# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 10:29:00 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: (S)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidic fluoride
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)C(C)=N[P@](C)(F)=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
 L2Y  L2Y  '(S)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidic fluoride'  ligand  28  12  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L2Y
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
 L2Y  C01  C  CH3   0  -0.653   4.4244  -50.3038  -30.8081
 L2Y  C02  C  CH2   0  -0.342   3.7493  -51.1966  -29.7788
 L2Y  C04  C  CH2   0  -0.313   1.9297  -52.4127  -30.9260
 L2Y  C05  C  CH3   0  -0.656   0.8492  -52.7864  -29.9244
 L2Y  C06  C  C     0   0.531   3.9552  -53.5930  -30.3141
 L2Y  C07  C  CH3   0  -0.787   5.3290  -53.5626  -29.7008
 L2Y  C11  C  CH3   0  -0.933   3.2818  -56.7869  -32.4917
 L2Y  N03  N  NT    0  -0.410   3.2658  -52.4499  -30.3442
 L2Y  N08  N  N     0  -0.661   3.3906  -54.6578  -30.8048
 L2Y  O12  O  O     0  -0.727   5.2849  -56.6133  -30.6017
 L2Y  P09  P  P     0   1.302   3.8888  -56.1939  -30.9105
 L2Y  F1   F  F     0  -0.444   2.8818  -56.9394  -29.8964
 L2Y  H1   H  HCH3  0   0.239   4.7005  -49.3536  -30.3514
 L2Y  H2   H  HCH3  0   0.231   5.3308  -50.7633  -31.2031
 L2Y  H3   H  HCH3  0   0.234   3.7614  -50.0906  -31.6472
 L2Y  H4   H  HCH2  0   0.271   4.4204  -51.3961  -28.9460
 L2Y  H5   H  HCH2  0   0.265   2.8873  -50.6834  -29.3499
 L2Y  H6   H  HCH2  0   0.250   1.7649  -51.4015  -31.3000
 L2Y  H7   H  HCH2  0   0.258   1.8989  -53.0826  -31.7824
 L2Y  H8   H  HCH3  0   0.234  -0.1318  -52.7338  -30.3972
 L2Y  H9   H  HCH3  0   0.235   0.9944  -53.8021  -29.5580
 L2Y  H10  H  HCH3  0   0.226   0.8422  -52.1085  -29.0694
 L2Y  H12  H  HCH3  0   0.278   5.2486  -53.5385  -28.6125
 L2Y  H13  H  HCH3  0   0.287   5.8886  -54.4495  -29.9750
 L2Y  H14  H  HCH3  0   0.264   5.8962  -52.6872  -30.0088
 L2Y  H15  H  HCH3  0   0.272   3.4350  -57.8619  -32.5786
 L2Y  H16  H  HCH3  0   0.273   2.2242  -56.5653  -32.6199
 L2Y  H17  H  HCH3  0   0.275   3.8348  -56.2975  -33.2929

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
 L2Y  C11  P09  single  1.795  0.020  1.795
 L2Y  N08  P09  single  1.618  0.020  1.618
 L2Y  N08  C06  double  1.301  0.020  1.301
 L2Y  P09  O12  double  1.490  0.020  1.490
 L2Y  C01  C02  single  1.521  0.020  1.521
 L2Y  N03  C04  single  1.458  0.020  1.458
 L2Y  N03  C06  single  1.335  0.020  1.335
 L2Y  N03  C02  single  1.457  0.020  1.457
 L2Y  C04  C05  single  1.520  0.020  1.520
 L2Y  C06  C07  single  1.505  0.020  1.505
 L2Y  P09  F1   single  1.612  0.020  1.612
 L2Y  C01  H1   single  0.970  0.020  1.090
 L2Y  C01  H2   single  0.970  0.020  1.090
 L2Y  C01  H3   single  0.970  0.020  1.090
 L2Y  C02  H4   single  0.970  0.020  1.090
 L2Y  C02  H5   single  0.970  0.020  1.090
 L2Y  C04  H6   single  0.970  0.020  1.090
 L2Y  C04  H7   single  0.970  0.020  1.090
 L2Y  C05  H8   single  0.970  0.020  1.090
 L2Y  C05  H9   single  0.970  0.020  1.090
 L2Y  C05  H10  single  0.970  0.020  1.090
 L2Y  C07  H12  single  0.970  0.020  1.090
 L2Y  C07  H13  single  0.970  0.020  1.090
 L2Y  C07  H14  single  0.970  0.020  1.090
 L2Y  C11  H15  single  0.970  0.020  1.090
 L2Y  C11  H16  single  0.970  0.020  1.090
 L2Y  C11  H17  single  0.970  0.020  1.090

