# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 16:45:20 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 1-[1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-6-yl]-3-phenyl-urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[B]1(O)OCc2ccc(NC(=O)Nc3ccccc3)cc12
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 KKH  KKH  1-[1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-6-yl]-3-phenyl-urea  ligand  35  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KKH
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
 KKH  C5   C  CR16  0  -0.231   3.0075   2.2304  -0.1618
 KKH  C4   C  CR16  0  -0.325   1.6481   2.2725  -0.2183
 KKH  C3   C  CR6   0   0.459   0.8734   1.0633  -0.1624
 KKH  C2   C  CR16  0  -0.406   1.5286  -0.1966  -0.0551
 KKH  C1   C  CR56  0   0.004   2.8929  -0.2335   0.0078
 KKH  C6   C  CR56  0  -0.034   3.6275   0.9747  -0.0407
 KKH  C7   C  CH2   0  -0.164   5.0847   0.6938   0.0588
 KKH  O1   O  O     0  -0.569   5.2480  -0.6619   0.2903
 KKH  C11  C  CR16  0  -0.246  -6.2435   0.2570   0.5810
 KKH  C10  C  CR16  0  -0.326  -4.9857   0.8348   0.5376
 KKH  C12  C  CR16  0  -0.262  -6.4693  -0.9736  -0.0214
 KKH  C13  C  CR16  0  -0.250  -5.4247  -1.6104  -0.6762
 KKH  C14  C  CR16  0  -0.290  -4.1610  -1.0392  -0.7353
 KKH  C9   C  CR6   0   0.362  -3.9369   0.1895  -0.1170
 KKH  O4   O  O     0  -0.446  -1.2618  -0.9095  -0.2747
 KKH  N1   N  NH1   0  -0.742  -0.4582   1.2454  -0.2074
 KKH  N2   N  NH1   0  -0.773  -2.7012   0.8562  -0.1514
 KKH  C8   C  C     0   0.766  -1.4833   0.2757  -0.2126
 KKH  B1   B  B     0   0.456   3.9751  -1.4502   0.1091
 KKH  O2   O  OB    0  -0.722   3.7078  -2.2699   1.2744
 KKH  H1   H  HCR6  0   0.284   3.5870   3.1436  -0.2028
 KKH  H2   H  HCR6  0   0.310   1.1307   3.2195  -0.3074
 KKH  H3   H  HCR6  0   0.301   0.9474  -1.1034  -0.0182
 KKH  H4   H  HCH2  0   0.230   5.5708   1.0401  -0.8720
 KKH  H5   H  HCH2  0   0.237   5.5305   1.3113   0.8553
 KKH  H6   H  H     0   0.438   4.7787  -2.6945  -1.2559
 KKH  H8   H  HCR6  0   0.276  -4.8133   1.7907   1.0177
 KKH  H9   H  HCR6  0   0.261  -7.4504  -1.4279   0.0138
 KKH  H10  H  HCR6  0   0.264  -5.5916  -2.5639  -1.1599
 KKH  H11  H  HCR6  0   0.277  -3.3763  -1.5483  -1.2724
 KKH  H12  H  HNH1  0   0.449  -0.7556   2.2126  -0.2620
 KKH  H13  H  HNH1  0   0.430  -2.7508   1.8488   0.0254
 KKH  H14  H  H     0   0.441   4.3489  -2.9817   1.3578
 KKH  O3   O  OB    0  -0.724   3.9787  -2.1697  -1.1591
 KKH  H7   H  HCR6  0   0.265  -7.0462   0.7703   1.0935

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
 KKH  C11  C10  aromatic  1.385  0.020  1.385
 KKH  C11  C12  aromatic  1.389  0.020  1.389
 KKH  C10  C9   aromatic  1.395  0.020  1.395
 KKH  C12  C13  aromatic  1.388  0.020  1.388
 KKH  C9   N2   single    1.405  0.020  1.405
 KKH  C9   C14  aromatic  1.394  0.020  1.394
 KKH  N2   C8   single    1.351  0.020  1.351
 KKH  N1   C8   single    1.411  0.020  1.411
 KKH  N1   C3   single    1.345  0.020  1.345
 KKH  C8   O4   double    1.207  0.020  1.207
