# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 04:13:43 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: [4-[(4~{S})-4-oxidanyl-5-oxidanylidene-1,3,2-dioxaborolan-2-yl]phenyl]methyl carbamimidothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)SCc1ccc(cc1)B2O[C@H](O)C(=O)O2
#
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
 J3T  J3T  '[4-[(4~{S})-4-oxidanyl-5-oxidanylidene-1,3,2-dioxaborolan-2-yl]phenyl]methyl carbamimidothioate'  ligand  29  18  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J3T
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
 J3T  C2   C  CR6   0   0.085  -1.6067  -0.1867   0.7009
 J3T  C3   C  CR16  0  -0.265  -0.9118   1.0126   0.8348
 J3T  C4   C  CR16  0  -0.292   0.4494   1.0661   0.5860
 J3T  C6   C  CH1   0   0.147   4.7740  -0.6220  -0.6252
 J3T  C7   C  C     0   0.498   4.7034   0.8497  -0.2072
 J3T  C8   C  CR16  0  -0.294   0.4441  -1.2736   0.0493
 J3T  C9   C  CR16  0  -0.265  -0.9168  -1.3281   0.2999
 J3T  N1   N  NH2   0  -0.806  -6.4440   0.3557  -1.1871
 J3T  N    N  N     0  -0.644  -5.9324  -0.0827   1.0855
 J3T  C    C  C     0   0.282  -5.6208   0.0998  -0.1319
 J3T  C1   C  CH2   0  -0.613  -3.0828  -0.2413   0.9563
 J3T  C5   C  CR6   0  -0.115   1.1522  -0.0762   0.1891
 J3T  B    B  B     0   0.653   2.6653  -0.0227  -0.0781
 J3T  O    O  O2    0  -0.460   3.4326  -1.0620  -0.4961
 J3T  O3   O  O2    0  -0.449   3.4278   1.1381   0.0924
 J3T  O2   O  O     0  -0.374   5.5998   1.6310  -0.1443
 J3T  H1   H  HCR6  0   0.261  -1.4385   1.9074   1.1434
 J3T  H2   H  HCR6  0   0.263   0.9653   2.0106   0.7065
 J3T  H3   H  HCH1  0   0.282   5.0678  -0.7106  -1.6768
 J3T  H4   H  HCR6  0   0.263   0.9561  -2.1777  -0.2558
 J3T  H5   H  HCR6  0   0.261  -1.4488  -2.2655   0.1903
 J3T  H6   H  HNH2  0   0.398  -7.4260   0.1683  -1.0573
 J3T  H7   H  HNH2  0   0.399  -6.1168   0.1670  -2.1211
 J3T  H8   H  H     0   0.334  -6.9412  -0.0765   1.2115
 J3T  H9   H  HCH2  0   0.296  -3.3925  -1.2266   1.3015
 J3T  H10  H  HCH2  0   0.297  -3.3887   0.4979   1.6944
 J3T  H11  H  HOH1  0   0.483   5.9533  -2.0783  -0.1973
 J3T  O1   O  OH1   0  -0.635   5.6271  -1.2745   0.2222
 J3T  S    S  S2    0   0.013  -3.9123   0.1270  -0.6189

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
 J3T  O2  C7   double    1.191  0.020  1.191
 J3T  C7  C6   single    1.531  0.020  1.531
 J3T  C7  O3   single    1.342  0.020  1.342
 J3T  O1  C6   single    1.368  0.020  1.368
 J3T  C6  O    single    1.418  0.020  1.418
 J3T  O3  B    single    1.399  0.020  1.399
 J3T  B   O    single    1.358  0.020  1.358
 J3T  B   C5   single    1.537  0.020  1.537
 J3T  C5  C4   aromatic  1.399  0.020  1.399
 J3T  C5  C8   aromatic  1.398  0.020  1.398
 J3T  C4  C3   aromatic  1.385  0.020  1.385
 J3T  C8  C9   aromatic  1.385  0.020  1.385
 J3T  C3  C2   aromatic  1.393  0.020  1.393
 J3T  C9  C2   aromatic  1.393  0.020  1.393
 J3T  C2  C1   single    1.499  0.020  1.499
 J3T  C1  S    single    1.818  0.020  1.818
 J3T  S   C    single    1.777  0.020  1.777
 J3T  N   C    double    1.270  0.020  1.270
 J3T  C   N1   single    1.363  0.020  1.363
 J3T  C3  H1   single    0.930  0.020  1.080
 J3T  C4  H2   single    0.930  0.020  1.080
 J3T  C6  H3   single    0.970  0.020  1.090
 J3T  C8  H4   single    0.930  0.020  1.080
 J3T  C9  H5   single    0.930  0.020  1.080
 J3T  N1  H6   single    0.890  0.020  1.040
