# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 18:02:03 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(phenylmethyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[B-]1(O)OCc2ccc(NC(=O)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
 R29  R29  1-[7,7-bis(oxidanyl)-8-oxa-7-boranuidabicyclo[4.3.0]nona-1,3,5-trien-4-yl]-3-(phenylmethyl)urea  ligand  38  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R29
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
 R29  C1   C  CR56   0   0.055  -2.9263   0.1717  -0.1994
 R29  C2   C  CR16   0  -0.371  -1.6921  -0.2886   0.2557
 R29  C3   C  CR6    0   0.320  -0.9363   0.4817   1.1419
 R29  C4   C  CR16   0  -0.347  -1.4370   1.7132   1.5776
 R29  C5   C  CR16   0  -0.274  -2.6711   2.1713   1.1388
 R29  C6   C  CR56   0  -0.103  -3.4017   1.3981   0.2478
 R29  C7   C  CH2    0  -0.203  -4.7504   1.6941  -0.3536
 R29  C8   C  C      0   0.688   1.2385  -0.7120   1.0610
 R29  C9   C  CH2    0  -0.328   3.5013  -1.6004   1.2610
 R29  C10  C  CR6    0  -0.005   4.2572  -0.7851   0.2395
 R29  C11  C  CR16   0  -0.203   4.3347  -1.1936  -1.0868
 R29  C12  C  CR16   0  -0.296   5.0325  -0.4392  -2.0226
 R29  C13  C  CR16   0  -0.136   5.6559   0.7402  -1.6402
 R29  C14  C  CR16   0  -0.333   5.5807   1.1590  -0.3166
 R29  C15  C  CR16   0  -0.209   4.8871   0.3997   0.6146
 R29  O1   O  O      0  -0.503  -5.0655   0.6334  -1.2034
 R29  O4   O  O      0  -0.441   1.1004  -1.2048  -0.0492
 R29  N1   N  NH1    0  -0.774   0.2933   0.0645   1.6766
 R29  N2   N  NH1    0  -0.668   2.3518  -0.9209   1.8123
 R29  B1   B  B     -1   0.148  -4.0309  -0.4595  -1.1990
 R29  O2   O  OB     0  -0.711  -3.4727  -0.6439  -2.5423
 R29  H1   H  HCR6   0   0.251  -1.3230  -1.2520  -0.0675
 R29  H2   H  HCR6   0   0.232  -0.8535   2.3144   2.2660
 R29  H3   H  HCR6   0   0.243  -3.0405   3.1274   1.4946
 R29  H4   H  HCH2   0   0.218  -5.5062   1.8204   0.4393
 R29  H5   H  HCH2   0   0.129  -4.7333   2.6543  -0.8948
 R29  H6   H  HCH2   0   0.247   3.1924  -2.5503   0.8237
 R29  H7   H  HCH2   0   0.264   4.1546  -1.8415   2.1006
 R29  H8   H  HCR6   0   0.261   3.8453  -2.1103  -1.3925
 R29  H9   H  HCR6   0   0.192   5.0837  -0.7709  -3.0519
 R29  H10  H  HCR6   0   0.267   6.1993   1.3298  -2.3672
 R29  H11  H  HCR6   0   0.239   6.0661   2.0766  -0.0096
 R29  H12  H  HCR6   0   0.271   4.8391   0.7321   1.6455
 R29  H13  H  H      0   0.417  -5.3088  -2.0264  -1.1646
 R29  H14  H  HNH1   0   0.370   0.5633   0.5219   2.5333
 R29  H15  H  HNH1   0   0.358   2.4802  -0.4152   2.6729
 R29  H16  H  H      0   0.409  -4.1578  -0.8951  -3.1688
 R29  O3   O  OB     0  -0.674  -4.5816  -1.6950  -0.6294

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
 R29  C9   C10  single    1.510  0.020  1.510
 R29  C9   N2   single    1.445  0.020  1.445
 R29  C11  C10  aromatic  1.390  0.020  1.390
 R29  C11  C12  aromatic  1.390  0.020  1.390
 R29  C10  C15  aromatic  1.393  0.020  1.393
 R29  C12  C13  aromatic  1.388  0.020  1.388
 R29  N2   C8   single    1.359  0.020  1.359
 R29  O4   C8   double    1.222  0.020  1.222
 R29  C8   N1   single    1.369  0.020  1.369
 R29  C15  C14  aromatic  1.387  0.020  1.387
