# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:34:32 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 1-oxidanyl-~{N},~{N}-bis(phenylmethyl)-3~{H}-2,1-benzoxaborole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB1OCc2ccc(cc12)C(=O)N(Cc3ccccc3)Cc4ccccc4
#
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
 S1E  S1E  1-oxidanyl-~{N},~{N}-bis(phenylmethyl)-3~{H}-2,1-benzoxaborole-6-carboxamide  ligand  47  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S1E
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
 S1E  O    O  O     0  -0.480   -7.3455  41.3610  -18.8398
 S1E  C    C  C     0   0.536   -7.1922  41.1057  -17.6536
 S1E  N    N  NT    0  -0.460   -7.9594  41.6646  -16.6846
 S1E  C15  C  CH2   0  -0.399   -8.9460  42.6720  -17.0473
 S1E  C16  C  CR6   0   0.117  -10.3573  42.1410  -17.0726
 S1E  C21  C  CR16  0  -0.297  -10.7033  41.0545  -17.8747
 S1E  C20  C  CR16  0  -0.236  -12.0068  40.5815  -17.8962
 S1E  C19  C  CR16  0  -0.266  -12.9869  41.1915  -17.1216
 S1E  C18  C  CR16  0  -0.239  -12.6518  42.2739  -16.3215
 S1E  C17  C  CR16  0  -0.306  -11.3431  42.7412  -16.2966
 S1E  C8   C  CH2   0  -0.359   -8.0445  41.1810  -15.3229
 S1E  C9   C  CR6   0   0.086   -7.5692  42.1623  -14.2765
 S1E  C14  C  CR16  0  -0.298   -6.7331  43.2320  -14.5772
 S1E  C13  C  CR16  0  -0.245   -6.2922  44.0899  -13.5765
 S1E  C12  C  CR16  0  -0.263   -6.6815  43.8878  -12.2606
 S1E  C11  C  CR16  0  -0.242   -7.5210  42.8241  -11.9522
 S1E  C10  C  CR16  0  -0.293   -7.9628  41.9721  -12.9534
 S1E  C1   C  CR6   0  -0.054   -6.1105  40.1491  -17.2572
 S1E  C4   C  CR16  0  -0.268   -5.1601  40.4585  -16.2800
 S1E  C5   C  CR16  0  -0.269   -4.1003  39.6061  -16.0097
 S1E  C6   C  CR56  0  -0.035   -4.0057  38.4270  -16.7319
 S1E  C7   C  CH2   0  -0.179   -2.9674  37.3483  -16.6375
 S1E  O1   O  O     0  -0.468   -3.3172  36.3795  -17.6174
 S1E  B    B  B     0   0.514   -4.4567  36.7456  -18.2876
 S1E  C3   C  CR56  0  -0.076   -4.9394  38.1047  -17.7131
 S1E  C2   C  CR16  0  -0.373   -5.9869  38.9708  -17.9876
 S1E  H1   H  HCH2  0   0.281   -8.6779  43.0822  -18.0191
 S1E  H2   H  HCH2  0   0.271   -8.8810  43.4935  -16.3301
 S1E  H3   H  HCR6  0   0.254   -9.9543  40.5757  -18.4933
 S1E  H4   H  HCR6  0   0.254  -12.2610  39.7370  -18.5240
 S1E  H5   H  HCR6  0   0.254  -14.0043  40.8227  -17.1420
 S1E  H6   H  HCR6  0   0.254  -13.4061  42.7537  -15.7109
 S1E  H7   H  HCR6  0   0.252  -11.0861  43.5831  -15.6642
 S1E  H8   H  HCH2  0   0.279   -9.0863  40.9181  -15.1136
 S1E  H9   H  HCH2  0   0.292   -7.4864  40.2496  -15.2327
 S1E  H10  H  HCR6  0   0.262   -6.4231  43.4102  -15.6002
 S1E  H11  H  HCR6  0   0.254   -5.6431  44.9183  -13.8300
 S1E  H12  H  HCR6  0   0.254   -6.3387  44.5558  -11.4810
 S1E  H13  H  HCR6  0   0.254   -7.8367  42.6609  -10.9297
 S1E  H14  H  HCR6  0   0.250   -8.6244  41.1497  -12.7053
 S1E  H15  H  HCR6  0   0.277   -5.2311  41.3871  -15.7288
 S1E  H16  H  HCR6  0   0.258   -3.3686  39.8709  -15.2566
 S1E  H17  H  HCH2  0   0.254   -2.9501  36.8818  -15.6486
