# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 13:29:54 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: [3-(benzyloxy)-4-methylphenyl]borinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(BO)cc1OCc2ccccc2
#
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
 7NM  7NM  '[3-(benzyloxy)-4-methylphenyl]borinic acid'  ligand  32  17  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7NM
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
 7NM  C01  C  CH3   0  -0.711  -0.6941   2.9301   0.3500
 7NM  C02  C  CR6   0  -0.020  -1.5514   1.7085   0.2153
 7NM  C03  C  CR6   0   0.381  -0.9686   0.4553  -0.0288
 7NM  O04  O  O2    0  -0.465   0.3782   0.4498  -0.1288
 7NM  C05  C  CH2   0  -0.254   1.0490  -0.7927  -0.2421
 7NM  C06  C  CR6   0   0.095   2.5250  -0.5314  -0.1824
 7NM  C07  C  CR16  0  -0.308   3.3645  -0.9794  -1.1951
 7NM  C08  C  CR16  0  -0.240   4.7364  -0.7653  -1.1246
 7NM  C09  C  CR16  0  -0.265   5.2782  -0.0899  -0.0410
 7NM  C10  C  CR16  0  -0.241   4.4435   0.3668   0.9733
 7NM  C11  C  CR16  0  -0.285   3.0767   0.1455   0.9044
 7NM  C12  C  CR16  0  -0.451  -1.7654  -0.6757  -0.1548
 7NM  C13  C  CR6   0  -0.043  -3.1590  -0.5980  -0.0407
 7NM  B14  B  B     0   0.260  -3.9913  -1.9018  -0.1999
 7NM  O15  O  OH1   0  -0.595  -5.3379  -1.8612  -0.1031
 7NM  C17  C  CR16  0  -0.334  -3.7333   0.6484   0.2040
 7NM  C18  C  CR16  0  -0.258  -2.9346   1.7770   0.3273
 7NM  H1   H  HCH3  0   0.245  -0.1437   3.1367  -0.5699
 7NM  H2   H  HCH3  0   0.243  -1.3005   3.8051   0.5787
 7NM  H3   H  HCH3  0   0.246   0.0469   2.8155   1.1426
 7NM  H4   H  HCH2  0   0.241   0.7523  -1.4577   0.5777
 7NM  H5   H  HCH2  0   0.242   0.7874  -1.2932  -1.1806
 7NM  H6   H  HCR6  0   0.255   2.9456  -1.4977  -2.0495
 7NM  H7   H  HCR6  0   0.258   5.3778  -1.1221  -1.9200
 7NM  H8   H  HCR6  0   0.258   6.3454   0.0813   0.0156
 7NM  H9   H  HCR6  0   0.257   4.8610   0.8923   1.8224
 7NM  H10  H  HCR6  0   0.252   2.4379   0.5010   1.7038
 7NM  H11  H  HCR6  0   0.273  -1.3200  -1.6432  -0.3529
 7NM  H12  H  H     0  -0.022  -3.4209  -2.9412  -0.4129
 7NM  H13  H  HOH1  0   0.493  -5.7499  -2.7213  -0.2261
 7NM  H14  H  HCR6  0   0.247  -4.8075   0.7481   0.2983
 7NM  H15  H  HCR6  0   0.247  -3.3924   2.7400   0.5213

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
 7NM  O15  B14  single    1.351  0.020  1.351
 7NM  B14  C13  single    1.555  0.020  1.555
 7NM  C07  C08  aromatic  1.390  0.020  1.390
 7NM  C07  C06  aromatic  1.390  0.020  1.390
 7NM  C05  C06  single    1.500  0.020  1.500
 7NM  C05  O04  single    1.417  0.020  1.417
 7NM  C08  C09  aromatic  1.387  0.020  1.387
 7NM  C13  C12  aromatic  1.400  0.020  1.400
 7NM  C13  C17  aromatic  1.394  0.020  1.394