 J3T  N1  H7   single    0.890  0.020  1.040
 J3T  N   H8   single    0.890  0.020  1.040
 J3T  C1  H9   single    0.970  0.020  1.090
 J3T  C1  H10  single    0.970  0.020  1.090
 J3T  O1  H11  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
 J3T  C1   C2  C9  120.46  3.000
 J3T  C1   C2  C3  120.43  3.000
 J3T  C9   C2  C3  119.10  3.000
 J3T  H1   C3  C4  119.82  3.000
 J3T  H1   C3  C2  119.75  3.000
 J3T  C4   C3  C2  120.43  3.000
 J3T  H2   C4  C5  120.29  3.000
 J3T  H2   C4  C3  118.82  3.000
 J3T  C5   C4  C3  120.89  3.000
 J3T  H3   C6  O1  112.88  3.000
 J3T  H3   C6  O   108.42  3.000
 J3T  O1   C6  O   112.68  3.000
 J3T  H3   C6  C7  110.61  3.000
 J3T  O    C6  C7  103.28  3.000
 J3T  O1   C6  C7  108.55  3.000
 J3T  O2   C7  O3  124.26  3.000
 J3T  O3   C7  C6  108.14  3.000
 J3T  O2   C7  C6  127.60  3.000
 J3T  H4   C8  C5  120.25  3.000
 J3T  H4   C8  C9  118.87  3.000
 J3T  C5   C8  C9  120.89  3.000
 J3T  H5   C9  C8  119.88  3.000
 J3T  H5   C9  C2  119.67  3.000
 J3T  C8   C9  C2  120.44  3.000
 J3T  H7   N1  H6  113.63  3.000
 J3T  H7   N1  C   119.11  3.000
 J3T  H6   N1  C   116.99  3.000
 J3T  H8   N   C   111.19  3.000
 J3T  S    C   N   120.06  3.000
 J3T  N    C   N1  128.40  3.000
 J3T  S    C   N1  111.46  3.000
 J3T  H10  C1  H9  108.64  3.000
 J3T  H10  C1  S   108.76  3.000
 J3T  H9   C1  S   109.16  3.000
 J3T  H10  C1  C2  111.56  3.000
 J3T  H9   C1  C2  111.54  3.000
 J3T  S    C1  C2  107.11  3.000
 J3T  B    C5  C8  120.72  3.000
 J3T  C8   C5  C4  118.25  3.000
 J3T  B    C5  C4  121.03  3.000
 J3T  O3   B   O   111.38  3.000
 J3T  O    B   C5  125.66  3.000
 J3T  O3   B   C5  122.96  3.000
 J3T  B    O   C6  108.98  3.000
 J3T  B    O3  C7  108.22  3.000
 J3T  H11  O1  C6  109.84  3.000
 J3T  C1   S   C   101.43  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
 J3T  CONST_01  C5  C4  C3  C2     0.00   0.0  0
 J3T  CONST_02  C5  C8  C9  C2     0.00   0.0  0
 J3T  CONST_03  C8  C5  C4  C3     0.00   0.0  0
 J3T  CONST_04  C8  C9  C2  C3     0.00   0.0  0
 J3T  CONST_05  C9  C8  C5  C4     0.00   0.0  0
 J3T  CONST_06  C9  C2  C3  C4     0.00   0.0  0
 J3T  CONST_07  B   C5  C4  C3   180.00   0.0  0
 J3T  CONST_08  B   C5  C8  C9   180.00   0.0  0
 J3T  CONST_09  C1  C2  C3  C4   180.00   0.0  0
 J3T  CONST_10  C1  C2  C9  C8   180.00   0.0  0
 J3T  CONST_11  H2  C4  C3  C2   180.00   0.0  0
 J3T  CONST_12  H4  C8  C9  C2   180.00   0.0  0
 J3T  CONST_13  H5  C9  C2  C3   180.00   0.0  0
 J3T  CONST_14  H1  C3  C2  C9   180.00   0.0  0
 J3T  CONST_15  H8  N   C   N1     0.00   0.0  0
 J3T  Var_01    O3  B   C5  C4     1.88  30.0  2
 J3T  Var_02    O2  C7  O3  B   -179.14  30.0  1
 J3T  Var_03    S   C1  C2  C3    89.13  30.0  2

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
 J3T  chir_01  C6  C7  O1  O  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
 J3T  plan-1  C2  0.020
 J3T  plan-1  C3  0.020
 J3T  plan-1  C4  0.020
 J3T  plan-1  C8  0.020
 J3T  plan-1  C9  0.020
 J3T  plan-1  C1  0.020
 J3T  plan-1  C5  0.020
 J3T  plan-1  B   0.020
 J3T  plan-1  H1  0.020
 J3T  plan-1  H2  0.020
 J3T  plan-1  H4  0.020
 J3T  plan-1  H5  0.020
 J3T  plan-2  C6  0.020
 J3T  plan-2  C7  0.020
 J3T  plan-2  O3  0.020
 J3T  plan-2  O2  0.020
 J3T  plan-3  N1  0.020
 J3T  plan-3  N   0.020
 J3T  plan-3  C   0.020
 J3T  plan-3  H6  0.020
 J3T  plan-3  H7  0.020
 J3T  plan-3  H8  0.020
 J3T  plan-3  S   0.020

