.000
 WXM  S17  C16  C15  111.30  3.000
 WXM  H14  N09  C10  118.56  3.000
 WXM  H14  N09  C08  116.11  3.000
 WXM  C10  N09  C08  125.33  3.000
 WXM  H16  O19  B18  109.60  3.000
 WXM  H17  O20  B18  109.05  3.000
 WXM  C05  O21  B18  115.78  3.000
 WXM  C16  S17  C13   92.37  3.000
 WXM  O11  C10  N09  124.53  3.000
 WXM  O11  C10  C12  120.35  3.000
 WXM  N09  C10  C12  115.12  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  Var_01    C08  C07  C06  C05   -27.01  30.0  1
 WXM  Var_02    C08  B18  O21  C05   -29.04  30.0  1
 WXM  Var_03    C14  C13  C12  C10  -105.27  30.0  2
 WXM  Var_04    O01  C02  C04  C05  -138.92  30.0  3
 WXM  Var_05    N09  C10  C12  C13  -135.71  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