 7NM  C12  C03  aromatic  1.389  0.020  1.389
 7NM  C06  C11  aromatic  1.394  0.020  1.394
 7NM  C09  C10  aromatic  1.391  0.020  1.391
 7NM  C17  C18  aromatic  1.388  0.020  1.388
 7NM  C11  C10  aromatic  1.386  0.020  1.386
 7NM  C03  O04  single    1.351  0.020  1.351
 7NM  C03  C02  aromatic  1.404  0.020  1.404
 7NM  C18  C02  aromatic  1.389  0.020  1.389
 7NM  C02  C01  single    1.498  0.020  1.498
 7NM  C01  H1   single    0.939  0.020  1.096
 7NM  C01  H2   single    0.939  0.020  1.096
 7NM  C01  H3   single    0.939  0.020  1.096
 7NM  C05  H4   single    0.939  0.020  1.096
 7NM  C05  H5   single    0.939  0.020  1.096
 7NM  C07  H6   single    0.929  0.020  1.085
 7NM  C08  H7   single    0.929  0.020  1.085
 7NM  C09  H8   single    0.929  0.020  1.085
 7NM  C10  H9   single    0.929  0.020  1.085
 7NM  C11  H10  single    0.929  0.020  1.085
 7NM  C12  H11  single    0.929  0.020  1.085
 7NM  B14  H12  single    1.023  0.020  1.195
 7NM  O15  H13  single    0.850  0.020  0.980
 7NM  C17  H14  single    0.930  0.020  1.080
 7NM  C18  H15  single    0.930  0.020  1.080

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
 7NM  H3   C01  H2   108.06  3.000
 7NM  H3   C01  H1   106.83  3.000
 7NM  H2   C01  H1   107.80  3.000
 7NM  H3   C01  C02  111.60  3.000
 7NM  H2   C01  C02  110.81  3.000
 7NM  H1   C01  C02  111.53  3.000
 7NM  C18  C02  C03  118.12  3.000
 7NM  C18  C02  C01  121.47  3.000
 7NM  C03  C02  C01  120.40  3.000
 7NM  C12  C03  O04  124.19  3.000
 7NM  O04  C03  C02  115.50  3.000
 7NM  C12  C03  C02  120.31  3.000
 7NM  C05  O04  C03  118.79  3.000
 7NM  H5   C05  H4   107.39  3.000
 7NM  H5   C05  C06  110.41  3.000
 7NM  H4   C05  C06  110.00  3.000
 7NM  H5   C05  O04  110.87  3.000
 7NM  H4   C05  O04  110.12  3.000
 7NM  C06  C05  O04  108.05  3.000
 7NM  C11  C06  C07  119.05  3.000
 7NM  C11  C06  C05  120.33  3.000
 7NM  C07  C06  C05  120.61  3.000
 7NM  H6   C07  C08  119.68  3.000
 7NM  H6   C07  C06  119.69  3.000
 7NM  C08  C07  C06  120.63  3.000
 7NM  H7   C08  C09  120.21  3.000
 7NM  H7   C08  C07  119.79  3.000
 7NM  C09  C08  C07  120.00  3.000
 7NM  H8   C09  C10  120.11  3.000
 7NM  H8   C09  C08  120.20  3.000
 7NM  C10  C09  C08  119.69  3.000
 7NM  H9   C10  C11  119.78  3.000
 7NM  H9   C10  C09  120.01  3.000
 7NM  C11  C10  C09  120.20  3.000
 7NM  H10  C11  C10  119.50  3.000
 7NM  H10  C11  C06  120.08  3.000
 7NM  C10  C11  C06  120.42  3.000
 7NM  H11  C12  C13  118.27  3.000
 7NM  H11  C12  C03  120.52  3.000
 7NM  C13  C12  C03  121.21  3.000
 7NM  C17  C13  B14  123.17  3.000
 7NM  C17  C13  C12  118.29  3.000
 7NM  B14  C13  C12  118.53  3.000
 7NM  H12  B14  O15  120.71  3.000
 7NM  H12  B14  C13  119.22  3.000