 KKH  C13  C14  aromatic  1.388  0.020  1.388
 KKH  C3   C4   aromatic  1.437  0.020  1.437
 KKH  C3   C2   aromatic  1.424  0.020  1.424
 KKH  C4   C5   aromatic  1.361  0.020  1.361
 KKH  C2   C1   aromatic  1.366  0.020  1.366
 KKH  C5   C6   aromatic  1.406  0.020  1.406
 KKH  O2   B1   single    1.450  0.020  1.450
 KKH  C6   C1   aromatic  1.415  0.020  1.415
 KKH  C6   C7   single    1.487  0.020  1.487
 KKH  C1   B1   single    1.631  0.020  1.631
 KKH  O1   C7   single    1.385  0.020  1.385
 KKH  O1   B1   single    1.508  0.020  1.508
 KKH  B1   O3   single    1.458  0.020  1.458
 KKH  C5   H1   single    0.930  0.020  1.080
 KKH  C4   H2   single    0.930  0.020  1.080
 KKH  C2   H3   single    0.930  0.020  1.080
 KKH  C7   H4   single    0.970  0.020  1.090
 KKH  C7   H5   single    0.970  0.020  1.090
 KKH  O3   H6   single    0.850  0.020  0.980
 KKH  C11  H7   single    0.930  0.020  1.080
 KKH  C10  H8   single    0.930  0.020  1.080
 KKH  C12  H9   single    0.930  0.020  1.080
 KKH  C13  H10  single    0.930  0.020  1.080
 KKH  C14  H11  single    0.930  0.020  1.080
 KKH  N1   H12  single    0.860  0.020  1.020
 KKH  N2   H13  single    0.860  0.020  1.020
 KKH  O2   H14  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
 KKH  H1   C5   C6   121.40  3.000
 KKH  H1   C5   C4   120.46  3.000
 KKH  C6   C5   C4   118.15  3.000
 KKH  H2   C4   C3   118.79  3.000
 KKH  H2   C4   C5   120.51  3.000
 KKH  C3   C4   C5   120.70  3.000
 KKH  N1   C3   C2   125.30  3.000
 KKH  C2   C3   C4   119.96  3.000
 KKH  N1   C3   C4   114.74  3.000
 KKH  H3   C2   C1   120.95  3.000
 KKH  H3   C2   C3   119.92  3.000
 KKH  C1   C2   C3   119.13  3.000
 KKH  B1   C1   C6   107.13  3.000
 KKH  B1   C1   C2   133.27  3.000
 KKH  C6   C1   C2   119.59  3.000
 KKH  C7   C6   C1   110.19  3.000
 KKH  C7   C6   C5   127.35  3.000
 KKH  C1   C6   C5   122.47  3.000
 KKH  H5   C7   H4   104.77  3.000
 KKH  H5   C7   O1   112.33  3.000
 KKH  H4   C7   O1   113.30  3.000
 KKH  H5   C7   C6   109.80  3.000
 KKH  H4   C7   C6   108.38  3.000
 KKH  O1   C7   C6   108.16  3.000
 KKH  B1   O1   C7   113.08  3.000
 KKH  H7   C11  C12  120.35  3.000
 KKH  H7   C11  C10  119.39  3.000
 KKH  C12  C11  C10  120.26  3.000
 KKH  H8   C10  C9   119.78  3.000
 KKH  H8   C10  C11  119.92  3.000
 KKH  C9   C10  C11  120.31  3.000
 KKH  H9   C12  C13  120.35  3.000
 KKH  H9   C12  C11  120.37  3.000
 KKH  C13  C12  C11  119.27  3.000
 KKH  H10  C13  C14  118.94  3.000
 KKH  H10  C13  C12  119.95  3.000
 KKH  C14  C13  C12  121.10  3.000
 KKH  H11  C14  C9   121.34  3.000
 KKH  H11  C14  C13  119.29  3.000
 KKH  C9   C14  C13  119.36  3.000
 KKH  N2   C9   C14  123.30  3.000
 KKH  C14  C9   C10  119.69  3.000
 KKH  N2   C9   C10  116.97  3.000
 KKH  H12  N1   C8   116.27  3.000
 KKH  H12  N1   C3   114.93  3.000
 KKH  C8   N1   C3   128.79  3.000
 KKH  H13  N2   C8   118.36  3.000
 KKH  H13  N2   C9   114.78  3.000
 KKH  C8   N2   C9   126.19  3.000
 KKH  N2   C8   N1   111.07  3.000