 S1E  O2   O  OH1   0  -0.607   -5.0208  36.0282  -19.2796
 S1E  H19  H  HCR6  0   0.260   -6.7109  38.7336  -18.7578
 S1E  H20  H  HOH1  0   0.489   -4.5656  35.2075  -19.4972
 S1E  H18  H  HCH2  0   0.254   -1.9621  37.7282  -16.8383

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
 S1E  O    C    double    1.223  0.020  1.223
 S1E  B    C3   single    1.552  0.020  1.552
 S1E  B    O1   single    1.372  0.020  1.372
 S1E  C20  C19  aromatic  1.390  0.020  1.390
 S1E  C20  C21  aromatic  1.387  0.020  1.387
 S1E  C2   C3   aromatic  1.387  0.020  1.387
 S1E  C2   C1   aromatic  1.392  0.020  1.392
 S1E  C3   C6   aromatic  1.392  0.020  1.392
 S1E  C19  C18  aromatic  1.387  0.020  1.387
 S1E  O1   C7   single    1.422  0.020  1.422
 S1E  C21  C16  aromatic  1.394  0.020  1.394
 S1E  C    C1   single    1.497  0.020  1.497
 S1E  C    N    single    1.357  0.020  1.357
 S1E  C1   C4   aromatic  1.398  0.020  1.398
 S1E  C6   C7   single    1.500  0.020  1.500
 S1E  C6   C5   aromatic  1.386  0.020  1.386
 S1E  C18  C17  aromatic  1.390  0.020  1.390
 S1E  C16  C15  single    1.508  0.020  1.508
 S1E  C16  C17  aromatic  1.391  0.020  1.391
 S1E  C15  N    single    1.456  0.020  1.456
 S1E  N    C8   single    1.447  0.020  1.447
 S1E  C4   C5   aromatic  1.387  0.020  1.387
 S1E  C8   C9   single    1.511  0.020  1.511
 S1E  C14  C9   aromatic  1.391  0.020  1.391
 S1E  C14  C13  aromatic  1.390  0.020  1.390
 S1E  C9   C10  aromatic  1.393  0.020  1.393
 S1E  C13  C12  aromatic  1.387  0.020  1.387
 S1E  C10  C11  aromatic  1.387  0.020  1.387
 S1E  C12  C11  aromatic  1.390  0.020  1.390
 S1E  C15  H1   single    0.970  0.020  1.090
 S1E  C15  H2   single    0.970  0.020  1.090
 S1E  C21  H3   single    0.930  0.020  1.080
 S1E  C20  H4   single    0.930  0.020  1.080
 S1E  C19  H5   single    0.930  0.020  1.080
 S1E  C18  H6   single    0.930  0.020  1.080
 S1E  C17  H7   single    0.930  0.020  1.080
 S1E  C8   H8   single    0.970  0.020  1.090
 S1E  C8   H9   single    0.970  0.020  1.090
 S1E  C14  H10  single    0.930  0.020  1.080
 S1E  C13  H11  single    0.930  0.020  1.080
 S1E  C12  H12  single    0.930  0.020  1.080
 S1E  C11  H13  single    0.930  0.020  1.080
 S1E  C10  H14  single    0.930  0.020  1.080
 S1E  C4   H15  single    0.930  0.020  1.080
 S1E  C5   H16  single    0.930  0.020  1.080
 S1E  C7   H17  single    0.970  0.020  1.090
 S1E  B    O2   single    1.348  0.020  1.348
 S1E  C2   H19  single    0.930  0.020  1.080
 S1E  O2   H20  single    0.850  0.020  0.980
 S1E  C7   H18  single    0.970  0.020  1.090

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
 S1E  C1   C    N    118.86  3.000
 S1E  N    C    O    122.41  3.000
 S1E  C1   C    O    118.73  3.000
 S1E  C8   N    C15  115.19  3.000
 S1E  C8   N    C    124.59  3.000
 S1E  C15  N    C    119.36  3.000
 S1E  H2   C15  H1   106.74  3.000
 S1E  H2   C15  C16  109.35  3.000
 S1E  H1   C15  C16  110.39  3.000
 S1E  H2   C15  N    108.45  3.000
 S1E  H1   C15  N    108.44  3.000
 S1E  C16  C15  N    113.25  3.000
