# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 22:28:03 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(C[n+]1cccc(c1)c2ccccc2)([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
 P2H  P2H  1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium  ligand  39  23  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P2H
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
 P2H  C7    C  CH2   0  -0.449  -0.8977  -0.1445  -1.3295
 P2H  C8    C  CT    0  -0.230  -1.5944   0.3049  -0.0317
 P2H  P9    P  P     0   1.342  -2.2947  -1.1299   0.9184
 P2H  O10   O  OH1   0  -0.745  -0.9536  -1.7313   1.5337
 P2H  O11   O  OH1   0  -0.666  -3.0165  -0.4887   2.1824
 P2H  N12   N  NR6   1  -0.291   0.3656  -0.8425  -1.0621
 P2H  O12   O  O     0  -0.654  -3.1075  -2.0074   0.0477
 P2H  C13   C  CR16  0   0.113   0.4054  -2.1820  -1.0961
 P2H  O13   O  OH1   0  -0.640  -0.7547   1.1239   0.7412
 P2H  C14   C  CR16  0  -0.370   1.5778  -2.8423  -0.8184
 P2H  P14   P  P     0   1.370  -3.0146   1.4317  -0.4380
 P2H  C15   C  CR16  0  -0.200   2.7068  -2.1119  -0.4873
 P2H  O15   O  OH1   0  -0.726  -2.3582   2.7629  -1.0051
 P2H  C16   C  CR6   0   0.024   2.6554  -0.7190  -0.4552
 P2H  O16   O  OH1   0  -0.734  -3.6156   0.7476  -1.7342
 P2H  C17   C  CR16  0  -0.001   1.4525  -0.1137  -0.7699
 P2H  O17   O  O     0  -0.702  -3.9148   1.5915   0.7385
 P2H  C18   C  CR6   0   0.104   3.8244   0.1078  -0.1045
 P2H  C19   C  CR16  0  -0.289   5.1005  -0.2579  -0.5308
 P2H  C20   C  CR16  0  -0.234   6.2000   0.5217  -0.2076
 P2H  C21   C  CR16  0  -0.245   6.0388   1.6730   0.5527
 P2H  C22   C  CR16  0  -0.223   4.7700   2.0419   0.9900
 P2H  C23   C  CR16  0  -0.338   3.6686   1.2645   0.6603
 P2H  H7    H  HCH2  0   0.344  -1.5309  -0.8047  -1.9158
 P2H  H7A   H  HCH2  0   0.337  -0.6557   0.7226  -1.9417
 P2H  H13   H  HCR6  0   0.345  -0.5104  -2.6934  -1.3535
 P2H  HO13  H  HOH1  0   0.484  -0.3773   0.6584   1.4992
 P2H  H14   H  HCR6  0   0.314   1.5960  -3.9218  -0.8500
 P2H  H15   H  HCR6  0   0.335   3.6247  -2.6286  -0.2387
 P2H  H17   H  HCR6  0   0.373   1.3408   0.9592  -0.8234
 P2H  H19   H  HCR6  0   0.215   5.2307  -1.1416  -1.1435
 P2H  H20   H  HCR6  0   0.280   7.1832   0.2340  -0.5533
 P2H  H21   H  HCR6  0   0.263   6.8978   2.2782   0.8086
 P2H  H22   H  HCR6  0   0.249   4.6353   2.9357   1.5839
 P2H  H23   H  HCR6  0   0.270   2.6891   1.5481   1.0268
 P2H  H131  H  HOH1  0   0.492  -1.0221  -2.5940   1.9739
 P2H  H141  H  HOH1  0   0.504  -3.5752   0.2795   1.9200
 P2H  H151  H  HOH1  0   0.488  -2.0728   3.4081  -0.3384
 P2H  H16   H  HOH1  0   0.489  -4.4491   1.1157  -2.0735

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
 P2H  C7   C8    single    1.540  0.020  1.540
 P2H  C7   N12   single    1.468  0.020  1.468
 P2H  C7   H7    single    0.970  0.020  1.090
 P2H  C7   H7A   single    0.970  0.020  1.090
 P2H  C8   P9    single    1.858  0.020  1.858
 P2H  C8   O13   single    1.405  0.020  1.405
 P2H  C8   P14   single    1.858  0.020  1.858
 P2H  P9   O10   single    1.593  0.020  1.593