 KKH  N1   C8   O4   122.79  3.000
 KKH  N2   C8   O4   126.14  3.000
 KKH  O2   B1   O3   114.87  3.000
 KKH  O3   B1   O1   111.12  3.000
 KKH  O2   B1   O1   110.77  3.000
 KKH  O3   B1   C1   108.40  3.000
 KKH  O1   B1   C1   100.23  3.000
 KKH  O2   B1   C1   110.45  3.000
 KKH  H14  O2   B1   111.43  3.000
 KKH  H6   O3   B1   111.04  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
 KKH  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 KKH  CONST_02  C2   C1   C6   C5      0.00   0.0  0
 KKH  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 KKH  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 KKH  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 KKH  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 KKH  CONST_07  C14  C9   C10  C11     0.00   0.0  0
 KKH  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 KKH  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 KKH  CONST_10  C13  C14  C9   C10     0.00   0.0  0
 KKH  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 KKH  CONST_12  C9   C14  C13  C12     0.00   0.0  0
 KKH  CONST_13  N1   C3   C4   C5    180.00   0.0  0
 KKH  CONST_14  N1   C3   C2   C1    180.00   0.0  0
 KKH  CONST_15  N2   C9   C10  C11   180.00   0.0  0
 KKH  CONST_16  N2   C9   C14  C13   180.00   0.0  0
 KKH  CONST_17  H3   C2   C3   C4    180.00   0.0  0
 KKH  CONST_18  H1   C5   C4   C3    180.00   0.0  0
 KKH  CONST_19  H2   C4   C3   C2    180.00   0.0  0
 KKH  CONST_20  H10  C13  C12  C11   180.00   0.0  0
 KKH  CONST_21  H9   C12  C11  C10   180.00   0.0  0
 KKH  CONST_22  H11  C14  C9   C10   180.00   0.0  0
 KKH  CONST_23  H8   C10  C11  C12   180.00   0.0  0
 KKH  CONST_24  H7   C11  C12  C13   180.00   0.0  0
 KKH  CONST_25  C8   N1   C3   C4    180.00   0.0  0
 KKH  CONST_26  C8   N1   C3   C2      0.00   0.0  0
 KKH  CONST_29  H12  N1   C3   C4      0.00   0.0  0
 KKH  CONST_31  O4   C8   N1   C3      0.00   0.0  0
 KKH  CONST_32  O4   C8   N2   C9      0.00   0.0  0
 KKH  CONST_33  N2   C8   N1   C3    180.00   0.0  0
 KKH  CONST_34  N1   C8   N2   C9    180.00   0.0  0
 KKH  Var_01    O1   C7   C6   C5    174.42  30.0  1
 KKH  Var_02    O1   B1   C1   C2   -173.90  30.0  1

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
 KKH  plan-1  C11  0.020
 KKH  plan-1  C10  0.020
 KKH  plan-1  C12  0.020
 KKH  plan-1  C13  0.020
 KKH  plan-1  C14  0.020
 KKH  plan-1  C9   0.020
 KKH  plan-1  N2   0.020
 KKH  plan-1  H8   0.020
 KKH  plan-1  H9   0.020
 KKH  plan-1  H10  0.020
 KKH  plan-1  H11  0.020
 KKH  plan-1  H7   0.020
 KKH  plan-2  C5   0.020
 KKH  plan-2  C4   0.020
 KKH  plan-2  C3   0.020
 KKH  plan-2  C2   0.020
 KKH  plan-2  C1   0.020
 KKH  plan-2  C6   0.020
 KKH  plan-2  C7   0.020
 KKH  plan-2  N1   0.020
 KKH  plan-2  B1   0.020
 KKH  plan-2  H1   0.020
 KKH  plan-2  H2   0.020
 KKH  plan-2  H3   0.020
 KKH  plan-3  C3   0.020
 KKH  plan-3  C9   0.020
 KKH  plan-3  O4   0.020
 KKH  plan-3  N1   0.020
 KKH  plan-3  N2   0.020
 KKH  plan-3  C8   0.020
 KKH  plan-3  H12  0.020
 KKH  plan-3  H13  0.020

