# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 12:15:12 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: methyl (R)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)C(C)=N[P@](C)(=O)OC
#
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
 L0S  L0S  'methyl (R)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidate'  ligand  32  13  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L0S
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
 L0S  C13  C  CH3   0  -0.414  -0.1723  65.5398  345.7542
 L0S  C01  C  CH3   0  -0.652  -6.4268  68.9980  347.0196
 L0S  C02  C  CH2   0  -0.341  -5.9241  68.3389  348.2946
 L0S  C04  C  CH2   0  -0.309  -6.1875  65.9062  347.9686
 L0S  C05  C  CH3   0  -0.657  -6.4016  65.2359  349.3158
 L0S  C06  C  C     0   0.520  -3.9668  66.8791  347.9369
 L0S  C07  C  CH3   0  -0.786  -3.1065  68.1142  348.0176
 L0S  N03  N  NT    0  -0.416  -5.2896  67.0507  348.0508
 L0S  N08  N  N     0  -0.651  -3.5150  65.6707  347.7783
 L0S  O11  O  O     0  -0.748  -0.9801  65.6632  348.7157
 L0S  O12  O  O2    0  -0.601  -1.5212  65.7013  346.1739
 L0S  P09  P  P     0   1.243  -1.9499  65.2104  347.6705
 L0S  H1   H  HCH3  0   0.242  -0.0961  65.9334  344.7425
 L0S  H2   H  HCH3  0   0.226   0.5200  66.0870  346.3954
 L0S  H3   H  HCH3  0   0.220   0.1273  64.4887  345.7349
 L0S  H4   H  HCH3  0   0.237  -6.9377  69.9314  347.2555
 L0S  H5   H  HCH3  0   0.230  -5.6058  69.2263  346.3390
 L0S  H6   H  HCH3  0   0.233  -7.1320  68.3541  346.4937
 L0S  H7   H  HCH2  0   0.270  -5.2403  68.9996  348.8231
 L0S  H8   H  HCH2  0   0.262  -6.7561  68.1667  348.9803
 L0S  H9   H  HCH2  0   0.247  -7.1377  66.2629  347.5678
 L0S  H10  H  HCH2  0   0.255  -5.7836  65.1926  347.2539
 L0S  H11  H  HCH3  0   0.232  -7.0973  64.4029  349.2125
 L0S  H12  H  HCH3  0   0.234  -5.4629  64.8475  349.7086
 L0S  H13  H  HCH3  0   0.224  -6.8218  65.9291  350.0459
 L0S  H14  H  HCH3  0   0.266  -3.5080  68.9301  347.4194
 L0S  H15  H  HCH3  0   0.279  -3.0422  68.4616  349.0500
 L0S  H16  H  HCH3  0   0.276  -2.0963  67.9197  347.6751
 L0S  C14  C  CH3   0  -0.918  -2.0430  63.4136  347.5504
 L0S  H17  H  HCH3  0   0.270  -2.4021  63.0038  348.4940
 L0S  H18  H  HCH3  0   0.264  -2.7262  63.1068  346.7602
 L0S  H19  H  HCH3  0   0.261  -1.0601  62.9864  347.3516

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
 L0S  C13  O12  single  1.422  0.020  1.422
 L0S  O12  P09  single  1.632  0.020  1.632
 L0S  C01  C02  single  1.521  0.020  1.521
 L0S  P09  N08  single  1.635  0.020  1.635
 L0S  P09  O11  double  1.496  0.020  1.496
 L0S  N08  C06  double  1.300  0.020  1.300
 L0S  C07  C06  single  1.507  0.020  1.507
 L0S  C06  N03  single  1.339  0.020  1.339
 L0S  N03  C04  single  1.457  0.020  1.457
 L0S  N03  C02  single  1.457  0.020  1.457
 L0S  C04  C05  single  1.520  0.020  1.520
 L0S  C13  H1   single  0.970  0.020  1.090
 L0S  C13  H2   single  0.970  0.020  1.090
 L0S  C13  H3   single  0.970  0.020  1.090
 L0S  C01  H4   single  0.970  0.020  1.090
 L0S  C01  H5   single  0.970  0.020  1.090
 L0S  C01  H6   single  0.970  0.020  1.090
 L0S  C02  H7   single  0.970  0.020  1.090
 L0S  C02  H8   single  0.970  0.020  1.090
 L0S  C04  H9   single  0.970  0.020  1.090
 L0S  C04  H10  single  0.970  0.020  1.090
 L0S  C05  H11  single  0.970  0.020  1.090
 L0S  C05  H12  single  0.970  0.020  1.090
 L0S  C05  H13  single  0.970  0.020  1.090
