# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 23:05:40 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: [(6-hydroxynaphthalen-2-yl)methylene]bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 RD2  RD2  '[(6-hydroxynaphthalen-2-yl)methylene]bis(phosphonic acid)'  ligand  32  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_RD2
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
 RD2  O1    O  OH1   0  -0.628   6.3022   0.0158   0.2078
 RD2  C2    C  CR6   0   0.368   4.9799   0.0120  -0.0386
 RD2  C3    C  CR16  0  -0.463   4.0263   0.1717   0.9361
 RD2  C4    C  CR66  0   0.132   2.6550   0.1610   0.6001
 RD2  C5    C  CR66  0   0.114   2.2645  -0.0126  -0.7505
 RD2  C6    C  CR16  0  -0.295   3.2725  -0.1770  -1.7298
 RD2  C7    C  CR16  0  -0.332   4.5938  -0.1668  -1.3890
 RD2  C9    C  CR16  0  -0.314   1.6415   0.3233   1.5744
 RD2  C10   C  CR16  0  -0.268   0.3202   0.3113   1.2280
 RD2  C11   C  CR6   0   0.114  -0.0750   0.1465  -0.1216
 RD2  C12   C  CR16  0  -0.367   0.8919  -0.0145  -1.0813
 RD2  C13   C  CH1   0  -0.938  -1.5287   0.1157  -0.5257
 RD2  P14   P  P     0   1.395  -2.2852  -1.5230  -0.2656
 RD2  P15   P  P     0   1.404  -2.5345   1.4374   0.2295
 RD2  O16   O  O     0  -0.692  -3.7258  -1.6034  -0.5871
 RD2  O17   O  OH1   0  -0.739  -1.4475  -2.5130  -1.2110
 RD2  O18   O  OH1   0  -0.734  -1.8567  -1.8516   1.2386
 RD2  O19   O  O     0  -0.698  -2.9845   1.1871   1.6165
 RD2  O20   O  OH1   0  -0.735  -1.6306   2.7591   0.1750
 RD2  O21   O  OH1   0  -0.732  -3.6761   1.6053  -0.8787
 RD2  H1    H  HOH1  0   0.476   6.4706   0.1534   1.1471
 RD2  H3    H  HCR6  0   0.269   4.3153   0.3118   1.9725
 RD2  H6    H  HCR6  0   0.261   2.9862  -0.3124  -2.7656
 RD2  H7    H  HCR6  0   0.271   5.3590  -0.2920  -2.1447
 RD2  H9    H  HCR6  0   0.256   1.9232   0.4593   2.6113
 RD2  H10   H  HCR6  0   0.259  -0.4275   0.4333   2.0002
 RD2  H121  H  HCR6  0   0.263   0.6112  -0.1372  -2.1217
 RD2  H23   H  HCH1  0   0.362  -1.5903   0.2661  -1.6103
 RD2  H2    H  HOH1  0   0.493  -0.5198  -2.6469  -0.9758
 RD2  H4    H  HOH1  0   0.501  -2.2985  -2.6244   1.6190
 RD2  H5    H  HOH1  0   0.494  -1.3514   3.0487  -0.7039
 RD2  H8    H  HOH1  0   0.499  -4.4552   2.0921  -0.5746

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
 RD2  O16  P14   double    1.478  0.020  1.478
 RD2  O17  P14   single    1.605  0.020  1.605
 RD2  C9   C10   aromatic  1.366  0.020  1.366
 RD2  C9   C4    aromatic  1.415  0.020  1.415
 RD2  C3   C4    aromatic  1.412  0.020  1.412
 RD2  C3   C2    aromatic  1.373  0.020  1.373
 RD2  P14  O18   single    1.598  0.020  1.598
 RD2  P14  C13   single    1.824  0.020  1.824
 RD2  O1   C2    single    1.345  0.020  1.345
 RD2  C10  C11   aromatic  1.416  0.020  1.416
 RD2  C4   C5    aromatic  1.417  0.020  1.417
 RD2  C2   C7    aromatic  1.416  0.020  1.416
 RD2  C11  C13   single    1.509  0.020  1.509
 RD2  C11  C12   aromatic  1.372  0.020  1.372
 RD2  C5   C12   aromatic  1.412  0.020  1.412
 RD2  C5   C6    aromatic  1.415  0.020  1.415
 RD2  O19  P15   double    1.480  0.020  1.480
 RD2  C7   C6    aromatic  1.365  0.020  1.365
 RD2  C13  P15   single    1.825  0.020  1.825
 RD2  P15  O21   single    1.600  0.020  1.600
 RD2  P15  O20   single    1.602  0.020  1.602
 RD2  O1   H1    single    0.850  0.020  0.980
 RD2  C3   H3    single    0.930  0.020  1.080
 RD2  C6   H6    single    0.930  0.020  1.080
 RD2  C7   H7    single    0.930  0.020  1.080
 RD2  C9   H9    single    0.930  0.020  1.080
 RD2  C10  H10   single    0.930  0.020  1.080
 RD2  C12  H121  single    0.930  0.020  1.080
 RD2  C13  H23   single    0.970  0.020  1.090
 RD2  O17  H2    single    0.850  0.020  0.980
 RD2  O18  H4    single    0.850  0.020  0.980
 RD2  O20  H5    single    0.850  0.020  0.980
 RD2  O21  H8    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
 RD2  H1    O1   C2   110.53  3.000
 RD2  C7    C2   C3   120.16  3.000
 RD2  C7    C2   O1   116.31  3.000
