# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 17:47:36 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-4-yl]-3-(phenylmethyl)thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[B-]1(O)OCc2ccc(NC(=S)NCc3ccccc3)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
 KL5  KL5  1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1(6),2,4-trien-4-yl]-3-(phenylmethyl)thiourea  ligand  38  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KL5
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
 KL5  C14  C  CR16   0  -0.241   6.5278  -1.7153  -0.3782
 KL5  C13  C  CR16   0  -0.264   7.0003  -1.2572   0.8436
 KL5  C12  C  CR16   0  -0.241   6.3564  -0.2027   1.4809
 KL5  C15  C  CR16   0  -0.294   5.4135  -1.1221  -0.9596
 KL5  C1   C  CR56   0  -0.044  -3.5137  -0.3442   0.1484
 KL5  C2   C  CR16   0  -0.438  -2.1535  -0.6134   0.0619
 KL5  C3   C  CR6    0   0.339  -1.2160   0.3928   0.2843
 KL5  C4   C  CR16   0  -0.284  -1.6375   1.6825   0.6047
 KL5  C5   C  CR16   0  -0.304  -2.9943   1.9666   0.6752
 KL5  C6   C  CR56   0  -0.093  -3.9149   0.9522   0.4468
 KL5  C7   C  CH2    0  -0.148  -5.4174   1.0422   0.4844
 KL5  C8   C  C      0   0.402   1.1412   0.6621  -0.4369
 KL5  C10  C  CR6    0   0.053   4.7652  -0.0648  -0.3305
 KL5  C11  C  CR16   0  -0.280   5.2460   0.3886   0.8965
 KL5  S1   S  S1     0  -0.428   0.8925   1.9690  -1.4638
 KL5  N1   N  NH1    0  -0.727   0.1556   0.0534   0.2562
 KL5  N2   N  NH1    0  -0.614   2.3580   0.1326  -0.2553
 KL5  B1   B  B     -1   0.416  -4.8396  -1.2541  -0.0373
 KL5  O1   O  O      0  -0.583  -5.9166  -0.2304   0.2090
 KL5  O2   O  OB     0  -0.736  -4.9157  -1.7709  -1.4070
 KL5  H1   H  HCR6   0   0.258   7.0257  -2.5338  -0.8817
 KL5  H2   H  HCR6   0   0.258   7.8682  -1.7174   1.2979
 KL5  H3   H  HCR6   0   0.258   6.7222   0.1609   2.4324
 KL5  H4   H  HCR6   0   0.255   5.0481  -1.4830  -1.9137
 KL5  H5   H  HCR6   0   0.239  -1.8006  -1.6114  -0.1821
 KL5  H6   H  HCR6   0   0.247  -0.9078   2.4561   0.7979
 KL5  H7   H  HCR6   0   0.233  -3.3159   2.9728   0.9220
 KL5  H8   H  HCH2   0   0.186  -5.7550   1.4100   1.4668
 KL5  H9   H  HCH2   0   0.186  -5.7761   1.7877  -0.2440
 KL5  H10  H  HCH2   0   0.258   3.6166   1.6595  -0.8884
 KL5  H11  H  HCH2   0   0.253   3.4907   0.3200  -2.0126
 KL5  H12  H  HCR6   0   0.255   4.7512   1.2140   1.3953
 KL5  H13  H  H      0   0.428  -5.7439  -2.7421   0.9918
 KL5  H14  H  HNH1   0   0.403   0.3873  -0.8215   0.7050
 KL5  H15  H  HNH1   0   0.403   2.4537  -0.6745   0.3441
 KL5  H16  H  H      0   0.427  -5.7104  -2.2973  -1.5344
 KL5  C9   C  CH2    0  -0.304   3.5520   0.5720  -0.9507
 KL5  O3   O  OB     0  -0.735  -4.8852  -2.3090   0.9789

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
 KL5  N2   C9   single    1.450  0.020  1.450
 KL5  N2   C8   single    1.339  0.020  1.339
 KL5  S1   C8   double    1.681  0.020  1.681
 KL5  C9   C10  single    1.504  0.020  1.504
 KL5  C8   N1   single    1.350  0.020  1.350
 KL5  C15  C10  aromatic  1.391  0.020  1.391
 KL5  C15  C14  aromatic  1.390  0.020  1.390
 KL5  C10  C11  aromatic  1.394  0.020  1.394
 KL5  N1   C3   single    1.413  0.020  1.413