 L0S  C07  H14  single  0.970  0.020  1.090
 L0S  C07  H15  single  0.970  0.020  1.090
 L0S  C07  H16  single  0.970  0.020  1.090
 L0S  P09  C14  single  1.803  0.020  1.803
 L0S  C14  H17  single  0.970  0.020  1.090
 L0S  C14  H18  single  0.970  0.020  1.090
 L0S  C14  H19  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
 L0S  H3   C13  H2   108.59  3.000
 L0S  H3   C13  H1   108.19  3.000
 L0S  H2   C13  H1   108.69  3.000
 L0S  H3   C13  O12  111.99  3.000
 L0S  H2   C13  O12  111.82  3.000
 L0S  H1   C13  O12  107.44  3.000
 L0S  H6   C01  H5   108.03  3.000
 L0S  H6   C01  H4   107.88  3.000
 L0S  H5   C01  H4   107.98  3.000
 L0S  H6   C01  C02  111.24  3.000
 L0S  H5   C01  C02  111.41  3.000
 L0S  H4   C01  C02  110.16  3.000
 L0S  H8   C02  H7   105.65  3.000
 L0S  H8   C02  N03  107.31  3.000
 L0S  H7   C02  N03  110.16  3.000
 L0S  H8   C02  C01  110.06  3.000
 L0S  H7   C02  C01  110.60  3.000
 L0S  N03  C02  C01  112.77  3.000
 L0S  H10  C04  H9   107.24  3.000
 L0S  H10  C04  N03  108.88  3.000
 L0S  H9   C04  N03  107.49  3.000
 L0S  H10  C04  C05  110.21  3.000
 L0S  H9   C04  C05  110.31  3.000
 L0S  N03  C04  C05  112.53  3.000
 L0S  H13  C05  H12  108.49  3.000
 L0S  H13  C05  H11  107.65  3.000
 L0S  H12  C05  H11  108.16  3.000
 L0S  H13  C05  C04  111.54  3.000
 L0S  H12  C05  C04  110.82  3.000
 L0S  H11  C05  C04  110.05  3.000
 L0S  N08  C06  N03  118.23  3.000
 L0S  N03  C06  C07  117.02  3.000
 L0S  N08  C06  C07  124.74  3.000
 L0S  H16  C07  H15  107.52  3.000
 L0S  H16  C07  H14  107.73  3.000
 L0S  H15  C07  H14  107.64  3.000
 L0S  H16  C07  C06  111.58  3.000
 L0S  H15  C07  C06  110.19  3.000
 L0S  H14  C07  C06  111.98  3.000
 L0S  C06  N03  C04  120.23  3.000
 L0S  C04  N03  C02  115.83  3.000
 L0S  C06  N03  C02  123.92  3.000
 L0S  P09  N08  C06  127.05  3.000
 L0S  P09  O12  C13  119.05  3.000
 L0S  C14  P09  O12  104.61  3.000
 L0S  C14  P09  O11  112.43  3.000
 L0S  O12  P09  O11  112.29  3.000
 L0S  C14  P09  N08  103.62  3.000
 L0S  O11  P09  N08  119.29  3.000
 L0S  O12  P09  N08  103.13  3.000
 L0S  H19  C14  H18  108.85  3.000
 L0S  H19  C14  H17  107.92  3.000
 L0S  H18  C14  H17  108.41  3.000
 L0S  H19  C14  P09  110.86  3.000
 L0S  H18  C14  P09  111.19  3.000
 L0S  H17  C14  P09  109.52  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
 L0S  CONST_01  N08  C06  N03  C02   180.00   0.0  0
 L0S  CONST_02  C07  C06  N03  C02     0.00   0.0  0
 L0S  CONST_03  N08  C06  N03  C04     0.00   0.0  0
 L0S  CONST_04  C07  C06  N03  C04   180.00   0.0  0
 L0S  CONST_05  P09  N08  C06  C07     0.00   0.0  0
 L0S  CONST_06  P09  N08  C06  N03   180.00   0.0  0
 L0S  Var_01    N08  P09  O12  C13   176.01  30.0  3
 L0S  Var_02    C06  N03  C02  C01    97.13  30.0  1
 L0S  Var_03    C05  C04  N03  C02   -90.92  30.0  3
 L0S  Var_04    O12  P09  N08  C06   -74.06  30.0  1
 L0S  Var_05    H14  C07  C06  N03   -45.03  30.0  3
 L0S  Var_06    H11  C05  C04  N03   178.58  30.0  3
 L0S  Var_07    H4   C01  C02  N03   177.09  30.0  3
 L0S  Var_08    H17  C14  P09  N08   -67.85  30.0  3
 L0S  Var_09    H1   C13  O12  P09  -179.51  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
 L0S  chir_01  P09  N08  O11  C14  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
 L0S  plan-1  C02  0.020
 L0S  plan-1  C04  0.020
 L0S  plan-1  C06  0.020
 L0S  plan-1  C07  0.020
 L0S  plan-1  N03  0.020
 L0S  plan-1  N08  0.020
 L0S  plan-1  P09  0.020