 S1E  C17  C16  C21  118.78  3.000
 S1E  C17  C16  C15  120.14  3.000
 S1E  C21  C16  C15  121.08  3.000
 S1E  H3   C21  C20  119.37  3.000
 S1E  H3   C21  C16  120.10  3.000
 S1E  C20  C21  C16  120.53  3.000
 S1E  H4   C20  C19  119.99  3.000
 S1E  H4   C20  C21  119.72  3.000
 S1E  C19  C20  C21  120.29  3.000
 S1E  H5   C19  C18  120.25  3.000
 S1E  H5   C19  C20  120.17  3.000
 S1E  C18  C19  C20  119.57  3.000
 S1E  H6   C18  C17  119.80  3.000
 S1E  H6   C18  C19  120.19  3.000
 S1E  C17  C18  C19  120.01  3.000
 S1E  H7   C17  C18  119.66  3.000
 S1E  H7   C17  C16  119.51  3.000
 S1E  C18  C17  C16  120.83  3.000
 S1E  H9   C8   H8   105.45  3.000
 S1E  H9   C8   C9   109.67  3.000
 S1E  H8   C8   C9   108.84  3.000
 S1E  H9   C8   N    109.47  3.000
 S1E  H8   C8   N    108.42  3.000
 S1E  C9   C8   N    114.58  3.000
 S1E  C10  C9   C14  118.69  3.000
 S1E  C10  C9   C8   118.69  3.000
 S1E  C14  C9   C8   122.61  3.000
 S1E  H10  C14  C13  119.17  3.000
 S1E  H10  C14  C9   120.17  3.000
 S1E  C13  C14  C9   120.66  3.000
 S1E  H11  C13  C12  120.13  3.000
 S1E  H11  C13  C14  119.60  3.000
 S1E  C12  C13  C14  120.27  3.000
 S1E  H12  C12  C11  120.25  3.000
 S1E  H12  C12  C13  120.30  3.000
 S1E  C11  C12  C13  119.44  3.000
 S1E  H13  C11  C10  119.76  3.000
 S1E  H13  C11  C12  120.08  3.000
 S1E  C10  C11  C12  120.16  3.000
 S1E  H14  C10  C11  119.68  3.000
 S1E  H14  C10  C9   119.54  3.000
 S1E  C11  C10  C9   120.77  3.000
 S1E  C2   C1   C4   119.60  3.000
 S1E  C4   C1   C    122.33  3.000
 S1E  C2   C1   C    117.78  3.000
 S1E  H15  C4   C5   118.58  3.000
 S1E  H15  C4   C1   120.09  3.000
 S1E  C5   C4   C1   121.32  3.000
 S1E  H16  C5   C6   121.62  3.000
 S1E  H16  C5   C4   120.11  3.000
 S1E  C6   C5   C4   118.26  3.000
 S1E  C3   C6   C7   110.00  3.000
 S1E  C7   C6   C5   128.77  3.000
 S1E  C3   C6   C5   121.23  3.000
 S1E  H18  C7   H17  107.45  3.000
 S1E  H18  C7   O1   109.66  3.000
 S1E  H17  C7   O1   109.66  3.000
 S1E  H18  C7   C6   112.02  3.000
 S1E  H17  C7   C6   112.00  3.000
 S1E  O1   C7   C6   106.04  3.000
 S1E  B    O1   C7   111.05  3.000
 S1E  O2   B    C3   127.46  3.000
 S1E  O2   B    O1   124.41  3.000
 S1E  C3   B    O1   108.13  3.000
 S1E  C2   C3   B    135.11  3.000
 S1E  C2   C3   C6   120.10  3.000
 S1E  B    C3   C6   104.77  3.000
 S1E  H19  C2   C3   120.58  3.000
 S1E  H19  C2   C1   119.95  3.000
 S1E  C3   C2   C1   119.47  3.000
 S1E  H20  O2   B    114.96  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
 S1E  CONST_01  C19  C20  C21  C16     0.00   0.0  0
 S1E  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 S1E  CONST_03  C18  C19  C20  C21     0.00   0.0  0
 S1E  CONST_04  C18  C17  C16  C21     0.00   0.0  0
 S1E  CONST_05  C17  C18  C19  C20     0.00   0.0  0
 S1E  CONST_06  C17  C16  C21  C20     0.00   0.0  0
 S1E  CONST_07  C12  C13  C14  C9      0.00   0.0  0
 S1E  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 S1E  CONST_09  C11  C10  C9   C14     0.00   0.0  0
 S1E  CONST_10  C11  C12  C13  C14     0.00   0.0  0