 P2H  P9   O11   single    1.591  0.020  1.591
 P2H  P9   O12   double    1.479  0.020  1.479
 P2H  N12  C13   aromatic  1.341  0.020  1.341
 P2H  N12  C17   aromatic  1.341  0.020  1.341
 P2H  C13  C14   aromatic  1.374  0.020  1.374
 P2H  C13  H13   single    0.930  0.020  1.080
 P2H  O13  HO13  single    0.850  0.020  0.980
 P2H  C14  C15   aromatic  1.385  0.020  1.385
 P2H  C14  H14   single    0.930  0.020  1.080
 P2H  P14  O15   single    1.589  0.020  1.589
 P2H  P14  O16   single    1.584  0.020  1.584
 P2H  P14  O17   double    1.490  0.020  1.490
 P2H  C15  C16   aromatic  1.394  0.020  1.394
 P2H  C15  H15   single    0.930  0.020  1.080
 P2H  C16  C17   aromatic  1.383  0.020  1.383
 P2H  C16  C18   single    1.474  0.020  1.474
 P2H  C17  H17   single    0.930  0.020  1.080
 P2H  C18  C19   aromatic  1.394  0.020  1.394
 P2H  C18  C23   aromatic  1.395  0.020  1.395
 P2H  C19  C20   aromatic  1.386  0.020  1.386
 P2H  C19  H19   single    0.930  0.020  1.080
 P2H  C20  C21   aromatic  1.389  0.020  1.389
 P2H  C20  H20   single    0.930  0.020  1.080
 P2H  C21  C22   aromatic  1.392  0.020  1.392
 P2H  C21  H21   single    0.930  0.020  1.080
 P2H  C22  C23   aromatic  1.388  0.020  1.388
 P2H  C22  H22   single    0.930  0.020  1.080
 P2H  C23  H23   single    0.930  0.020  1.080
 P2H  O10  H131  single    0.850  0.020  0.980
 P2H  O11  H141  single    0.850  0.020  0.980
 P2H  O15  H151  single    0.850  0.020  0.980
 P2H  O16  H16   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
 P2H  H7A   C7   H7   108.06  3.000
 P2H  H7A   C7   N12  106.85  3.000
 P2H  H7    C7   N12  108.11  3.000
 P2H  H7A   C7   C8   110.00  3.000
 P2H  H7    C7   C8   111.62  3.000
 P2H  N12   C7   C8   112.00  3.000
 P2H  P14   C8   O13  102.92  3.000
 P2H  P14   C8   P9   106.98  3.000
 P2H  O13   C8   P9   113.22  3.000
 P2H  P14   C8   C7   109.78  3.000
 P2H  O13   C8   C7   111.31  3.000
 P2H  P9    C8   C7   112.09  3.000
 P2H  O12   P9   O11  117.23  3.000
 P2H  O12   P9   O10  117.77  3.000
 P2H  O11   P9   O10  103.13  3.000
 P2H  O12   P9   C8   111.36  3.000
 P2H  O11   P9   C8   105.43  3.000
 P2H  O10   P9   C8    99.88  3.000
 P2H  H131  O10  P9   116.81  3.000
 P2H  H141  O11  P9   111.10  3.000
 P2H  C17   N12  C13  121.64  3.000
 P2H  C17   N12  C7   118.61  3.000
 P2H  C13   N12  C7   119.74  3.000
 P2H  H13   C13  C14  122.97  3.000
 P2H  H13   C13  N12  117.00  3.000
 P2H  C14   C13  N12  120.03  3.000
 P2H  HO13  O13  C8   112.59  3.000
 P2H  H14   C14  C15  121.36  3.000
 P2H  H14   C14  C13  119.26  3.000
 P2H  C15   C14  C13  119.38  3.000
 P2H  O17   P14  O16  117.59  3.000
 P2H  O17   P14  O15  116.20  3.000
 P2H  O16   P14  O15  103.09  3.000
 P2H  O17   P14  C8   110.74  3.000
 P2H  O16   P14  C8   101.95  3.000
 P2H  O15   P14  C8   105.69  3.000
 P2H  H15   C15  C16  120.19  3.000
 P2H  H15   C15  C14  119.64  3.000
 P2H  C16   C15  C14  120.16  3.000
 P2H  H151  O15  P14  115.67  3.000
 P2H  C18   C16  C17  119.90  3.000
 P2H  C18   C16  C15  122.45  3.000
 P2H  C17   C16  C15  117.65  3.000
 P2H  H16   O16  P14  116.57  3.000
