# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 19:29:35 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: {[6-(phosphonooxy)naphthalen-2-yl]methylene}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)Oc1ccc2cc(ccc2c1)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
 RD1  RD1  '{[6-(phosphonooxy)naphthalen-2-yl]methylene}bis(phosphonic acid)'  ligand  37  24  .  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_RD1
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
 RD1  C8   C  CR16  0  -0.304  -1.7492   0.9688  -1.7745
 RD1  C7   C  CR16  0  -0.315  -3.0729   1.0534  -1.4474
 RD1  C6   C  CR6   0   0.359  -3.4813   0.7760  -0.1278
 RD1  C5   C  CR16  0  -0.375  -2.5859   0.4212   0.8400
 RD1  C8A  C  CR66  0   0.136  -0.7869   0.5985  -0.8067
 RD1  C1   C  CR16  0  -0.355   0.5835   0.4873  -1.1265
 RD1  C4A  C  CR66  0   0.119  -1.2135   0.3283   0.5170
 RD1  C4   C  CR16  0  -0.295  -0.2443  -0.0396   1.4770
 RD1  C3   C  CR16  0  -0.309   1.0772  -0.1373   1.1406
 RD1  C2   C  CR6   0   0.131   1.5090   0.1203  -0.1843
 RD1  O1   O  O2    0  -0.615  -4.8216   0.9037   0.1726
 RD1  C9   C  CH1   0  -0.957   2.9586  -0.0075  -0.5856
 RD1  P10  P  P     0   1.441  -5.7418  -0.4211   0.2508
 RD1  P11  P  P     0   1.398   3.9177   1.4071   0.0530
 RD1  P12  P  P     0   1.402   3.6793  -1.6613  -0.2912
 RD1  O13  O  O     0  -0.686  -5.3080  -1.4467   1.2128
 RD1  O14  O  OH1   0  -0.722  -7.1111   0.3396   0.5153
 RD1  O15  O  OH1   0  -0.731  -5.7736  -1.0259  -1.2232
 RD1  O16  O  OH1   0  -0.736   5.3873   0.9845  -0.4183
 RD1  O17  O  O     0  -0.689   3.4087   2.7158  -0.4085
 RD1  O18  O  OH1   0  -0.740   3.8914   1.3503   1.6526
 RD1  O19  O  OH1   0  -0.730   2.4621  -2.6982  -0.3710
 RD1  O20  O  O     0  -0.682   4.7435  -2.0640  -1.2317
 RD1  O21  O  OH1   0  -0.757   4.0946  -1.5394   1.2579
 RD1  H8   H  HCR6  0   0.269  -1.4281   1.1817  -2.7862
 RD1  H7   H  HCR6  0   0.279  -3.8081   1.3397  -2.1884
 RD1  H5   H  HCR6  0   0.278  -2.9156   0.2173   1.8510
 RD1  H11  H  HCR6  0   0.267   0.8958   0.6911  -2.1441
 RD1  H4   H  HCR6  0   0.267  -0.5583  -0.2488   2.4918
 RD1  H3   H  HCR6  0   0.272   1.7875  -0.4189   1.9068
 RD1  H1   H  HOH1  0   0.510  -7.8455  -0.2446   0.7504
 RD1  H2   H  HOH1  0   0.500  -6.1525  -0.4621  -1.9111
 RD1  H6   H  HOH1  0   0.502   6.0784   1.6362  -0.2315
 RD1  H12  H  HOH1  0   0.493   4.2299   0.5303   2.0410
 RD1  H13  H  HOH1  0   0.496   1.7244  -2.5544   0.2376
 RD1  H15  H  HOH1  0   0.509   4.5627  -2.3051   1.6233
 RD1  H9   H  HCH1  0   0.372   3.0169   0.1017  -1.6751

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
 RD1  C8   C7   aromatic  1.366  0.020  1.366
 RD1  C8   C8A  aromatic  1.414  0.020  1.414
 RD1  C7   C6   aromatic  1.409  0.020  1.409
 RD1  C6   C5   aromatic  1.365  0.020  1.365
 RD1  C6   O1   single    1.380  0.020  1.380
 RD1  C5   C4A  aromatic  1.413  0.020  1.413
