# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 10:44:14 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: [1-(3-chlorophenyl)-1H-pyrazol-4-yl]boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1cnn(c1)c2cccc(Cl)c2
#
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
 NL9  NL9  '[1-(3-chlorophenyl)-1H-pyrazol-4-yl]boronic acid'  ligand  23  15  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NL9
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
 NL9  B03  B   B     0   0.480   3.9720  -0.7830  -0.1130
 NL9  O04  O   OH1   0  -0.633   5.1582  -0.1388   0.0688
 NL9  O05  O   OH1   0  -0.634   3.8334  -2.0984  -0.4375
 NL9  C06  C   CR5   0  -0.320   2.6780   0.0523   0.0611
 NL9  C07  C   CR15  0  -0.088   2.5370   1.4216   0.3908
 NL9  N08  N   N     0  -0.269   1.2811   1.8006   0.4317
 NL9  N09  N   NR5   0  -0.398   0.5759   0.6999   0.1361
 NL9  C10  C   CR6   0   0.384  -0.8282   0.7554   0.0731
 NL9  C11  C   CR16  0  -0.290  -1.4614   1.9580  -0.2197
 NL9  C12  C   CR16  0  -0.251  -2.8445   1.9964  -0.2880
 NL9  C13  C   CR16  0  -0.226  -3.6060   0.8553  -0.0798
 NL9  C14  C   CR6   0  -0.031  -2.9506  -0.3302   0.2105
 NL9  CL1  CL  CL    0  -0.117  -3.8739  -1.7683   0.4891
 NL9  C16  C   CR16  0  -0.274  -1.5703  -0.3973   0.3016
 NL9  C17  C   CR15  0  -0.009   1.3746  -0.3640  -0.0943
 NL9  H1   H   HOH1  0   0.482   5.9486  -0.6765  -0.0404
 NL9  H2   H   HOH1  0   0.482   4.6515  -2.5899  -0.5593
 NL9  H3   H   HCR5  0   0.266   3.3176   2.1373   0.6027
 NL9  H4   H   HCR6  0   0.282  -0.8800   2.8511  -0.3978
 NL9  H5   H   HCR6  0   0.277  -3.3393   2.9300  -0.5189
 NL9  H6   H   HCR6  0   0.285  -4.6847   0.8911  -0.1400
 NL9  H7   H   HCR6  0   0.301  -1.0900  -1.3294   0.5649
 NL9  H8   H   HCR5  0   0.301   0.9744  -1.3252  -0.3742

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
 NL9  O05  B03  single    1.362  0.020  1.362
 NL9  O04  B03  single    1.362  0.020  1.362
 NL9  B03  C06  single    1.550  0.020  1.550
 NL9  C06  C07  aromatic  1.416  0.020  1.416
 NL9  C06  C17  aromatic  1.377  0.020  1.377
 NL9  C07  N08  aromatic  1.312  0.020  1.312
 NL9  C17  N09  aromatic  1.350  0.020  1.350
 NL9  N08  N09  aromatic  1.340  0.020  1.340
 NL9  N09  C10  single    1.407  0.020  1.407
 NL9  C10  C11  aromatic  1.390  0.020  1.390
 NL9  C10  C16  aromatic  1.390  0.020  1.390
 NL9  C11  C12  aromatic  1.385  0.020  1.385
 NL9  C16  C14  aromatic  1.385  0.020  1.385
 NL9  C12  C13  aromatic  1.388  0.020  1.388
 NL9  C14  C13  aromatic  1.385  0.020  1.385
 NL9  C14  CL1  single    1.732  0.020  1.732
 NL9  O04  H1   single    0.850  0.020  0.980
 NL9  O05  H2   single    0.850  0.020  0.980
 NL9  C07  H3   single    0.930  0.020  1.080
 NL9  C11  H4   single    0.930  0.020  1.080
 NL9  C12  H5   single    0.930  0.020  1.080
 NL9  C13  H6   single    0.930  0.020  1.080
 NL9  C16  H7   single    0.930  0.020  1.080
 NL9  C17  H8   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
 NL9  C06  B03  O05  117.53  3.000
 NL9  C06  B03  O04  117.21  3.000
 NL9  O05  B03  O04  125.26  3.000