 S1E  CONST_11  C10  C9   C14  C13     0.00   0.0  0
 S1E  CONST_12  C10  C11  C12  C13     0.00   0.0  0
 S1E  CONST_13  C6   C3   C2   C1      0.00   0.0  0
 S1E  CONST_14  C6   C5   C4   C1      0.00   0.0  0
 S1E  CONST_15  C3   C2   C1   C4      0.00   0.0  0
 S1E  CONST_16  C3   C6   C5   C4      0.00   0.0  0
 S1E  CONST_17  C2   C3   C6   C5      0.00   0.0  0
 S1E  CONST_18  C2   C1   C4   C5      0.00   0.0  0
 S1E  CONST_19  C3   C2   C1   C     180.00   0.0  0
 S1E  CONST_20  C5   C4   C1   C     180.00   0.0  0
 S1E  CONST_21  C20  C21  C16  C15   180.00   0.0  0
 S1E  CONST_22  C18  C17  C16  C15   180.00   0.0  0
 S1E  CONST_23  C13  C14  C9   C8    180.00   0.0  0
 S1E  CONST_24  C11  C10  C9   C8    180.00   0.0  0
 S1E  CONST_25  H4   C20  C21  C16   180.00   0.0  0
 S1E  CONST_26  H6   C18  C17  C16   180.00   0.0  0
 S1E  CONST_27  H5   C19  C20  C21   180.00   0.0  0
 S1E  CONST_28  H7   C17  C16  C21   180.00   0.0  0
 S1E  CONST_29  H3   C21  C20  C19   180.00   0.0  0
 S1E  CONST_30  H11  C13  C14  C9    180.00   0.0  0
 S1E  CONST_31  H13  C11  C10  C9    180.00   0.0  0
 S1E  CONST_32  H14  C10  C9   C14   180.00   0.0  0
 S1E  CONST_33  H12  C12  C13  C14   180.00   0.0  0
 S1E  CONST_34  H10  C14  C13  C12   180.00   0.0  0
 S1E  CONST_35  H16  C5   C4   C1    180.00   0.0  0
 S1E  CONST_36  H19  C2   C1   C4    180.00   0.0  0
 S1E  CONST_37  H15  C4   C5   C6    180.00   0.0  0
 S1E  CONST_38  C1   C    N    C15   180.00   0.0  0
 S1E  CONST_40  C15  N    C    O       0.00   0.0  0
 S1E  Var_01    O1   C7   C6   C5   -178.62  30.0  1
 S1E  Var_02    O1   B    C3   C6      0.33  30.0  1
 S1E  Var_03    C3   B    O1   C7      0.10  30.0  1
 S1E  Var_04    C2   C1   C    O     -45.35  30.0  2
 S1E  Var_05    C21  C16  C15  N     -56.75  30.0  2
 S1E  Var_06    C14  C9   C8   N     -19.99  30.0  2
 S1E  Var_07    C16  C15  N    C     102.90  30.0  2
 S1E  Var_08    C9   C8   N    C     117.71  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
 S1E  plan-1  C15  0.020
 S1E  plan-1  C16  0.020
 S1E  plan-1  C21  0.020
 S1E  plan-1  C20  0.020
 S1E  plan-1  C19  0.020
 S1E  plan-1  C18  0.020
 S1E  plan-1  C17  0.020
 S1E  plan-1  H3   0.020
 S1E  plan-1  H4   0.020
 S1E  plan-1  H5   0.020
 S1E  plan-1  H6   0.020
 S1E  plan-1  H7   0.020
 S1E  plan-2  C8   0.020
 S1E  plan-2  C9   0.020
 S1E  plan-2  C14  0.020
 S1E  plan-2  C13  0.020
 S1E  plan-2  C12  0.020
 S1E  plan-2  C11  0.020
 S1E  plan-2  C10  0.020
 S1E  plan-2  H10  0.020
 S1E  plan-2  H11  0.020
 S1E  plan-2  H12  0.020
 S1E  plan-2  H13  0.020
 S1E  plan-2  H14  0.020
 S1E  plan-3  C    0.020
 S1E  plan-3  C1   0.020
 S1E  plan-3  C4   0.020
 S1E  plan-3  C5   0.020
 S1E  plan-3  C6   0.020
 S1E  plan-3  C7   0.020
 S1E  plan-3  B    0.020
 S1E  plan-3  C3   0.020
 S1E  plan-3  C2   0.020
 S1E  plan-3  H15  0.020
 S1E  plan-3  H16  0.020
 S1E  plan-3  H19  0.020
 S1E  plan-4  O    0.020
 S1E  plan-4  C    0.020
 S1E  plan-4  N    0.020
 S1E  plan-4  C15  0.020
 S1E  plan-4  C8   0.020
 S1E  plan-4  C1   0.020