 KL5  C14  C13  aromatic  1.388  0.020  1.388
 KL5  C3   C2   aromatic  1.393  0.020  1.393
 KL5  C3   C4   aromatic  1.394  0.020  1.394
 KL5  O2   B1   single    1.466  0.020  1.466
 KL5  C2   C1   aromatic  1.389  0.020  1.389
 KL5  C11  C12  aromatic  1.387  0.020  1.387
 KL5  C13  C12  aromatic  1.390  0.020  1.390
 KL5  C4   C5   aromatic  1.388  0.020  1.388
 KL5  C1   B1   single    1.619  0.020  1.619
 KL5  C1   C6   aromatic  1.389  0.020  1.389
 KL5  B1   O1   single    1.506  0.020  1.506
 KL5  B1   O3   single    1.465  0.020  1.465
 KL5  C5   C6   aromatic  1.389  0.020  1.389
 KL5  C6   C7   single    1.506  0.020  1.506
 KL5  O1   C7   single    1.394  0.020  1.394
 KL5  C14  H1   single    0.930  0.020  1.080
 KL5  C13  H2   single    0.930  0.020  1.080
 KL5  C12  H3   single    0.930  0.020  1.080
 KL5  C15  H4   single    0.930  0.020  1.080
 KL5  C2   H5   single    0.930  0.020  1.080
 KL5  C4   H6   single    0.930  0.020  1.080
 KL5  C5   H7   single    0.930  0.020  1.080
 KL5  C7   H8   single    0.970  0.020  1.090
 KL5  C7   H9   single    0.970  0.020  1.090
 KL5  C9   H10  single    0.970  0.020  1.090
 KL5  C9   H11  single    0.970  0.020  1.090
 KL5  C11  H12  single    0.930  0.020  1.080
 KL5  O3   H13  single    0.850  0.020  0.980
 KL5  N1   H14  single    0.860  0.020  1.020
 KL5  N2   H15  single    0.860  0.020  1.020
 KL5  O2   H16  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
 KL5  H1   C14  C15  119.80  3.000
 KL5  H1   C14  C13  120.17  3.000
 KL5  C15  C14  C13  120.03  3.000
 KL5  H2   C13  C12  120.10  3.000
 KL5  H2   C13  C14  120.15  3.000
 KL5  C12  C13  C14  119.75  3.000
 KL5  H3   C12  C11  119.85  3.000
 KL5  H3   C12  C13  120.09  3.000
 KL5  C11  C12  C13  120.06  3.000
 KL5  H4   C15  C10  119.62  3.000
 KL5  H4   C15  C14  119.78  3.000
 KL5  C10  C15  C14  120.60  3.000
 KL5  B1   C1   C6   108.21  3.000
 KL5  C6   C1   C2   118.49  3.000
 KL5  B1   C1   C2   133.30  3.000
 KL5  H5   C2   C3   118.73  3.000
 KL5  H5   C2   C1   120.67  3.000
 KL5  C3   C2   C1   120.60  3.000
 KL5  N1   C3   C4   121.34  3.000
 KL5  C4   C3   C2   120.09  3.000
 KL5  N1   C3   C2   118.46  3.000
 KL5  H6   C4   C5   120.28  3.000
 KL5  H6   C4   C3   119.94  3.000
 KL5  C5   C4   C3   119.78  3.000
 KL5  H7   C5   C6   121.22  3.000
 KL5  H7   C5   C4   119.42  3.000
 KL5  C6   C5   C4   119.35  3.000
 KL5  C7   C6   C5   127.86  3.000
 KL5  C7   C6   C1   110.44  3.000
 KL5  C5   C6   C1   121.69  3.000
 KL5  H9   C7   H8   105.29  3.000
 KL5  H9   C7   O1   111.74  3.000
 KL5  H8   C7   O1   111.78  3.000
 KL5  H9   C7   C6   110.40  3.000
 KL5  H8   C7   C6   110.36  3.000
 KL5  O1   C7   C6   107.32  3.000
 KL5  N2   C8   N1   114.55  3.000
 KL5  N1   C8   S1   123.80  3.000
 KL5  N2   C8   S1   121.65  3.000
 KL5  C11  C10  C9   120.24  3.000
 KL5  C11  C10  C15  119.00  3.000
 KL5  C9   C10  C15  120.76  3.000
 KL5  H12  C11  C10  119.69  3.000
 KL5  H12  C11  C12  119.75  3.000
 KL5  C10  C11  C12  120.56  3.000
 KL5  H14  N1   C8   116.81  3.000
 KL5  H14  N1   C3   114.95  3.000
 KL5  C8   N1   C3   127.63  3.000
 KL5  H15  N2   C9   116.67  3.000
 KL5  H15  N2   C8   118.85  3.000
 KL5  C9   N2   C8   124.28  3.000
