# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 09:08:56 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 3-[(2R)-2-(acetylamino)-2-(dihydroxyboranyl)ethyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1cccc(c1)C(O)=O)B(O)O
#
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
 BJI  BJI  '3-[(2R)-2-(acetylamino)-2-(dihydroxyboranyl)ethyl]benzoic acid'  ligand  32  18  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BJI
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
 BJI  C2    C  CH2   0  -0.553   0.7596  -1.2566   0.7913
 BJI  C1    C  CH1   0  -0.246   0.5742  -0.1371   1.8271
 BJI  N1    N  NH1   0  -0.635   0.3867  -0.7183   3.1412
 BJI  C3    C  C     0   0.557  -0.3047  -0.0672   4.0790
 BJI  C4    C  CH3   0  -0.769  -0.3879  -0.7110   5.4349
 BJI  O2    O  O     0  -0.512  -0.8492   1.0096   3.8317
 BJI  C11   C  C     0   0.533  -0.9883  -0.2053  -3.7572
 BJI  O3    O  OH1   0  -0.594  -0.7189   0.3893  -4.9113
 BJI  O4    O  O     0  -0.439  -2.0473  -0.7373  -3.5222
 BJI  B     B  B     0   0.530  -0.6823   0.7829   1.4396
 BJI  OB1   O  OH1   0  -0.634  -1.8787   0.1528   1.2578
 BJI  C6    C  CR16  0  -0.293   2.1882  -0.1054  -0.9277
 BJI  C5    C  CR6   0   0.117   0.9703  -0.6909  -0.5852
 BJI  C7    C  CR16  0  -0.227   2.3826   0.4545  -2.1813
 BJI  C10   C  CR16  0  -0.298  -0.0462  -0.7045  -1.5313
 BJI  C8    C  CR16  0  -0.277   1.3619   0.4385  -3.1197
 BJI  C9    C  CR6   0  -0.073   0.1400  -0.1471  -2.7951
 BJI  OB2   O  OH1   0  -0.620  -0.5437   2.0777   1.0193
 BJI  H21   H  HCH2  0   0.258   1.6219  -1.8716   1.0675
 BJI  H22   H  HCH2  0   0.258  -0.1137  -1.9108   0.7990
 BJI  H1    H  HCH1  0   0.243   1.4950   0.4644   1.8344
 BJI  HN1   H  HNH1  0   0.397   0.8888  -1.5571   3.3870
 BJI  H41   H  HCH3  0   0.267  -1.4340  -0.8431   5.7099
 BJI  H42   H  HCH3  0   0.252   0.1090  -1.6779   5.4814
 BJI  H43   H  HCH3  0   0.268   0.0633  -0.0532   6.1777
 BJI  HO3   H  HOH1  0   0.487  -1.4816   0.3196  -5.5045
 BJI  HOB1  H  HOH1  0   0.479  -2.5721   0.7338   0.9299
 BJI  H6    H  HCR6  0   0.260   2.9964  -0.0911  -0.2056
 BJI  H7    H  HCR6  0   0.264   3.3348   0.9030  -2.4316
 BJI  H10   H  HCR6  0   0.258  -0.9984  -1.1542  -1.2802
 BJI  H8    H  HCR6  0   0.267   1.5300   0.8769  -4.0935
 BJI  HOB2  H  HOH1  0   0.473   0.3484   2.4126   1.1427

