# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 15:46:41 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: {[4-(phosphonooxy)phenyl]methylene}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1ccc(cc1)C([P](O)(O)=O)[P](O)(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
 RD3  RD3  '{[4-(phosphonooxy)phenyl]methylene}bis(phosphonic acid)'  ligand  31  20  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RD3
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
 RD3  C1   C  CH1   0  -0.964   2.0367   0.0312  -0.5492
 RD3  C2   C  CR6   0   0.146   0.5607   0.2742  -0.3508
 RD3  C3   C  CR16  0  -0.297  -0.2211   0.6407  -1.4412
 RD3  C4   C  CR16  0  -0.299  -1.5816   0.8686  -1.3021
 RD3  C5   C  CR6   0   0.345  -2.1637   0.7329  -0.0532
 RD3  C6   C  CR16  0  -0.296  -1.4047   0.3746   1.0495
 RD3  C7   C  CR16  0  -0.267  -0.0451   0.1554   0.8984
 RD3  P8   P  P     0   1.412   2.9961   1.3723   0.2287
 RD3  P9   P  P     0   1.397   2.5254  -1.6677  -0.0907
 RD3  O10  O  O2    0  -0.614  -3.5110   0.9893   0.0960
 RD3  P11  P  P     0   1.441  -4.5523  -0.2435   0.0725
 RD3  O12  O  O     0  -0.689  -4.2641  -1.3436   1.0071
 RD3  O14  O  OH1   0  -0.723  -5.8572   0.6319   0.3076
 RD3  O15  O  OH1   0  -0.731  -4.5675  -0.7867  -1.4254
 RD3  O16  O  O     0  -0.682   2.7159   1.6553   1.6501
 RD3  O17  O  OH1   0  -0.753   4.4848   0.8886  -0.1375
 RD3  O18  O  OH1   0  -0.732   2.6864   2.6734  -0.6512
 RD3  O19  O  O     0  -0.688   1.5506  -2.7023  -0.4948
 RD3  O20  O  OH1   0  -0.740   3.9370  -1.9344  -0.7972
 RD3  O21  O  OH1   0  -0.735   2.7977  -1.5079   1.4794
 RD3  H3   H  HCR6  0   0.269   0.2312   0.7453  -2.4195
 RD3  H4   H  HCR6  0   0.278  -2.1759   1.1580  -2.1589
 RD3  H6   H  HCR6  0   0.280  -1.8661   0.2796   2.0233
 RD3  H7   H  HCR6  0   0.270   0.5351  -0.1166   1.7690
 RD3  H2   H  HOH1  0   0.509  -6.6563   0.1118   0.4706
 RD3  H5   H  HOH1  0   0.500  -4.8252  -0.1514  -2.1075
 RD3  H9   H  HOH1  0   0.507   5.1957   1.3790   0.3004
 RD3  H10  H  HOH1  0   0.495   2.9140   2.6230  -1.5889
 RD3  H12  H  HOH1  0   0.492   4.6250  -1.2789  -0.6092
 RD3  H13  H  HOH1  0   0.501   2.9511  -2.3411   1.9483
 RD3  H1   H  HCH1  0   0.367   2.2486   0.0765  -1.6243

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
 RD3  C1   C2   single    1.509  0.020  1.509
 RD3  C1   P8   single    1.823  0.020  1.823
 RD3  C1   P9   single    1.826  0.020  1.826
 RD3  C2   C3   aromatic  1.391  0.020  1.391
 RD3  C2   C7   aromatic  1.393  0.020  1.393
 RD3  C3   C4   aromatic  1.386  0.020  1.386
 RD3  C4   C5   aromatic  1.385  0.020  1.385
 RD3  C5   C6   aromatic  1.386  0.020  1.386
 RD3  C5   O10  single    1.380  0.020  1.380
 RD3  C6   C7   aromatic  1.385  0.020  1.385
 RD3  P8   O16  double    1.476  0.020  1.476
 RD3  P8   O17  single    1.608  0.020  1.608
 RD3  P8   O18  single    1.601  0.020  1.601
 RD3  P9   O19  double    1.478  0.020  1.478
 RD3  P9   O20  single    1.601  0.020  1.601
 RD3  P9   O21  single    1.602  0.020  1.602
 RD3  O10  P11  single    1.614  0.020  1.614
 RD3  P11  O12  double    1.472  0.020  1.472
 RD3  P11  O14  single    1.589  0.020  1.589
 RD3  P11  O15  single    1.593  0.020  1.593
 RD3  C1   H1   single    0.970  0.020  1.090
 RD3  C3   H3   single    0.930  0.020  1.080
 RD3  C4   H4   single    0.930  0.020  1.080
 RD3  C6   H6   single    0.930  0.020  1.080