 P2H  H17   C17  C16  122.42  3.000
 P2H  H17   C17  N12  116.44  3.000
 P2H  C16   C17  N12  121.12  3.000
 P2H  C23   C18  C19  119.16  3.000
 P2H  C23   C18  C16  120.45  3.000
 P2H  C19   C18  C16  120.39  3.000
 P2H  H19   C19  C20  119.69  3.000
 P2H  H19   C19  C18  119.80  3.000
 P2H  C20   C19  C18  120.48  3.000
 P2H  H20   C20  C21  120.07  3.000
 P2H  H20   C20  C19  119.81  3.000
 P2H  C21   C20  C19  120.11  3.000
 P2H  H21   C21  C22  120.09  3.000
 P2H  H21   C21  C20  120.08  3.000
 P2H  C22   C21  C20  119.83  3.000
 P2H  H22   C22  C23  119.64  3.000
 P2H  H22   C22  C21  120.34  3.000
 P2H  C23   C22  C21  120.02  3.000
 P2H  H23   C23  C22  119.37  3.000
 P2H  H23   C23  C18  120.22  3.000
 P2H  C22   C23  C18  120.39  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
 P2H  CONST_01  C15  C14  C13  N12    0.00   0.0  0
 P2H  CONST_02  C15  C16  C17  N12    0.00   0.0  0
 P2H  CONST_03  C18  C16  C17  N12  180.00   0.0  0
 P2H  CONST_04  C16  C17  N12  C13    0.00   0.0  0
 P2H  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 P2H  CONST_06  C17  N12  C13  C14    0.00   0.0  0
 P2H  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 P2H  CONST_08  C18  C16  C15  C14  180.00   0.0  0
 P2H  CONST_11  C20  C19  C18  C16  180.00   0.0  0
 P2H  CONST_12  C22  C23  C18  C16  180.00   0.0  0
 P2H  CONST_15  C21  C20  C19  C18    0.00   0.0  0
 P2H  CONST_16  C21  C22  C23  C18    0.00   0.0  0
 P2H  CONST_17  C22  C23  C18  C19    0.00   0.0  0
 P2H  CONST_18  C22  C21  C20  C19    0.00   0.0  0
 P2H  CONST_19  C23  C18  C19  C20    0.00   0.0  0
 P2H  CONST_20  C23  C22  C21  C20    0.00   0.0  0
 P2H  CONST_21  C14  C13  N12  C7   180.00   0.0  0
 P2H  CONST_22  C16  C17  N12  C7   180.00   0.0  0
 P2H  CONST_23  H14  C14  C13  N12  180.00   0.0  0
 P2H  CONST_24  H17  C17  N12  C13  180.00   0.0  0
 P2H  CONST_25  H15  C15  C14  C13  180.00   0.0  0
 P2H  CONST_26  H13  C13  C14  C15  180.00   0.0  0
 P2H  CONST_27  H19  C19  C18  C16    0.00   0.0  0
 P2H  CONST_28  H23  C23  C18  C16    0.00   0.0  0
 P2H  CONST_29  H20  C20  C19  C18  180.00   0.0  0
 P2H  CONST_30  H22  C22  C23  C18  180.00   0.0  0
 P2H  CONST_31  H21  C21  C20  C19  180.00   0.0  0
 P2H  Var_01    C13  N12  C7   C8   100.05  30.0  2
 P2H  Var_02    N12  C7   C8   P9   -71.20  30.0  3
 P2H  Var_03    O10  P9   C8   C7    75.41  30.0  3
 P2H  Var_04    O15  P14  C8   C7   -68.31  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
 P2H  plan-1  C7   0.020
 P2H  plan-1  N12  0.020
 P2H  plan-1  C13  0.020
 P2H  plan-1  C14  0.020
 P2H  plan-1  C15  0.020
 P2H  plan-1  C16  0.020
 P2H  plan-1  C17  0.020
 P2H  plan-1  C18  0.020
 P2H  plan-1  H13  0.020
 P2H  plan-1  H14  0.020
 P2H  plan-1  H15  0.020
 P2H  plan-1  H17  0.020
 P2H  plan-2  C16  0.020
 P2H  plan-2  C18  0.020
 P2H  plan-2  C19  0.020
 P2H  plan-2  C20  0.020
 P2H  plan-2  C21  0.020
 P2H  plan-2  C22  0.020
 P2H  plan-2  C23  0.020
 P2H  plan-2  H19  0.020
 P2H  plan-2  H20  0.020
 P2H  plan-2  H21  0.020
 P2H  plan-2  H22  0.020
 P2H  plan-2  H23  0.020