 KL5  O2   B1   O1   110.81  3.000
 KL5  O1   B1   O3   110.71  3.000
 KL5  O2   B1   O3   113.11  3.000
 KL5  O3   B1   C1   110.53  3.000
 KL5  O1   B1   C1   100.65  3.000
 KL5  O2   B1   C1   110.35  3.000
 KL5  B1   O1   C7   113.36  3.000
 KL5  H16  O2   B1   111.08  3.000
 KL5  H11  C9   H10  106.77  3.000
 KL5  H11  C9   N2   110.48  3.000
 KL5  H10  C9   N2   108.87  3.000
 KL5  H11  C9   C10  110.38  3.000
 KL5  H10  C9   C10  110.53  3.000
 KL5  N2   C9   C10  109.76  3.000
 KL5  H13  O3   B1   111.18  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
 KL5  CONST_01  C11  C10  C15  C14     0.00   0.0  0
 KL5  CONST_02  C11  C12  C13  C14     0.00   0.0  0
 KL5  CONST_03  C10  C15  C14  C13     0.00   0.0  0
 KL5  CONST_04  C10  C11  C12  C13     0.00   0.0  0
 KL5  CONST_05  C15  C10  C11  C12     0.00   0.0  0
 KL5  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 KL5  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 KL5  CONST_08  C4   C5   C6   C1      0.00   0.0  0
 KL5  CONST_09  C5   C4   C3   C2      0.00   0.0  0
 KL5  CONST_10  C5   C6   C1   C2      0.00   0.0  0
 KL5  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 KL5  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 KL5  CONST_13  C9   C10  C15  C14   180.00   0.0  0
 KL5  CONST_14  C9   C10  C11  C12   180.00   0.0  0
 KL5  CONST_15  N1   C3   C2   C1    180.00   0.0  0
 KL5  CONST_16  N1   C3   C4   C5    180.00   0.0  0
 KL5  CONST_17  H3   C12  C13  C14   180.00   0.0  0
 KL5  CONST_18  H4   C15  C14  C13   180.00   0.0  0
 KL5  CONST_19  H12  C11  C12  C13   180.00   0.0  0
 KL5  CONST_20  H1   C14  C13  C12   180.00   0.0  0
 KL5  CONST_21  H2   C13  C14  C15   180.00   0.0  0
 KL5  CONST_22  H7   C5   C6   C1    180.00   0.0  0
 KL5  CONST_23  H6   C4   C3   C2    180.00   0.0  0
 KL5  CONST_24  H5   C2   C3   C4    180.00   0.0  0
 KL5  CONST_28  N2   C8   N1   C3    180.00   0.0  0
 KL5  CONST_29  S1   C8   N1   C3      0.00   0.0  0
 KL5  CONST_30  S1   C8   N2   C9      0.00   0.0  0
 KL5  CONST_31  N1   C8   N2   C9    180.00   0.0  0
 KL5  CONST_32  H15  N2   C8   S1    180.00   0.0  0
 KL5  Var_01    O1   C7   C6   C1      0.31  30.0  1
 KL5  Var_02    O1   B1   C1   C2   -179.67  30.0  1
 KL5  Var_03    N2   C9   C10  C15   104.14  30.0  2
 KL5  Var_04    C10  C9   N2   C8    169.95  30.0  3

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
 KL5  plan-1  C14  0.020
 KL5  plan-1  C13  0.020
 KL5  plan-1  C12  0.020
 KL5  plan-1  C15  0.020
 KL5  plan-1  C10  0.020
 KL5  plan-1  C11  0.020
 KL5  plan-1  H1   0.020
 KL5  plan-1  H2   0.020
 KL5  plan-1  H3   0.020
 KL5  plan-1  H4   0.020
 KL5  plan-1  H12  0.020
 KL5  plan-1  C9   0.020
 KL5  plan-2  C1   0.020
 KL5  plan-2  C2   0.020
 KL5  plan-2  C3   0.020
 KL5  plan-2  C4   0.020
 KL5  plan-2  C5   0.020
 KL5  plan-2  C6   0.020
 KL5  plan-2  C7   0.020
 KL5  plan-2  N1   0.020
 KL5  plan-2  B1   0.020
 KL5  plan-2  H5   0.020
 KL5  plan-2  H6   0.020
 KL5  plan-2  H7   0.020
 KL5  plan-3  C3   0.020
 KL5  plan-3  C8   0.020
 KL5  plan-3  S1   0.020
 KL5  plan-3  N1   0.020
 KL5  plan-3  N2   0.020
 KL5  plan-3  H14  0.020
 KL5  plan-3  H15  0.020
 KL5  plan-3  C9   0.020