 RD1  C8A  C1   aromatic  1.412  0.020  1.412
 RD1  C8A  C4A  aromatic  1.417  0.020  1.417
 RD1  C1   C2   aromatic  1.371  0.020  1.371
 RD1  C4A  C4   aromatic  1.413  0.020  1.413
 RD1  C4   C3   aromatic  1.367  0.020  1.367
 RD1  C3   C2   aromatic  1.417  0.020  1.417
 RD1  C2   C9   single    1.510  0.020  1.510
 RD1  O1   P10  single    1.615  0.020  1.615
 RD1  C9   P11  single    1.825  0.020  1.825
 RD1  C9   P12  single    1.828  0.020  1.828
 RD1  P10  O13  double    1.472  0.020  1.472
 RD1  P10  O14  single    1.589  0.020  1.589
 RD1  P10  O15  single    1.594  0.020  1.594
 RD1  P11  O16  single    1.600  0.020  1.600
 RD1  P11  O17  double    1.478  0.020  1.478
 RD1  P11  O18  single    1.601  0.020  1.601
 RD1  P12  O19  single    1.601  0.020  1.601
 RD1  P12  O20  double    1.476  0.020  1.476
 RD1  P12  O21  single    1.608  0.020  1.608
 RD1  C8   H8   single    0.930  0.020  1.080
 RD1  C7   H7   single    0.930  0.020  1.080
 RD1  C5   H5   single    0.930  0.020  1.080
 RD1  C1   H11  single    0.930  0.020  1.080
 RD1  C4   H4   single    0.930  0.020  1.080
 RD1  C3   H3   single    0.930  0.020  1.080
 RD1  C9   H9   single    0.970  0.020  1.090
 RD1  O14  H1   single    0.850  0.020  0.980
 RD1  O15  H2   single    0.850  0.020  0.980
 RD1  O16  H6   single    0.850  0.020  0.980
 RD1  O18  H12  single    0.850  0.020  0.980
 RD1  O19  H13  single    0.850  0.020  0.980
 RD1  O21  H15  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
 RD1  H8   C8   C8A  119.29  3.000
 RD1  H8   C8   C7   119.93  3.000
 RD1  C8A  C8   C7   120.78  3.000
 RD1  H7   C7   C6   119.76  3.000
 RD1  H7   C7   C8   120.70  3.000
 RD1  C6   C7   C8   119.53  3.000
 RD1  O1   C6   C5   120.46  3.000
 RD1  O1   C6   C7   117.86  3.000
 RD1  C5   C6   C7   121.66  3.000
 RD1  H5   C5   C4A  119.79  3.000
 RD1  H5   C5   C6   120.73  3.000
 RD1  C4A  C5   C6   119.48  3.000
 RD1  C4A  C8A  C1   119.27  3.000
 RD1  C4A  C8A  C8   118.98  3.000
 RD1  C1   C8A  C8   121.75  3.000
 RD1  H11  C1   C2   120.08  3.000
 RD1  H11  C1   C8A  118.53  3.000
 RD1  C2   C1   C8A  121.39  3.000
 RD1  C4   C4A  C8A  118.55  3.000
 RD1  C4   C4A  C5   121.88  3.000
 RD1  C8A  C4A  C5   119.57  3.000
 RD1  H4   C4   C3   119.81  3.000
 RD1  H4   C4   C4A  119.23  3.000
 RD1  C3   C4   C4A  120.96  3.000
 RD1  H3   C3   C2   120.62  3.000
 RD1  H3   C3   C4   118.61  3.000
 RD1  C2   C3   C4   120.77  3.000
 RD1  C9   C2   C3   121.72  3.000
 RD1  C9   C2   C1   119.23  3.000
 RD1  C3   C2   C1   119.05  3.000
 RD1  P10  O1   C6   119.23  3.000
 RD1  H9   C9   P12  103.25  3.000
 RD1  H9   C9   P11  104.04  3.000
 RD1  P12  C9   P11  115.97  3.000
 RD1  H9   C9   C2   107.86  3.000
 RD1  P12  C9   C2   114.36  3.000
 RD1  P11  C9   C2   110.25  3.000
 RD1  O15  P10  O14  108.58  3.000
 RD1  O15  P10  O13  110.24  3.000
 RD1  O14  P10  O13  118.62  3.000
 RD1  O15  P10  O1   106.14  3.000
