# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:40:19 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: (3-nitrophenyl)boronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OB(O)c1cccc(c1)[N+]([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
 NPB  NPB  '(3-nitrophenyl)boronic acid'  ligand  18  12  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NPB
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
 NPB  B     B  B      0   0.527   2.5690   0.5392   0.0195
 NPB  OB1   O  OH1    0  -0.631   3.6888  -0.2278  -0.0104
 NPB  OB2   O  OH1    0  -0.631   2.5411   1.8965   0.0443
 NPB  CP1   C  CR6    0  -0.073   1.1841  -0.2092   0.0212
 NPB  CP2   C  CR16   0  -0.345  -0.0107   0.5078   0.0290
 NPB  CP3   C  CR6    0   0.278  -1.2225  -0.1661   0.0264
 NPB  NT    N  N      1   0.330  -2.4605   0.6003   0.0335
 NPB  O1    O  O      0  -0.379  -3.5054  -0.0072   0.0385
 NPB  O2    O  O     -1  -0.380  -2.3849   1.8066   0.0327
 NPB  CP4   C  CR16   0  -0.288  -1.2909  -1.5525   0.0168
 NPB  CP5   C  CR16   0  -0.224  -0.1065  -2.2684   0.0097
 NPB  CP6   C  CR16   0  -0.297   1.1125  -1.6040   0.0117
 NPB  HO11  H  HOH1   0   0.488   4.5264   0.2461  -0.0124
 NPB  HO21  H  HOH1   0   0.487   3.3962   2.3377   0.0392
 NPB  HC21  H  HCR6   0   0.292   0.0068   1.5884   0.0365
 NPB  HC41  H  HCR6   0   0.299  -2.2392  -2.0695   0.0148
 NPB  HC51  H  HCR6   0   0.276  -0.1378  -3.3492   0.0021
 NPB  HC61  H  HCR6   0   0.271   2.0220  -2.1907   0.0065

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
 NPB  B    OB1   single    1.358  0.020  1.358
 NPB  B    OB2   single    1.358  0.020  1.358
 NPB  B    CP1   single    1.574  0.020  1.574
 NPB  OB1  HO11  single    0.850  0.020  0.980
 NPB  OB2  HO21  single    0.850  0.020  0.980
 NPB  CP1  CP2   aromatic  1.393  0.020  1.393
 NPB  CP1  CP6   aromatic  1.397  0.020  1.397
 NPB  CP2  CP3   aromatic  1.387  0.020  1.387
 NPB  CP2  HC21  single    0.930  0.020  1.080
 NPB  CP3  NT    single    1.456  0.020  1.456
 NPB  CP3  CP4   aromatic  1.388  0.020  1.388
 NPB  NT   O1    double    1.209  0.020  1.209
 NPB  NT   O2    single    1.209  0.020  1.209
 NPB  CP4  CP5   aromatic  1.384  0.020  1.384
 NPB  CP4  HC41  single    0.930  0.020  1.080
 NPB  CP5  CP6   aromatic  1.388  0.020  1.388
 NPB  CP5  HC51  single    0.930  0.020  1.080
 NPB  CP6  HC61  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
 NPB  CP1   B    OB2  117.20  3.000
 NPB  CP1   B    OB1  117.20  3.000
 NPB  OB2   B    OB1  125.60  3.000
 NPB  HO11  OB1  B    116.08  3.000
 NPB  HO21  OB2  B    116.10  3.000
 NPB  CP6   CP1  CP2  118.03  3.000
 NPB  CP6   CP1  B    121.32  3.000
 NPB  CP2   CP1  B    120.65  3.000
 NPB  HC21  CP2  CP3  120.01  3.000
 NPB  HC21  CP2  CP1  120.04  3.000
 NPB  CP3   CP2  CP1  119.95  3.000
 NPB  CP4   CP3  NT   118.94  3.000
 NPB  CP4   CP3  CP2  121.90  3.000
 NPB  NT    CP3  CP2  119.16  3.000
 NPB  O2    NT   O1   123.76  3.000
 NPB  O2    NT   CP3  118.18  3.000
 NPB  O1    NT   CP3  118.06  3.000
 NPB  HC41  CP4  CP5  120.25  3.000
 NPB  HC41  CP4  CP3  121.42  3.000
 NPB  CP5   CP4  CP3  118.33  3.000
 NPB  HC51  CP5  CP6  120.25  3.000
 NPB  HC51  CP5  CP4  119.50  3.000
 NPB  CP6   CP5  CP4  120.25  3.000
 NPB  HC61  CP6  CP5  118.59  3.000
 NPB  HC61  CP6  CP1  119.88  3.000
 NPB  CP5   CP6  CP1  121.53  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
 NPB  CONST_01  CP4   CP3  CP2  CP1     0.00   0.0  0
 NPB  CONST_02  CP4   CP5  CP6  CP1     0.00   0.0  0
 NPB  CONST_03  CP5   CP6  CP1  CP2     0.00   0.0  0
 NPB  CONST_04  CP5   CP4  CP3  CP2     0.00   0.0  0
 NPB  CONST_05  CP6   CP1  CP2  CP3     0.00   0.0  0
 NPB  CONST_06  CP6   CP5  CP4  CP3     0.00   0.0  0
 NPB  CONST_07  CP3   CP2  CP1  B     180.00   0.0  0
 NPB  CONST_08  CP5   CP6  CP1  B     180.00   0.0  0
 NPB  CONST_09  NT    CP3  CP2  CP1   180.00   0.0  0
 NPB  CONST_10  CP5   CP4  CP3  NT    180.00   0.0  0
 NPB  CONST_11  HC51  CP5  CP6  CP1   180.00   0.0  0
 NPB  CONST_12  HC61  CP6  CP1  CP2   180.00   0.0  0
 NPB  CONST_13  HC41  CP4  CP3  CP2   180.00   0.0  0
 NPB  CONST_14  HC21  CP2  CP3  CP4   180.00   0.0  0
 NPB  CONST_15  O1    NT   CP3  CP2   180.00   0.0  0
 NPB  CONST_16  O2    NT   CP3  CP2     0.00   0.0  0
 NPB  CONST_17  CP4   CP3  NT   O1      0.00   0.0  0
 NPB  CONST_18  CP4   CP3  NT   O2    180.00   0.0  0
 NPB  Var_01    CP2   CP1  B    OB1  -178.95  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
 NPB  plan-1  B     0.020
 NPB  plan-1  CP1   0.020
 NPB  plan-1  CP2   0.020
 NPB  plan-1  CP3   0.020
 NPB  plan-1  NT    0.020
 NPB  plan-1  CP4   0.020
 NPB  plan-1  CP5   0.020
 NPB  plan-1  CP6   0.020
 NPB  plan-1  HC21  0.020
 NPB  plan-1  HC41  0.020
 NPB  plan-1  HC51  0.020
 NPB  plan-1  HC61  0.020
 NPB  plan-2  CP3   0.020
 NPB  plan-2  NT    0.020
 NPB  plan-2  O1    0.020
 NPB  plan-2  O2    0.020

