# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 02:01:33 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (3-formylbut-3-en-1-yl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CCC(=C)C=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
 CYX  CYX  '(3-formylbut-3-en-1-yl)phosphonic acid'  ligand  19  10  .  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_CYX
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
 CYX  C1   C  C1    0   0.129   0.5675  -0.4098  -3.0598
 CYX  C2   C  C     0   0.052  -0.6080   0.0540  -2.3058
 CYX  O3   O  O     0  -0.387   1.7045  -0.3573  -2.6499
 CYX  C4   C  C2    0  -0.529  -1.7917  -0.0311  -2.9161
 CYX  C5   C  CH2   0  -0.510  -0.4153   0.5919  -0.9195
 CYX  C6   C  CH2   0  -0.752  -0.1162  -0.5278   0.0852
 CYX  P7   P  P     0   1.374   0.0962   0.1214   1.7520
 CYX  O8   O  OH1   0  -0.744   0.3441  -1.2292   2.5871
 CYX  O9   O  OH1   0  -0.753  -1.3315   0.7034   2.2184
 CYX  O10  O  O     0  -0.719   1.1206   1.1829   1.9035
 CYX  H11  H  H     0   0.200   0.3410  -0.8177  -4.0612
 CYX  H41  H  H     0   0.270  -1.8812  -0.4349  -3.9174
 CYX  H42  H  H     0   0.271  -2.7069   0.3006  -2.4437
 CYX  H51  H  HCH2  0   0.263  -1.3161   1.1282  -0.6190
 CYX  H52  H  HCH2  0   0.264   0.4029   1.3150  -0.9159
 CYX  H61  H  HCH2  0   0.294   0.8047  -1.0483  -0.1832
 CYX  H62  H  HCH2  0   0.293  -0.9188  -1.2689   0.0832
 CYX  H81  H  HOH1  0   0.494   0.5958  -1.0840   3.5098
 CYX  H91  H  HOH1  0   0.489  -2.0640   0.0740   2.1938

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
 CYX  C1  C2   single  1.472  0.020  1.472
 CYX  C1  O3   double  1.210  0.020  1.210
 CYX  C1  H11  single  0.930  0.020  1.080
 CYX  C2  C4   double  1.335  0.020  1.335
 CYX  C2  C5   single  1.499  0.020  1.499
 CYX  C4  H41  single  0.930  0.020  1.080
 CYX  C4  H42  single  0.930  0.020  1.080
 CYX  C5  C6   single  1.534  0.020  1.534
 CYX  C5  H51  single  0.970  0.020  1.090
 CYX  C5  H52  single  0.970  0.020  1.090
 CYX  C6  P7   single  1.801  0.020  1.801
 CYX  C6  H61  single  0.970  0.020  1.090
 CYX  C6  H62  single  0.970  0.020  1.090
 CYX  P7  O8   single  1.607  0.020  1.607
 CYX  P7  O9   single  1.611  0.020  1.611
 CYX  P7  O10  double  1.483  0.020  1.483
 CYX  O8  H81  single  0.850  0.020  0.980
 CYX  O9  H91  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
 CYX  H11  C1  O3   121.06  3.000
 CYX  H11  C1  C2   114.65  3.000
 CYX  O3   C1  C2   124.29  3.000
 CYX  C5   C2  C4   124.03  3.000
 CYX  C5   C2  C1   118.96  3.000
 CYX  C4   C2  C1   117.01  3.000
 CYX  H42  C4  H41  116.61  3.000
 CYX  H42  C4  C2   122.07  3.000
 CYX  H41  C4  C2   121.31  3.000
 CYX  H52  C5  H51  107.00  3.000
 CYX  H52  C5  C6   109.58  3.000
 CYX  H51  C5  C6   109.85  3.000
 CYX  H52  C5  C2   109.69  3.000
 CYX  H51  C5  C2   108.97  3.000
 CYX  C6   C5  C2   111.64  3.000
 CYX  H62  C6  H61  107.21  3.000
 CYX  H62  C6  P7   109.44  3.000
 CYX  H61  C6  P7   107.45  3.000
 CYX  H62  C6  C5   110.53  3.000
 CYX  H61  C6  C5   110.59  3.000
 CYX  P7   C6  C5   111.47  3.000
 CYX  O10  P7  O9   108.91  3.000
 CYX  O10  P7  O8   116.22  3.000
 CYX  O9   P7  O8   106.85  3.000
 CYX  O10  P7  C6   115.72  3.000
 CYX  O9   P7  C6   107.07  3.000
 CYX  O8   P7  C6   101.31  3.000
 CYX  H81  O8  P7   114.18  3.000
 CYX  H91  O9  P7   115.42  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
 CYX  Var_01  C6   C5  C2  C1   -73.65  30.0  3
 CYX  Var_02  P7   C6  C5  C2  -179.37  30.0  3
 CYX  Var_03  C4   C2  C1  O3   177.79  30.0  2
 CYX  Var_04  O8   P7  C6  C5   178.28  30.0  3
 CYX  Var_05  H41  C4  C2  C1     0.70   0.0  2

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
 CYX  plan-1  C1   0.020
 CYX  plan-1  C2   0.020
 CYX  plan-1  O3   0.020
 CYX  plan-1  H11  0.020
 CYX  plan-2  C1   0.020
 CYX  plan-2  C2   0.020
 CYX  plan-2  C4   0.020
 CYX  plan-2  C5   0.020
 CYX  plan-2  H41  0.020
 CYX  plan-2  H42  0.020