 R29  N1   C3   single    1.404  0.020  1.404
 R29  C13  C14  aromatic  1.390  0.020  1.390
 R29  C4   C3   aromatic  1.399  0.020  1.399
 R29  C4   C5   aromatic  1.388  0.020  1.388
 R29  C3   C2   aromatic  1.396  0.020  1.396
 R29  C5   C6   aromatic  1.388  0.020  1.388
 R29  C2   C1   aromatic  1.394  0.020  1.394
 R29  C6   C1   aromatic  1.389  0.020  1.389
 R29  C6   C7   single    1.506  0.020  1.506
 R29  C1   B1   single    1.618  0.020  1.618
 R29  O2   B1   single    1.466  0.020  1.466
 R29  O1   C7   single    1.395  0.020  1.395
 R29  O1   B1   single    1.505  0.020  1.505
 R29  B1   O3   single    1.468  0.020  1.468
 R29  C2   H1   single    0.930  0.020  1.080
 R29  C4   H2   single    0.930  0.020  1.080
 R29  C5   H3   single    0.930  0.020  1.080
 R29  C7   H4   single    0.970  0.020  1.090
 R29  C7   H5   single    0.970  0.020  1.090
 R29  C9   H6   single    0.970  0.020  1.090
 R29  C9   H7   single    0.970  0.020  1.090
 R29  C11  H8   single    0.930  0.020  1.080
 R29  C12  H9   single    0.930  0.020  1.080
 R29  C13  H10  single    0.930  0.020  1.080
 R29  C14  H11  single    0.930  0.020  1.080
 R29  C15  H12  single    0.930  0.020  1.080
 R29  O3   H13  single    0.850  0.020  0.980
 R29  N1   H14  single    0.860  0.020  1.020
 R29  N2   H15  single    0.860  0.020  1.020
 R29  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
 R29  B1   C1   C6   108.03  3.000
 R29  B1   C1   C2   132.65  3.000
 R29  C6   C1   C2   119.31  3.000
 R29  H1   C2   C3   119.77  3.000
 R29  H1   C2   C1   119.94  3.000
 R29  C3   C2   C1   120.29  3.000
 R29  N1   C3   C4   117.15  3.000
 R29  C4   C3   C2   119.31  3.000
 R29  N1   C3   C2   123.49  3.000
 R29  H2   C4   C5   119.76  3.000
 R29  H2   C4   C3   119.55  3.000
 R29  C5   C4   C3   120.69  3.000
 R29  H3   C5   C6   121.49  3.000
 R29  H3   C5   C4   119.34  3.000
 R29  C6   C5   C4   119.17  3.000
 R29  C7   C6   C5   128.20  3.000
 R29  C7   C6   C1   110.57  3.000
 R29  C5   C6   C1   121.22  3.000
 R29  H5   C7   H4   105.30  3.000
 R29  H5   C7   O1   111.52  3.000
 R29  H4   C7   O1   111.73  3.000
 R29  H5   C7   C6   110.69  3.000
 R29  H4   C7   C6   110.43  3.000
 R29  O1   C7   C6   107.22  3.000
 R29  N2   C8   N1   113.83  3.000
 R29  N1   C8   O4   123.98  3.000
 R29  N2   C8   O4   122.18  3.000
 R29  H7   C9   H6   106.61  3.000
 R29  H7   C9   N2   106.66  3.000
 R29  H6   C9   N2   109.71  3.000
 R29  H7   C9   C10  109.90  3.000
 R29  H6   C9   C10  109.93  3.000
 R29  N2   C9   C10  113.74  3.000
 R29  C15  C10  C11  118.79  3.000
 R29  C15  C10  C9   120.23  3.000
 R29  C11  C10  C9   120.99  3.000
 R29  H8   C11  C12  119.74  3.000
 R29  H8   C11  C10  119.53  3.000
 R29  C12  C11  C10  120.73  3.000
 R29  H9   C12  C13  120.07  3.000
 R29  H9   C12  C11  119.84  3.000
 R29  C13  C12  C11  120.08  3.000
 R29  H10  C13  C14  120.17  3.000
 R29  H10  C13  C12  120.22  3.000
 R29  C14  C13  C12  119.61  3.000
 R29  H11  C14  C15  119.85  3.000
 R29  H11  C14  C13  120.07  3.000
 R29  C15  C14  C13  120.08  3.000
 R29  H12  C15  C14  119.51  3.000
 R29  H12  C15  C10  119.78  3.000
 R29  C14  C15  C10  120.71  3.000
 R29  B1   O1   C7   113.27  3.000