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
 L2Y  H3   C01  H2   108.00  3.000
 L2Y  H3   C01  H1   107.82  3.000
 L2Y  H2   C01  H1   107.98  3.000
 L2Y  H3   C01  C02  111.45  3.000
 L2Y  H2   C01  C02  111.52  3.000
 L2Y  H1   C01  C02  109.92  3.000
 L2Y  H5   C02  H4   105.82  3.000
 L2Y  H5   C02  N03  107.15  3.000
 L2Y  H4   C02  N03  110.11  3.000
 L2Y  H5   C02  C01  109.92  3.000
 L2Y  H4   C02  C01  110.61  3.000
 L2Y  N03  C02  C01  112.93  3.000
 L2Y  H7   C04  H6   107.27  3.000
 L2Y  H7   C04  N03  108.93  3.000
 L2Y  H6   C04  N03  107.40  3.000
 L2Y  H7   C04  C05  110.31  3.000
 L2Y  H6   C04  C05  110.27  3.000
 L2Y  N03  C04  C05  112.47  3.000
 L2Y  H10  C05  H9   108.45  3.000
 L2Y  H10  C05  H8   107.70  3.000
 L2Y  H9   C05  H8   108.11  3.000
 L2Y  H10  C05  C04  111.60  3.000
 L2Y  H9   C05  C04  110.86  3.000
 L2Y  H8   C05  C04  110.00  3.000
 L2Y  N08  C06  N03  117.90  3.000
 L2Y  N03  C06  C07  117.60  3.000
 L2Y  N08  C06  C07  124.49  3.000
 L2Y  H14  C07  H13  108.52  3.000
 L2Y  H14  C07  H12  107.64  3.000
 L2Y  H13  C07  H12  107.96  3.000
 L2Y  H14  C07  C06  112.14  3.000
 L2Y  H13  C07  C06  110.59  3.000
 L2Y  H12  C07  C06  109.85  3.000
 L2Y  H17  C11  H16  108.37  3.000
 L2Y  H17  C11  H15  108.25  3.000
 L2Y  H16  C11  H15  109.16  3.000
 L2Y  H17  C11  P09  109.14  3.000
 L2Y  H16  C11  P09  111.42  3.000
 L2Y  H15  C11  P09  110.42  3.000
 L2Y  C06  N03  C04  120.27  3.000
 L2Y  C06  N03  C02  123.79  3.000
 L2Y  C04  N03  C02  115.90  3.000
 L2Y  P09  N08  C06  131.89  3.000
 L2Y  F1   P09  O12  108.95  3.000
 L2Y  F1   P09  N08  101.86  3.000
 L2Y  O12  P09  N08  122.83  3.000
 L2Y  F1   P09  C11  100.96  3.000
 L2Y  O12  P09  C11  113.98  3.000
 L2Y  N08  P09  C11  105.49  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
 L2Y  CONST_01  N08  C06  N03  C02   180.00   0.0  0
 L2Y  CONST_02  C07  C06  N03  C02     0.00   0.0  0
 L2Y  CONST_03  N08  C06  N03  C04     0.00   0.0  0
 L2Y  CONST_04  C07  C06  N03  C04   180.00   0.0  0
 L2Y  CONST_05  P09  N08  C06  C07     0.00   0.0  0
 L2Y  CONST_06  P09  N08  C06  N03   180.00   0.0  0
 L2Y  Var_01    C04  N03  C02  C01   -86.65  30.0  2
 L2Y  Var_02    C05  C04  N03  C02   -91.70  30.0  3
 L2Y  Var_03    C11  P09  N08  C06  -142.75  30.0  3
 L2Y  Var_04    H8   C05  C04  N03   179.32  30.0  3
 L2Y  Var_05    H12  C07  C06  N03    76.70  30.0  3
 L2Y  Var_06    H1   C01  C02  N03   175.87  30.0  3
 L2Y  Var_07    H15  C11  P09  N08  -171.00  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 L2Y  chir_01  P09  N08  O12  F1  both

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
 L2Y  plan-1  C02  0.020
 L2Y  plan-1  C04  0.020
 L2Y  plan-1  C06  0.020
 L2Y  plan-1  C07  0.020
 L2Y  plan-1  N03  0.020
 L2Y  plan-1  N08  0.020
 L2Y  plan-1  P09  0.020