 RD2  C3    C2   O1   123.54  3.000
 RD2  H3    C3   C4   119.15  3.000
 RD2  H3    C3   C2   120.54  3.000
 RD2  C4    C3   C2   120.32  3.000
 RD2  C9    C4   C5   118.23  3.000
 RD2  C5    C4   C3   119.71  3.000
 RD2  C9    C4   C3   122.06  3.000
 RD2  C12   C5   C6   122.02  3.000
 RD2  C6    C5   C4   118.54  3.000
 RD2  C12   C5   C4   119.44  3.000
 RD2  H6    C6   C7   119.72  3.000
 RD2  H6    C6   C5   119.21  3.000
 RD2  C7    C6   C5   121.07  3.000
 RD2  H7    C7   C6   120.61  3.000
 RD2  H7    C7   C2   119.18  3.000
 RD2  C6    C7   C2   120.21  3.000
 RD2  H9    C9   C10  119.70  3.000
 RD2  H9    C9   C4   119.16  3.000
 RD2  C10   C9   C4   121.14  3.000
 RD2  H10   C10  C11  120.04  3.000
 RD2  H10   C10  C9   119.12  3.000
 RD2  C11   C10  C9   120.84  3.000
 RD2  C13   C11  C12  119.29  3.000
 RD2  C12   C11  C10  118.93  3.000
 RD2  C13   C11  C10  121.77  3.000
 RD2  H121  C12  C11  120.12  3.000
 RD2  H121  C12  C5   118.46  3.000
 RD2  C11   C12  C5   121.41  3.000
 RD2  H23   C13  P15  106.20  3.000
 RD2  H23   C13  P14  103.95  3.000
 RD2  P15   C13  P14  111.30  3.000
 RD2  H23   C13  C11  108.43  3.000
 RD2  P15   C13  C11  113.92  3.000
 RD2  P14   C13  C11  112.32  3.000
 RD2  O18   P14  O17  106.72  3.000
 RD2  O18   P14  O16  117.05  3.000
 RD2  O17   P14  O16  110.31  3.000
 RD2  O18   P14  C13  101.99  3.000
 RD2  O17   P14  C13  104.70  3.000
 RD2  O16   P14  C13  114.97  3.000
 RD2  O21   P15  O20  107.00  3.000
 RD2  O20   P15  O19  110.06  3.000
 RD2  O21   P15  O19  116.75  3.000
 RD2  O20   P15  C13  105.82  3.000
 RD2  O21   P15  C13  100.53  3.000
 RD2  O19   P15  C13  115.67  3.000
 RD2  H2    O17  P14  116.31  3.000
 RD2  H4    O18  P14  114.30  3.000
 RD2  H5    O20  P15  116.17  3.000
 RD2  H8    O21  P15  114.18  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
 RD2  CONST_01  C9    C4   C3   C2   180.00   0.0  0
 RD2  CONST_02  C5    C4   C3   C2     0.00   0.0  0
 RD2  CONST_03  C5    C6   C7   C2     0.00   0.0  0
 RD2  CONST_04  C10   C9   C4   C3   180.00   0.0  0
 RD2  CONST_05  C12   C5   C4   C3   180.00   0.0  0
 RD2  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 RD2  CONST_07  C6    C7   C2   C3     0.00   0.0  0
 RD2  CONST_08  C11   C10  C9   C4     0.00   0.0  0
 RD2  CONST_09  C7    C2   C3   C4     0.00   0.0  0
 RD2  CONST_10  C11   C12  C5   C4     0.00   0.0  0
 RD2  CONST_11  C7    C6   C5   C4     0.00   0.0  0
 RD2  CONST_12  C10   C9   C4   C5     0.00   0.0  0
 RD2  CONST_13  C10   C11  C12  C5     0.00   0.0  0
 RD2  CONST_14  C9    C4   C5   C6   180.00   0.0  0
 RD2  CONST_15  C11   C12  C5   C6   180.00   0.0  0
 RD2  CONST_16  C12   C5   C6   C7   180.00   0.0  0
 RD2  CONST_17  C12   C11  C10  C9     0.00   0.0  0
 RD2  CONST_18  C12   C5   C4   C9     0.00   0.0  0
 RD2  CONST_19  C4    C3   C2   O1   180.00   0.0  0
 RD2  CONST_20  C6    C7   C2   O1   180.00   0.0  0
 RD2  CONST_21  C13   C11  C12  C5   180.00   0.0  0
 RD2  CONST_22  C13   C11  C10  C9   180.00   0.0  0
 RD2  CONST_23  H6    C6   C7   C2   180.00   0.0  0
 RD2  CONST_24  H9    C9   C4   C3     0.00   0.0  0
 RD2  CONST_25  H7    C7   C2   C3   180.00   0.0  0
 RD2  CONST_26  H10   C10  C9   C4   180.00   0.0  0
 RD2  CONST_27  H121  C12  C5   C4   180.00   0.0  0
 RD2  CONST_28  H3    C3   C4   C5   180.00   0.0  0
 RD2  Var_01    P14   C13  C11  C10  -81.56  30.0  2
 RD2  Var_02    O16   P14  C13  C11  177.44  30.0  3
 RD2  Var_03    O19   P15  C13  C11  -80.91  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
 RD2  plan-1  O1    0.020
 RD2  plan-1  C2    0.020
 RD2  plan-1  C3    0.020
 RD2  plan-1  C4    0.020
 RD2  plan-1  C5    0.020
 RD2  plan-1  C6    0.020
 RD2  plan-1  C7    0.020
 RD2  plan-1  C9    0.020
 RD2  plan-1  C10   0.020
 RD2  plan-1  C11   0.020
 RD2  plan-1  C12   0.020
 RD2  plan-1  C13   0.020
 RD2  plan-1  H3    0.020
 RD2  plan-1  H6    0.020
 RD2  plan-1  H7    0.020
 RD2  plan-1  H9    0.020
 RD2  plan-1  H10   0.020
 RD2  plan-1  H121  0.020