 NL9  H1   O04  B03  115.85  3.000
 NL9  H2   O05  B03  115.91  3.000
 NL9  C17  C06  C07  102.97  3.000
 NL9  C17  C06  B03  127.92  3.000
 NL9  C07  C06  B03  129.10  3.000
 NL9  H3   C07  N08  119.62  3.000
 NL9  H3   C07  C06  127.93  3.000
 NL9  N08  C07  C06  112.45  3.000
 NL9  N09  N08  C07  105.04  3.000
 NL9  C17  N09  C10  127.87  3.000
 NL9  C10  N09  N08  120.18  3.000
 NL9  C17  N09  N08  111.94  3.000
 NL9  C16  C10  C11  120.59  3.000
 NL9  C16  C10  N09  119.54  3.000
 NL9  C11  C10  N09  119.88  3.000
 NL9  H4   C11  C12  120.41  3.000
 NL9  H4   C11  C10  120.31  3.000
 NL9  C12  C11  C10  119.28  3.000
 NL9  H5   C12  C13  119.40  3.000
 NL9  H5   C12  C11  119.42  3.000
 NL9  C13  C12  C11  121.18  3.000
 NL9  H6   C13  C14  120.81  3.000
 NL9  H6   C13  C12  120.80  3.000
 NL9  C14  C13  C12  118.39  3.000
 NL9  C16  C14  CL1  118.72  3.000
 NL9  CL1  C14  C13  119.48  3.000
 NL9  C16  C14  C13  121.79  3.000
 NL9  H7   C16  C14  120.04  3.000
 NL9  H7   C16  C10  121.18  3.000
 NL9  C14  C16  C10  118.76  3.000
 NL9  H8   C17  N09  121.82  3.000
 NL9  H8   C17  C06  130.55  3.000
 NL9  N09  C17  C06  107.60  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
 NL9  CONST_01  N09  N08  C07  C06    0.00   0.0  0
 NL9  CONST_02  N08  N09  C17  C06    0.00   0.0  0
 NL9  CONST_03  C10  N09  C17  C06  180.00   0.0  0
 NL9  CONST_04  N09  C17  C06  C07    0.00   0.0  0
 NL9  CONST_05  C17  N09  N08  C07    0.00   0.0  0
 NL9  CONST_06  C10  N09  N08  C07  180.00   0.0  0
 NL9  CONST_07  C17  C06  C07  N08    0.00   0.0  0
 NL9  CONST_10  C12  C11  C10  N09  180.00   0.0  0
 NL9  CONST_11  C14  C16  C10  N09  180.00   0.0  0
 NL9  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 NL9  CONST_13  C13  C14  C16  C10    0.00   0.0  0
 NL9  CONST_15  C14  C16  C10  C11    0.00   0.0  0
 NL9  CONST_16  C14  C13  C12  C11    0.00   0.0  0
 NL9  CONST_17  C16  C10  C11  C12    0.00   0.0  0
 NL9  CONST_18  C16  C14  C13  C12    0.00   0.0  0
 NL9  CONST_20  N08  C07  C06  B03  180.00   0.0  0
 NL9  CONST_21  N09  C17  C06  B03  180.00   0.0  0
 NL9  CONST_22  CL1  C14  C16  C10  180.00   0.0  0
 NL9  CONST_23  CL1  C14  C13  C12  180.00   0.0  0
 NL9  CONST_24  H8   C17  C06  C07  180.00   0.0  0
 NL9  CONST_25  H3   C07  N08  N09  180.00   0.0  0
 NL9  CONST_26  H4   C11  C10  N09    0.00   0.0  0
 NL9  CONST_27  H7   C16  C10  N09    0.00   0.0  0
 NL9  CONST_28  H5   C12  C11  C10  180.00   0.0  0
 NL9  CONST_29  H6   C13  C12  C11  180.00   0.0  0
 NL9  Var_01    C07  C06  B03  O04   -0.07  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
 NL9  plan-1  B03  0.020
 NL9  plan-1  C06  0.020
 NL9  plan-1  C07  0.020
 NL9  plan-1  N08  0.020
 NL9  plan-1  N09  0.020
 NL9  plan-1  C10  0.020
 NL9  plan-1  C17  0.020
 NL9  plan-1  H3   0.020
 NL9  plan-1  H8   0.020
 NL9  plan-2  N09  0.020
 NL9  plan-2  C10  0.020
 NL9  plan-2  C11  0.020
 NL9  plan-2  C12  0.020
 NL9  plan-2  C13  0.020
 NL9  plan-2  C14  0.020
 NL9  plan-2  CL1  0.020
 NL9  plan-2  C16  0.020
 NL9  plan-2  H4   0.020
 NL9  plan-2  H5   0.020
 NL9  plan-2  H6   0.020
 NL9  plan-2  H7   0.020