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
 BJI  C2   C1    single    1.536  0.020  1.536
 BJI  C2   C5    single    1.503  0.020  1.503
 BJI  C2   H21   single    0.970  0.020  1.090
 BJI  C2   H22   single    0.970  0.020  1.090
 BJI  C1   N1    single    1.449  0.020  1.449
 BJI  C1   B     single    1.605  0.020  1.605
 BJI  C1   H1    single    0.970  0.020  1.090
 BJI  N1   C3    single    1.335  0.020  1.335
 BJI  N1   HN1   single    0.860  0.020  1.020
 BJI  C3   C4    single    1.503  0.020  1.503
 BJI  C3   O2    double    1.232  0.020  1.232
 BJI  C4   H41   single    0.970  0.020  1.090
 BJI  C4   H42   single    0.970  0.020  1.090
 BJI  C4   H43   single    0.970  0.020  1.090
 BJI  C11  O3    single    1.326  0.020  1.326
 BJI  C11  O4    double    1.208  0.020  1.208
 BJI  C11  C9    single    1.484  0.020  1.484
 BJI  O3   HO3   single    0.850  0.020  0.980
 BJI  B    OB1   single    1.364  0.020  1.364
 BJI  B    OB2   single    1.368  0.020  1.368
 BJI  OB1  HOB1  single    0.850  0.020  0.980
 BJI  C6   C5    aromatic  1.394  0.020  1.394
 BJI  C6   C7    aromatic  1.387  0.020  1.387
 BJI  C6   H6    single    0.930  0.020  1.080
 BJI  C5   C10   aromatic  1.389  0.020  1.389
 BJI  C7   C8    aromatic  1.386  0.020  1.386
 BJI  C7   H7    single    0.930  0.020  1.080
 BJI  C10  C9    aromatic  1.394  0.020  1.394
 BJI  C10  H10   single    0.930  0.020  1.080
 BJI  C8   C9    aromatic  1.393  0.020  1.393
 BJI  C8   H8    single    0.930  0.020  1.080
 BJI  OB2  HOB2  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
 BJI  H22   C2   H21  106.97  3.000
 BJI  H22   C2   C5   110.14  3.000
 BJI  H21   C2   C5   109.40  3.000
 BJI  H22   C2   C1   109.60  3.000
 BJI  H21   C2   C1   109.53  3.000
 BJI  C5    C2   C1   111.11  3.000
 BJI  H1    C1   B    110.10  3.000
 BJI  H1    C1   N1   108.76  3.000
 BJI  B     C1   N1   110.34  3.000
 BJI  H1    C1   C2   107.57  3.000
 BJI  B     C1   C2   110.45  3.000
 BJI  N1    C1   C2   109.56  3.000
 BJI  HN1   N1   C3   119.51  3.000
 BJI  HN1   N1   C1   119.37  3.000
 BJI  C3    N1   C1   120.57  3.000
 BJI  O2    C3   C4   122.07  3.000
 BJI  O2    C3   N1   120.96  3.000
 BJI  C4    C3   N1   116.97  3.000
 BJI  H43   C4   H42  108.55  3.000
 BJI  H43   C4   H41  107.37  3.000
 BJI  H42   C4   H41  108.66  3.000
 BJI  H43   C4   C3   109.47  3.000
 BJI  H42   C4   C3   113.20  3.000
 BJI  H41   C4   C3   109.43  3.000
 BJI  C9    C11  O4   123.88  3.000
 BJI  C9    C11  O3   113.10  3.000
 BJI  O4    C11  O3   123.02  3.000
 BJI  HO3   O3   C11  109.92  3.000
 BJI  OB2   B    OB1  119.00  3.000
 BJI  OB2   B    C1   122.50  3.000
 BJI  OB1   B    C1   117.00  3.000
 BJI  HOB1  OB1  B    113.48  3.000
 BJI  H6    C6   C7   119.50  3.000
 BJI  H6    C6   C5   119.56  3.000
 BJI  C7    C6   C5   120.94  3.000
 BJI  C10   C5   C6   118.44  3.000
 BJI  C10   C5   C2   121.18  3.000
 BJI  C6    C5   C2   120.37  3.000
 BJI  H7    C7   C8   119.74  3.000
 BJI  H7    C7   C6   119.99  3.000
 BJI  C8    C7   C6   120.27  3.000
 BJI  H10   C10  C9   119.60  3.000
 BJI  H10   C10  C5   119.33  3.000
 BJI  C9    C10  C5   121.07  3.000
 BJI  H8    C8   C9   121.11  3.000
 BJI  H8    C8   C7   119.37  3.000
 BJI  C9    C8   C7   119.52  3.000
 BJI  C8    C9   C10  119.77  3.000
 BJI  C8    C9   C11  122.15  3.000
 BJI  C10   C9   C11  118.08  3.000
 BJI  HOB2  OB2  B    112.60  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
 BJI  CONST_01  C9   C10  C5   C6      0.00   0.0  0
 BJI  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 BJI  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 BJI  CONST_04  C8   C9   C10  C5      0.00   0.0  0
 BJI  CONST_05  C10  C5   C6   C7      0.00   0.0  0
 BJI  CONST_06  C10  C9   C8   C7      0.00   0.0  0
 BJI  CONST_07  C7   C6   C5   C2    180.00   0.0  0
 BJI  CONST_08  C9   C10  C5   C2    180.00   0.0  0
 BJI  CONST_09  C5   C10  C9   C11   180.00   0.0  0
 BJI  CONST_10  C7   C8   C9   C11   180.00   0.0  0
 BJI  CONST_11  H10  C10  C5   C6    180.00   0.0  0
 BJI  CONST_12  H8   C8   C7   C6    180.00   0.0  0
 BJI  CONST_13  H7   C7   C6   C5    180.00   0.0  0
 BJI  CONST_14  H6   C6   C5   C10   180.00   0.0  0
 BJI  CONST_15  HO3  O3   C11  C9    180.00   0.0  0
 BJI  CONST_16  C4   C3   N1   C1    180.00   0.0  0
 BJI  CONST_17  O2   C3   N1   C1      0.00   0.0  0
 BJI  CONST_18  HN1  N1   C3   C4      0.00   0.0  0
 BJI  Var_01    C6   C5   C2   C1     74.36  30.0  2
 BJI  Var_02    C10  C9   C11  O3    178.02  30.0  2
 BJI  Var_03    H41  C4   C3   N1   -123.56  30.0  3

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
 BJI  chir_01  C1  C2  N1  B  positiv

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
 BJI  plan-1  C2   0.020
 BJI  plan-1  C11  0.020
 BJI  plan-1  C6   0.020
 BJI  plan-1  C5   0.020
 BJI  plan-1  C7   0.020
 BJI  plan-1  C10  0.020
 BJI  plan-1  C8   0.020
 BJI  plan-1  C9   0.020
 BJI  plan-1  H6   0.020
 BJI  plan-1  H7   0.020
 BJI  plan-1  H10  0.020
 BJI  plan-1  H8   0.020
 BJI  plan-2  C1   0.020
 BJI  plan-2  N1   0.020
 BJI  plan-2  C3   0.020
 BJI  plan-2  C4   0.020
 BJI  plan-2  O2   0.020
 BJI  plan-2  HN1  0.020
 BJI  plan-3  C11  0.020
 BJI  plan-3  O3   0.020
 BJI  plan-3  O4   0.020
 BJI  plan-3  C9   0.020
 BJI  plan-3  HO3  0.020