 RD1  O14  P10  O1    96.11  3.000
 RD1  O13  P10  O1   115.81  3.000
 RD1  O18  P11  O17  109.74  3.000
 RD1  O18  P11  O16  107.46  3.000
 RD1  O17  P11  O16  117.27  3.000
 RD1  O18  P11  C9   108.27  3.000
 RD1  O17  P11  C9   113.34  3.000
 RD1  O16  P11  C9   100.07  3.000
 RD1  O21  P12  O20  116.62  3.000
 RD1  O21  P12  O19  107.06  3.000
 RD1  O20  P12  O19  109.85  3.000
 RD1  O21  P12  C9   100.86  3.000
 RD1  O20  P12  C9   115.37  3.000
 RD1  O19  P12  C9   106.15  3.000
 RD1  H1   O14  P10  113.93  3.000
 RD1  H2   O15  P10  116.40  3.000
 RD1  H6   O16  P11  114.90  3.000
 RD1  H12  O18  P11  115.15  3.000
 RD1  H13  O19  P12  116.89  3.000
 RD1  H15  O21  P12  115.34  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
 RD1  CONST_01  C5   C6   C7   C8     0.00   0.0  0
 RD1  CONST_02  C2   C1   C8A  C8   180.00   0.0  0
 RD1  CONST_03  C5   C4A  C8A  C8     0.00   0.0  0
 RD1  CONST_04  C4   C4A  C8A  C8   180.00   0.0  0
 RD1  CONST_05  C1   C8A  C8   C7   180.00   0.0  0
 RD1  CONST_06  C4A  C8A  C8   C7     0.00   0.0  0
 RD1  CONST_07  C4A  C5   C6   C7     0.00   0.0  0
 RD1  CONST_08  C8A  C8   C7   C6     0.00   0.0  0
 RD1  CONST_09  C8A  C4A  C5   C6     0.00   0.0  0
 RD1  CONST_10  C4   C4A  C5   C6   180.00   0.0  0
 RD1  CONST_11  C1   C8A  C4A  C5   180.00   0.0  0
 RD1  CONST_12  C3   C4   C4A  C5   180.00   0.0  0
 RD1  CONST_13  C3   C2   C1   C8A    0.00   0.0  0
 RD1  CONST_14  C3   C4   C4A  C8A    0.00   0.0  0
 RD1  CONST_15  C4   C4A  C8A  C1     0.00   0.0  0
 RD1  CONST_16  C4   C3   C2   C1     0.00   0.0  0
 RD1  CONST_17  C2   C1   C8A  C4A    0.00   0.0  0
 RD1  CONST_18  C2   C3   C4   C4A    0.00   0.0  0
 RD1  CONST_19  O1   C6   C7   C8   180.00   0.0  0
 RD1  CONST_20  C9   C2   C1   C8A  180.00   0.0  0
 RD1  CONST_21  O1   C6   C5   C4A  180.00   0.0  0
 RD1  CONST_22  C9   C2   C3   C4   180.00   0.0  0
 RD1  CONST_23  H11  C1   C8A  C8     0.00   0.0  0
 RD1  CONST_24  H5   C5   C6   C7   180.00   0.0  0
 RD1  CONST_25  H8   C8   C7   C6   180.00   0.0  0
 RD1  CONST_26  H7   C7   C6   C5   180.00   0.0  0
 RD1  CONST_27  H4   C4   C4A  C5     0.00   0.0  0
 RD1  CONST_28  H3   C3   C2   C1   180.00   0.0  0
 RD1  Var_01    P11  C9   C2   C1   105.50  30.0  2
 RD1  Var_02    O13  P10  O1   C6    57.58  30.0  3
 RD1  Var_03    O16  P11  C9   C2   176.56  30.0  3
 RD1  Var_04    O19  P12  C9   C2    27.42  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
 RD1  plan-1  C8   0.020
 RD1  plan-1  C7   0.020
 RD1  plan-1  C6   0.020
 RD1  plan-1  C5   0.020
 RD1  plan-1  C8A  0.020
 RD1  plan-1  C1   0.020
 RD1  plan-1  C4A  0.020
 RD1  plan-1  C4   0.020
 RD1  plan-1  C3   0.020
 RD1  plan-1  C2   0.020
 RD1  plan-1  O1   0.020
 RD1  plan-1  C9   0.020
 RD1  plan-1  H8   0.020
 RD1  plan-1  H7   0.020
 RD1  plan-1  H5   0.020
 RD1  plan-1  H11  0.020
 RD1  plan-1  H4   0.020
 RD1  plan-1  H3   0.020