 7NM  O15  B14  C13  120.07  3.000
 7NM  H13  O15  B14  113.02  3.000
 7NM  H14  C17  C18  119.22  3.000
 7NM  H14  C17  C13  120.42  3.000
 7NM  C18  C17  C13  120.37  3.000
 7NM  H15  C18  C17  119.69  3.000
 7NM  H15  C18  C02  118.60  3.000
 7NM  C17  C18  C02  121.71  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
 7NM  CONST_01  C13  C12  C03  C02     0.00   0.0  0
 7NM  CONST_02  C13  C17  C18  C02     0.00   0.0  0
 7NM  CONST_03  C17  C13  C12  C03     0.00   0.0  0
 7NM  CONST_04  C17  C18  C02  C03     0.00   0.0  0
 7NM  CONST_05  C09  C08  C07  C06     0.00   0.0  0
 7NM  CONST_06  C09  C10  C11  C06     0.00   0.0  0
 7NM  CONST_07  C10  C09  C08  C07     0.00   0.0  0
 7NM  CONST_08  C10  C11  C06  C07     0.00   0.0  0
 7NM  CONST_09  C11  C06  C07  C08     0.00   0.0  0
 7NM  CONST_10  C11  C10  C09  C08     0.00   0.0  0
 7NM  CONST_11  C18  C17  C13  C12     0.00   0.0  0
 7NM  CONST_12  C18  C02  C03  C12     0.00   0.0  0
 7NM  CONST_13  C12  C03  C02  C01   180.00   0.0  0
 7NM  CONST_14  C17  C18  C02  C01   180.00   0.0  0
 7NM  CONST_15  B14  C13  C12  C03   180.00   0.0  0
 7NM  CONST_16  C13  C12  C03  O04   180.00   0.0  0
 7NM  CONST_17  C18  C02  C03  O04   180.00   0.0  0
 7NM  CONST_18  C08  C07  C06  C05   180.00   0.0  0
 7NM  CONST_19  C10  C11  C06  C05   180.00   0.0  0
 7NM  CONST_20  C18  C17  C13  B14   180.00   0.0  0
 7NM  CONST_21  H11  C12  C03  C02   180.00   0.0  0
 7NM  CONST_22  H14  C17  C18  C02   180.00   0.0  0
 7NM  CONST_23  H15  C18  C02  C03   180.00   0.0  0
 7NM  CONST_24  H7   C08  C07  C06   180.00   0.0  0
 7NM  CONST_25  H9   C10  C11  C06   180.00   0.0  0
 7NM  CONST_26  H8   C09  C08  C07   180.00   0.0  0
 7NM  CONST_27  H10  C11  C06  C07   180.00   0.0  0
 7NM  CONST_28  H6   C07  C08  C09   180.00   0.0  0
 7NM  Var_01    C06  C05  O04  C03  -173.76  30.0  2
 7NM  Var_02    C07  C06  C05  O04  -125.00  30.0  2
 7NM  Var_03    C12  C03  O04  C05    -6.32  30.0  3
 7NM  Var_04    O15  B14  C13  C12  -179.63  30.0  2
 7NM  Var_05    H1   C01  C02  C03    62.32  30.0  2

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
 7NM  plan-1  C05  0.020
 7NM  plan-1  C06  0.020
 7NM  plan-1  C07  0.020
 7NM  plan-1  C08  0.020
 7NM  plan-1  C09  0.020
 7NM  plan-1  C10  0.020
 7NM  plan-1  C11  0.020
 7NM  plan-1  H6   0.020
 7NM  plan-1  H7   0.020
 7NM  plan-1  H8   0.020
 7NM  plan-1  H9   0.020
 7NM  plan-1  H10  0.020
 7NM  plan-2  C01  0.020
 7NM  plan-2  C02  0.020
 7NM  plan-2  C03  0.020
 7NM  plan-2  O04  0.020
 7NM  plan-2  C12  0.020
 7NM  plan-2  C13  0.020
 7NM  plan-2  B14  0.020
 7NM  plan-2  C17  0.020
 7NM  plan-2  C18  0.020
 7NM  plan-2  H11  0.020
 7NM  plan-2  H14  0.020
 7NM  plan-2  H15  0.020

