# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 19:41:05 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: (3S)-2,1-benzoxaborole-1,3(3H)-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB1O[C@H](O)c2ccccc12
#
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
 ZMD  ZMD  (3S)-2,1-benzoxaborole-1,3(3H)-diol  ligand  18  11  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZMD
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
 ZMD  C10  C  CR16  0  -0.278  63.7785  50.1955  23.2497
 ZMD  B04  B  B     0   0.508  62.1386  52.5475  25.5426
 ZMD  C02  C  CR15  0   0.264  63.9344  52.6428  24.0922
 ZMD  C06  C  CR56  0  -0.091  62.2756  51.1370  24.9046
 ZMD  C07  C  CR16  0  -0.344  61.5963  49.9284  25.0037
 ZMD  C08  C  CR16  0  -0.230  62.0115  48.8566  24.2246
 ZMD  C09  C  CR16  0  -0.265  63.0925  48.9915  23.3545
 ZMD  C11  C  CR56  0  -0.043  63.3553  51.2531  24.0372
 ZMD  O01  O  OH1   0  -0.644  63.8941  53.2121  22.8364
 ZMD  O03  O  O     0  -0.489  63.1163  53.3554  25.0159
 ZMD  O05  O  OH1   0  -0.604  61.2376  52.9543  26.4582
 ZMD  H1   H  HCR6  0   0.256  64.6166  50.2932  22.5707
 ZMD  H2   H  HCR5  0   0.232  64.9535  52.6422  24.4981
 ZMD  H3   H  HCR6  0   0.256  60.7529  49.8169  25.6741
 ZMD  H4   H  HCR6  0   0.257  61.4944  47.9077  24.2876
 ZMD  H5   H  HCR6  0   0.261  63.3991  48.1468  22.7509
 ZMD  H6   H  HOH1  0   0.466  64.4535  53.9968  22.8197
 ZMD  H7   H  HOH1  0   0.489  61.3204  53.8761  26.7260

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
 ZMD  O01  C02  single    1.379  0.020  1.379
 ZMD  C10  C09  aromatic  1.390  0.020  1.390
 ZMD  C10  C11  aromatic  1.385  0.020  1.385
 ZMD  C09  C08  aromatic  1.394  0.020  1.394
 ZMD  C11  C02  single    1.507  0.020  1.507
 ZMD  C11  C06  aromatic  1.390  0.020  1.390
 ZMD  C08  C07  aromatic  1.389  0.020  1.389
 ZMD  C02  O03  single    1.425  0.020  1.425
 ZMD  C06  C07  aromatic  1.390  0.020  1.390
 ZMD  C06  B04  single    1.554  0.020  1.554
 ZMD  O03  B04  single    1.373  0.020  1.373
 ZMD  B04  O05  single    1.347  0.020  1.347
 ZMD  C10  H1   single    0.930  0.020  1.080
 ZMD  C02  H2   single    0.970  0.020  1.090
 ZMD  C07  H3   single    0.930  0.020  1.080
 ZMD  C08  H4   single    0.930  0.020  1.080
 ZMD  C09  H5   single    0.930  0.020  1.080
 ZMD  O01  H6   single    0.850  0.020  0.980
 ZMD  O05  H7   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
 ZMD  H1   C10  C11  121.60  3.000
 ZMD  H1   C10  C09  120.50  3.000
 ZMD  C11  C10  C09  117.90  3.000
 ZMD  O05  B04  O03  123.99  3.000
 ZMD  O05  B04  C06  127.73  3.000
 ZMD  O03  B04  C06  108.28  3.000
 ZMD  H2   C02  O03  107.09  3.000
 ZMD  H2   C02  O01  111.36  3.000
 ZMD  O03  C02  O01  111.53  3.000
 ZMD  H2   C02  C11  111.72  3.000
 ZMD  O03  C02  C11  105.32  3.000
 ZMD  O01  C02  C11  109.65  3.000
 ZMD  C11  C06  C07  119.79  3.000
 ZMD  C07  C06  B04  135.79  3.000
 ZMD  C11  C06  B04  104.41  3.000
 ZMD  H3   C07  C08  120.04  3.000
 ZMD  H3   C07  C06  120.94  3.000
 ZMD  C08  C07  C06  119.02  3.000
 ZMD  H4   C08  C09  119.44  3.000
 ZMD  H4   C08  C07  120.08  3.000
 ZMD  C09  C08  C07  120.48  3.000
 ZMD  H5   C09  C08  119.48  3.000
 ZMD  H5   C09  C10  119.62  3.000
 ZMD  C08  C09  C10  120.91  3.000
 ZMD  C06  C11  C02  110.66  3.000
 ZMD  C06  C11  C10  121.90  3.000
 ZMD  C02  C11  C10  127.43  3.000
 ZMD  H6   O01  C02  109.56  3.000
 ZMD  C02  O03  B04  111.30  3.000
 ZMD  H7   O05  B04  114.86  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
 ZMD  CONST_01  C07  C08  C09  C10     0.00   0.0  0
 ZMD  CONST_02  C07  C06  C11  C10     0.00   0.0  0
 ZMD  CONST_03  C09  C10  C11  C06     0.00   0.0  0
 ZMD  CONST_04  C09  C08  C07  C06     0.00   0.0  0
 ZMD  CONST_05  C11  C10  C09  C08     0.00   0.0  0
 ZMD  CONST_06  C11  C06  C07  C08     0.00   0.0  0
 ZMD  CONST_07  H4   C08  C09  C10   180.00   0.0  0
 ZMD  CONST_08  H3   C07  C06  B04     0.00   0.0  0
 ZMD  CONST_09  H1   C10  C11  C02     0.00   0.0  0
 ZMD  CONST_10  H5   C09  C08  C07   180.00   0.0  0
 ZMD  Var_01    C06  B04  O03  C02    -0.99  30.0  1
 ZMD  Var_02    O03  B04  C06  C07  -178.82  30.0  1

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
 ZMD  chir_01  C02  O01  C11  O03  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
 ZMD  plan-1  C10  0.020
 ZMD  plan-1  B04  0.020
 ZMD  plan-1  C02  0.020
 ZMD  plan-1  C06  0.020
 ZMD  plan-1  C07  0.020
 ZMD  plan-1  C08  0.020
 ZMD  plan-1  C09  0.020
 ZMD  plan-1  C11  0.020
 ZMD  plan-1  H1   0.020
 ZMD  plan-1  H3   0.020
 ZMD  plan-1  H4   0.020
 ZMD  plan-1  H5   0.020

