# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 07:01:55 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (4-methyl-3-nitro-phenyl)boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1[N+]([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
 UK2  UK2  '(4-methyl-3-nitro-phenyl)boronic acid'  ligand  21  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_UK2
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
 UK2  B02  B  B      0   0.522  -3.3100  2.8390  -59.3983
 UK2  C03  C  CR6    0  -0.101  -4.6688  3.6220  -59.2592
 UK2  C04  C  CR16   0  -0.289  -5.2868  4.1966  -60.3726
 UK2  C05  C  CR16   0  -0.271  -6.4843  4.8817  -60.2636
 UK2  C06  C  CR6    0   0.091  -7.1592  5.0100  -59.0504
 UK2  C07  C  CH3    0  -0.714  -8.4548  5.7651  -59.0150
 UK2  C08  C  CR6    0   0.220  -6.5312  4.4287  -57.9463
 UK2  C12  C  CR16   0  -0.348  -5.3124  3.7698  -58.0363
 UK2  N09  N  N      1   0.324  -7.1406  4.4859  -56.6253
 UK2  O01  O  OH1    0  -0.623  -2.5065  2.5275  -58.3481
 UK2  O10  O  O     -1  -0.374  -6.4055  4.5799  -55.6699
 UK2  O11  O  O      0  -0.369  -8.3444  4.4188  -56.5476
 UK2  O13  O  OH1    0  -0.624  -2.9389  2.4592  -60.6462
 UK2  H1   H  HCR6   0   0.267  -4.8243  4.1194  -61.3482
 UK2  H2   H  HCR6   0   0.268  -6.9191  5.3348  -61.1457
 UK2  H3   H  HCH3   0   0.264  -9.3050  5.0899  -58.9254
 UK2  H4   H  HCH3   0   0.254  -8.5085  6.4712  -58.1876
 UK2  H5   H  HCH3   0   0.254  -8.5731  6.3261  -59.9399
 UK2  H6   H  HCR6   0   0.278  -4.8887  3.3451  -57.1354
 UK2  H7   H  HOH1   0   0.485  -2.0911  2.0033  -60.6844
 UK2  H8   H  HOH1   0   0.486  -2.7851  2.8618  -57.4917

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
 UK2  O13  B02  single    1.356  0.020  1.356
 UK2  C04  C05  aromatic  1.384  0.020  1.384
 UK2  C04  C03  aromatic  1.397  0.020  1.397
 UK2  C05  C06  aromatic  1.394  0.020  1.394
 UK2  B02  C03  single    1.574  0.020  1.574
 UK2  B02  O01  single    1.359  0.020  1.359
 UK2  C03  C12  aromatic  1.390  0.020  1.390
 UK2  C06  C07  single    1.500  0.020  1.500
 UK2  C06  C08  aromatic  1.397  0.020  1.397
 UK2  C12  C08  aromatic  1.388  0.020  1.388
 UK2  C08  N09  single    1.456  0.020  1.456
 UK2  N09  O11  double    1.208  0.020  1.208
 UK2  N09  O10  single    1.209  0.020  1.209
 UK2  C04  H1   single    0.930  0.020  1.080
 UK2  C05  H2   single    0.930  0.020  1.080
 UK2  C07  H3   single    0.970  0.020  1.090
 UK2  C07  H4   single    0.970  0.020  1.090
 UK2  C07  H5   single    0.970  0.020  1.090
 UK2  C12  H6   single    0.930  0.020  1.080
 UK2  O13  H7   single    0.850  0.020  0.980
 UK2  O01  H8   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
 UK2  O13  B02  O01  119.03  3.000
 UK2  O01  B02  C03  123.79  3.000
 UK2  O13  B02  C03  117.18  3.000
 UK2  C12  C03  C04  116.91  3.000
 UK2  C12  C03  B02  122.03  3.000
 UK2  C04  C03  B02  121.06  3.000
 UK2  H1   C04  C05  118.43  3.000
 UK2  H1   C04  C03  119.99  3.000
 UK2  C05  C04  C03  121.58  3.000
 UK2  H2   C05  C06  118.42  3.000
 UK2  H2   C05  C04  119.37  3.000
 UK2  C06  C05  C04  122.20  3.000
 UK2  C08  C06  C07  125.39  3.000
 UK2  C08  C06  C05  115.59  3.000
 UK2  C07  C06  C05  119.01  3.000
 UK2  H5   C07  H4   107.83  3.000
 UK2  H5   C07  H3   107.74  3.000
 UK2  H4   C07  H3   107.50  3.000
 UK2  H5   C07  C06  109.48  3.000
 UK2  H4   C07  C06  112.76  3.000
 UK2  H3   C07  C06  111.35  3.000
 UK2  N09  C08  C12  116.41  3.000
 UK2  N09  C08  C06  120.84  3.000
 UK2  C12  C08  C06  122.75  3.000
 UK2  H6   C12  C08  118.42  3.000
 UK2  H6   C12  C03  120.62  3.000
 UK2  C08  C12  C03  120.93  3.000
 UK2  O11  N09  O10  124.00  3.000
 UK2  O10  N09  C08  117.74  3.000
 UK2  O11  N09  C08  118.25  3.000
 UK2  H8   O01  B02  115.97  3.000
 UK2  H7   O13  B02  114.20  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
 UK2  CONST_01  C06  C05  C04  C03    0.00   0.0  0
 UK2  CONST_02  C06  C08  C12  C03    0.00   0.0  0
 UK2  CONST_03  C08  C06  C05  C04    0.00   0.0  0
 UK2  CONST_04  C08  C12  C03  C04    0.00   0.0  0
 UK2  CONST_05  C12  C03  C04  C05    0.00   0.0  0
 UK2  CONST_06  C12  C08  C06  C05    0.00   0.0  0
 UK2  CONST_07  C05  C04  C03  B02  180.00   0.0  0
 UK2  CONST_08  C08  C12  C03  B02  180.00   0.0  0
 UK2  CONST_09  N09  C08  C12  C03  180.00   0.0  0
 UK2  CONST_10  C07  C06  C05  C04  180.00   0.0  0
 UK2  CONST_11  N09  C08  C06  C05  180.00   0.0  0
 UK2  CONST_12  C12  C08  C06  C07  180.00   0.0  0
 UK2  CONST_13  H2   C05  C04  C03  180.00   0.0  0
 UK2  CONST_14  H6   C12  C03  C04  180.00   0.0  0
 UK2  CONST_15  H1   C04  C05  C06  180.00   0.0  0
 UK2  Var_01    O13  B02  C03  C04  -15.95  30.0  2
 UK2  Var_02    H3   C07  C06  C05  105.37  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
 UK2  plan-1  B02  0.020
 UK2  plan-1  C03  0.020
 UK2  plan-1  C04  0.020
 UK2  plan-1  C05  0.020
 UK2  plan-1  C06  0.020
 UK2  plan-1  C07  0.020
 UK2  plan-1  C08  0.020
 UK2  plan-1  C12  0.020
 UK2  plan-1  N09  0.020
 UK2  plan-1  H1   0.020
 UK2  plan-1  H2   0.020
 UK2  plan-1  H6   0.020
 UK2  plan-2  C08  0.020
 UK2  plan-2  N09  0.020
 UK2  plan-2  O10  0.020
 UK2  plan-2  O11  0.020