 R29  H14  N1   C8   117.03  3.000
 R29  H14  N1   C3   115.04  3.000
 R29  C8   N1   C3   126.99  3.000
 R29  H15  N2   C9   117.46  3.000
 R29  H15  N2   C8   119.99  3.000
 R29  C9   N2   C8   120.87  3.000
 R29  O2   B1   O3   113.11  3.000
 R29  O3   B1   O1   110.77  3.000
 R29  O2   B1   O1   110.51  3.000
 R29  O3   B1   C1   110.17  3.000
 R29  O1   B1   C1   100.83  3.000
 R29  O2   B1   C1   110.80  3.000
 R29  H16  O2   B1   111.01  3.000
 R29  H13  O3   B1   110.96  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
 R29  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 R29  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 R29  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 R29  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 R29  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 R29  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 R29  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 R29  CONST_08  C13  C14  C15  C10     0.00   0.0  0
 R29  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 R29  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 R29  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 R29  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 R29  CONST_13  N1   C3   C2   C1    180.00   0.0  0
 R29  CONST_14  N1   C3   C4   C5    180.00   0.0  0
 R29  CONST_15  C12  C11  C10  C9    180.00   0.0  0
 R29  CONST_16  C14  C15  C10  C9    180.00   0.0  0
 R29  CONST_17  H3   C5   C6   C1    180.00   0.0  0
 R29  CONST_18  H2   C4   C3   C2    180.00   0.0  0
 R29  CONST_19  H1   C2   C3   C4    180.00   0.0  0
 R29  CONST_20  H9   C12  C11  C10   180.00   0.0  0
 R29  CONST_21  H11  C14  C15  C10   180.00   0.0  0
 R29  CONST_22  H12  C15  C10  C11   180.00   0.0  0
 R29  CONST_23  H10  C13  C12  C11   180.00   0.0  0
 R29  CONST_24  H8   C11  C12  C13   180.00   0.0  0
 R29  CONST_28  O4   C8   N1   C3      0.00   0.0  0
 R29  CONST_29  N2   C8   N1   C3    180.00   0.0  0
 R29  CONST_30  O4   C8   N2   C9      0.00   0.0  0
 R29  CONST_31  N1   C8   N2   C9    180.00   0.0  0
 R29  CONST_32  H15  N2   C8   O4    180.00   0.0  0
 R29  Var_01    O1   C7   C6   C1     -1.51  30.0  1
 R29  Var_02    O1   B1   C1   C2   -179.27  30.0  1
 R29  Var_03    N2   C9   C10  C11  -115.63  30.0  2
 R29  Var_04    C10  C9   N2   C8     71.18  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
 R29  plan-1  C9   0.020
 R29  plan-1  C10  0.020
 R29  plan-1  C11  0.020
 R29  plan-1  C12  0.020
 R29  plan-1  C13  0.020
 R29  plan-1  C14  0.020
 R29  plan-1  C15  0.020
 R29  plan-1  H8   0.020
 R29  plan-1  H9   0.020
 R29  plan-1  H10  0.020
 R29  plan-1  H11  0.020
 R29  plan-1  H12  0.020
 R29  plan-2  C1   0.020
 R29  plan-2  C2   0.020
 R29  plan-2  C3   0.020
 R29  plan-2  C4   0.020
 R29  plan-2  C5   0.020
 R29  plan-2  C6   0.020
 R29  plan-2  C7   0.020
 R29  plan-2  N1   0.020
 R29  plan-2  B1   0.020
 R29  plan-2  H1   0.020
 R29  plan-2  H2   0.020
 R29  plan-2  H3   0.020
 R29  plan-3  C3   0.020
 R29  plan-3  C8   0.020
 R29  plan-3  C9   0.020
 R29  plan-3  O4   0.020
 R29  plan-3  N1   0.020
 R29  plan-3  N2   0.020
 R29  plan-3  H14  0.020
 R29  plan-3  H15  0.020

