# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:35:23 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: benzylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Cc1ccccc1
#
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
 B85  B85  'benzylphosphonic acid    '  ligand  20  11  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B85
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
 B85  C1    C  CR16  0  -0.285   1.5005  -1.2307   0.2668
 B85  C2    C  CR16  0  -0.243   2.7796  -1.1869  -0.2696
 B85  C3    C  CR16  0  -0.267   3.4184   0.0326  -0.4528
 B85  C4    C  CR16  0  -0.241   2.7709   1.2065  -0.0911
 B85  C5    C  CR16  0  -0.296   1.4921   1.1600   0.4471
 B85  C6    C  CR6   0   0.114   0.8461  -0.0585   0.6370
 B85  C7    C  CH2   0  -0.831  -0.5448  -0.1078   1.2028
 B85  P8    P  P     0   1.370  -1.7654  -0.1269  -0.1288
 B85  O9    O  O     0  -0.709  -1.6503  -1.2473  -1.0911
 B85  O10   O  OH1   0  -0.745  -3.1360  -0.0442   0.7062
 B85  O11   O  OH1   0  -0.745  -1.6165   1.2660  -0.9205
 B85  H1    H  HCR6  0   0.253   1.0123  -2.1864   0.4121
 B85  H2    H  HCR6  0   0.257   3.2782  -2.1080  -0.5429
 B85  H3    H  HCR6  0   0.257   4.4162   0.0678  -0.8706
 B85  H4    H  HCR6  0   0.257   3.2615   2.1615  -0.2279
 B85  H5    H  HCR6  0   0.251   0.9986   2.0817   0.7312
 B85  H7    H  HCH2  0   0.311  -0.6940  -1.0114   1.7982
 B85  H7A   H  HCH2  0   0.310  -0.7357   0.7426   1.8611
 B85  HO10  H  HOH1  0   0.495  -3.9324  -0.1621   0.1698
 B85  HO11  H  HOH1  0   0.489  -1.7437   2.0644  -0.3922

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
 B85  C6   C1    aromatic  1.393  0.020  1.393
 B85  C2   C1    aromatic  1.388  0.020  1.388
 B85  C1   H1    single    0.930  0.020  1.080
 B85  C3   C2    aromatic  1.389  0.020  1.389
 B85  C2   H2    single    0.930  0.020  1.080
 B85  C4   C3    aromatic  1.389  0.020  1.389
 B85  C3   H3    single    0.930  0.020  1.080
 B85  C4   C5    aromatic  1.388  0.020  1.388
 B85  C4   H4    single    0.930  0.020  1.080
 B85  C5   C6    aromatic  1.392  0.020  1.392
 B85  C5   H5    single    0.930  0.020  1.080
 B85  C6   C7    single    1.502  0.020  1.502
 B85  P8   C7    single    1.806  0.020  1.806
 B85  C7   H7    single    0.970  0.020  1.090
 B85  C7   H7A   single    0.970  0.020  1.090
 B85  O9   P8    double    1.481  0.020  1.481
 B85  O11  P8    single    1.609  0.020  1.609
 B85  P8   O10   single    1.607  0.020  1.607
 B85  O10  HO10  single    0.850  0.020  0.980
 B85  O11  HO11  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
 B85  H1    C1   C6   119.69  3.000
 B85  H1    C1   C2   119.68  3.000
 B85  C6    C1   C2   120.62  3.000
 B85  H2    C2   C3   120.13  3.000
 B85  H2    C2   C1   119.69  3.000
 B85  C3    C2   C1   120.17  3.000
 B85  H3    C3   C4   120.20  3.000
 B85  H3    C3   C2   120.23  3.000
 B85  C4    C3   C2   119.57  3.000
 B85  H4    C4   C5   119.74  3.000
 B85  H4    C4   C3   120.11  3.000
 B85  C5    C4   C3   120.15  3.000
 B85  H5    C5   C6   119.83  3.000
 B85  H5    C5   C4   119.52  3.000
 B85  C6    C5   C4   120.64  3.000
 B85  C7    C6   C5   120.65  3.000
 B85  C7    C6   C1   120.50  3.000
 B85  C5    C6   C1   118.84  3.000
 B85  H7A   C7   H7   106.96  3.000
 B85  H7A   C7   P8   109.54  3.000
 B85  H7    C7   P8   107.50  3.000
 B85  H7A   C7   C6   111.30  3.000
 B85  H7    C7   C6   111.03  3.000
 B85  P8    C7   C6   110.39  3.000
 B85  O11   P8   O10  106.86  3.000
 B85  O10   P8   O9   116.28  3.000
 B85  O11   P8   O9   109.14  3.000
 B85  O10   P8   C7   101.11  3.000
 B85  O11   P8   C7   106.92  3.000
 B85  O9    P8   C7   115.74  3.000
 B85  HO10  O10  P8   114.06  3.000
 B85  HO11  O11  P8   115.74  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
 B85  CONST_01  C4  C5  C6  C1    0.00   0.0  0
 B85  CONST_02  C4  C3  C2  C1    0.00   0.0  0
 B85  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 B85  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 B85  CONST_05  C6  C1  C2  C3    0.00   0.0  0
 B85  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 B85  CONST_07  C7  C6  C1  C2  180.00   0.0  0
 B85  CONST_08  C7  C6  C5  C4  180.00   0.0  0
 B85  CONST_09  H5  C5  C6  C1  180.00   0.0  0
 B85  CONST_10  H3  C3  C2  C1  180.00   0.0  0
 B85  CONST_11  H4  C4  C3  C2  180.00   0.0  0
 B85  CONST_12  H1  C1  C2  C3  180.00   0.0  0
 B85  CONST_13  H2  C2  C3  C4  180.00   0.0  0
 B85  Var_01    P8  C7  C6  C1  -85.44  30.0  2
 B85  Var_02    O9  P8  C7  C6   58.35  30.0  1

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
 B85  plan-1  C1  0.020
 B85  plan-1  C2  0.020
 B85  plan-1  C3  0.020
 B85  plan-1  C4  0.020
 B85  plan-1  C5  0.020
 B85  plan-1  C6  0.020
 B85  plan-1  C7  0.020
 B85  plan-1  H1  0.020
 B85  plan-1  H2  0.020
 B85  plan-1  H3  0.020
 B85  plan-1  H4  0.020
 B85  plan-1  H5  0.020