 RD3  C7   H7   single    0.930  0.020  1.080
 RD3  O14  H2   single    0.850  0.020  0.980
 RD3  O15  H5   single    0.850  0.020  0.980
 RD3  O17  H9   single    0.850  0.020  0.980
 RD3  O18  H10  single    0.850  0.020  0.980
 RD3  O20  H12  single    0.850  0.020  0.980
 RD3  O21  H13  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
 RD3  H1   C1   P9   103.46  3.000
 RD3  H1   C1   P8   106.63  3.000
 RD3  P9   C1   P8   115.87  3.000
 RD3  H1   C1   C2   108.14  3.000
 RD3  P9   C1   C2   112.24  3.000
 RD3  P8   C1   C2   109.89  3.000
 RD3  C7   C2   C3   118.75  3.000
 RD3  C7   C2   C1   121.97  3.000
 RD3  C3   C2   C1   119.28  3.000
 RD3  H3   C3   C4   118.98  3.000
 RD3  H3   C3   C2   119.94  3.000
 RD3  C4   C3   C2   121.08  3.000
 RD3  H4   C4   C5   120.63  3.000
 RD3  H4   C4   C3   120.23  3.000
 RD3  C5   C4   C3   119.14  3.000
 RD3  O10  C5   C6   119.79  3.000
 RD3  O10  C5   C4   119.33  3.000
 RD3  C6   C5   C4   120.86  3.000
 RD3  H6   C6   C7   120.19  3.000
 RD3  H6   C6   C5   120.36  3.000
 RD3  C7   C6   C5   119.44  3.000
 RD3  H7   C7   C6   118.60  3.000
 RD3  H7   C7   C2   120.67  3.000
 RD3  C6   C7   C2   120.73  3.000
 RD3  O18  P8   O17  107.36  3.000
 RD3  O18  P8   O16  109.68  3.000
 RD3  O17  P8   O16  116.92  3.000
 RD3  O18  P8   C1   105.16  3.000
 RD3  O17  P8   C1    99.72  3.000
 RD3  O16  P8   C1   116.87  3.000
 RD3  O21  P9   O20  107.42  3.000
 RD3  O21  P9   O19  116.75  3.000
 RD3  O20  P9   O19  110.14  3.000
 RD3  O21  P9   C1   101.47  3.000
 RD3  O20  P9   C1   106.27  3.000
 RD3  O19  P9   C1   113.96  3.000
 RD3  P11  O10  C5   119.11  3.000
 RD3  O15  P11  O14  108.61  3.000
 RD3  O15  P11  O12  110.12  3.000
 RD3  O14  P11  O12  118.59  3.000
 RD3  O15  P11  O10  106.27  3.000
 RD3  O14  P11  O10   96.13  3.000
 RD3  O12  P11  O10  115.81  3.000
 RD3  H2   O14  P11  114.03  3.000
 RD3  H5   O15  P11  116.21  3.000
 RD3  H9   O17  P8   115.12  3.000
 RD3  H10  O18  P8   116.45  3.000
 RD3  H12  O20  P9   115.33  3.000
 RD3  H13  O21  P9   114.57  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
 RD3  CONST_01  C5   C4   C3   C2    0.00   0.0  0
 RD3  CONST_02  C5   C6   C7   C2    0.00   0.0  0
 RD3  CONST_03  C6   C7   C2   C3    0.00   0.0  0
 RD3  CONST_04  C6   C5   C4   C3    0.00   0.0  0
 RD3  CONST_05  C7   C2   C3   C4    0.00   0.0  0
 RD3  CONST_06  C7   C6   C5   C4    0.00   0.0  0
 RD3  CONST_07  C4   C3   C2   C1  180.00   0.0  0
 RD3  CONST_08  C6   C7   C2   C1  180.00   0.0  0
 RD3  CONST_09  O10  C5   C4   C3  180.00   0.0  0
 RD3  CONST_10  O10  C5   C6   C7  180.00   0.0  0
 RD3  CONST_11  H4   C4   C3   C2  180.00   0.0  0
 RD3  CONST_12  H6   C6   C7   C2  180.00   0.0  0
 RD3  CONST_13  H7   C7   C2   C3  180.00   0.0  0
 RD3  CONST_14  H3   C3   C4   C5  180.00   0.0  0
 RD3  Var_01    P8   C1   C2   C3  109.22  30.0  2
 RD3  Var_02    O16  P8   C1   C2   53.67  30.0  3
 RD3  Var_03    O19  P9   C1   C2   39.76  30.0  3
 RD3  Var_04    O12  P11  O10  C5   53.01  30.0  3

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
 RD3  plan-1  C1   0.020
 RD3  plan-1  C2   0.020
 RD3  plan-1  C3   0.020
 RD3  plan-1  C4   0.020
 RD3  plan-1  C5   0.020
 RD3  plan-1  C6   0.020
 RD3  plan-1  C7   0.020
 RD3  plan-1  O10  0.020
 RD3  plan-1  H3   0.020
 RD3  plan-1  H4   0.020
 RD3  plan-1  H6   0.020
 RD3  plan-1  H7   0.020

