# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:23:10 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: dodecyl(dimethyl)oxo-lambda~5~-phosphane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC[P](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
 9PD  9PD  dodecyl(dimethyl)oxo-lambda~5~-phosphane  ligand  47  16  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9PD
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
 9PD  C01  C  CH3   0  -0.666  -14.3864  -28.4932  -24.7018
 9PD  C02  C  CH2   0  -0.426  -14.7485  -29.8969  -25.1718
 9PD  C03  C  CH2   0  -0.416  -13.8131  -30.9852  -24.6509
 9PD  C04  C  CH2   0  -0.416  -13.8665  -31.1888  -23.1409
 9PD  C05  C  CH2   0  -0.421  -12.9731  -32.3258  -22.6614
 9PD  C06  C  CH2   0  -0.431  -13.0053  -32.5084  -21.1461
 9PD  C07  C  CH2   0  -0.429  -12.1600  -33.6790  -20.6263
 9PD  C08  C  CH2   0  -0.422  -12.9270  -34.9850  -20.4258
 9PD  C09  C  CH2   0  -0.420  -13.5707  -35.5585  -21.6813
 9PD  C10  C  CH2   0  -0.418  -14.2365  -36.9077  -21.4352
 9PD  C11  C  CH2   0  -0.445  -15.1249  -37.3769  -22.5852
 9PD  C12  C  CH2   0  -0.680  -14.4507  -37.4849  -23.9548
 9PD  P13  P  P     0   1.028  -13.0289  -38.6201  -24.0473
 9PD  C14  C  CH3   0  -0.895  -12.7722  -38.8819  -25.8238
 9PD  C15  C  CH3   0  -0.911  -13.6321  -40.2134  -23.4258
 9PD  O16  O  O     0  -0.746  -11.7874  -38.1361  -23.3417
 9PD  H1   H  HCH3  0   0.226  -15.0450  -27.7458  -25.1460
 9PD  H2   H  HCH3  0   0.220  -14.4656  -28.3907  -23.6187
 9PD  H3   H  HCH3  0   0.214  -13.3625  -28.2385  -24.9825
 9PD  H4   H  HCH2  0   0.219  -14.7402  -29.9191  -26.2651
 9PD  H5   H  HCH2  0   0.209  -15.7755  -30.1297  -24.8733
 9PD  H6   H  HCH2  0   0.214  -14.0620  -31.9316  -25.1420
 9PD  H7   H  HCH2  0   0.205  -12.7851  -30.7507  -24.9497
 9PD  H8   H  HCH2  0   0.211  -13.5789  -30.2660  -22.6267
 9PD  H9   H  HCH2  0   0.204  -14.9012  -31.3916  -22.8412
 9PD  H10  H  HCH2  0   0.216  -13.2681  -33.2533  -23.1620
 9PD  H11  H  HCH2  0   0.208  -11.9405  -32.1331  -22.9735
 9PD  H12  H  HCH2  0   0.218  -12.6600  -31.5773  -20.6870
 9PD  H13  H  HCH2  0   0.209  -14.0431  -32.6320  -20.8151
 9PD  H14  H  HCH2  0   0.210  -11.3192  -33.8503  -21.3072
 9PD  H15  H  HCH2  0   0.223  -11.7139  -33.4041  -19.6669
 9PD  H16  H  HCH2  0   0.206  -13.7023  -34.8273  -19.6674
 9PD  H17  H  HCH2  0   0.212  -12.2443  -35.7305  -20.0038
 9PD  H18  H  HCH2  0   0.213  -12.8112  -35.6653  -22.4614
 9PD  H19  H  HCH2  0   0.210  -14.3177  -34.8572  -22.0684
 9PD  H20  H  HCH2  0   0.218  -14.8608  -36.8444  -20.5384
 9PD  H21  H  HCH2  0   0.216  -13.4682  -37.6550  -21.2177
 9PD  H22  H  HCH2  0   0.238  -15.9624  -36.6810  -22.6865
 9PD  H23  H  HCH2  0   0.234  -15.5725  -38.3407  -22.3278
 9PD  H24  H  HCH2  0   0.268  -14.0936  -36.5098  -24.2975
 9PD  H25  H  HCH2  0   0.272  -15.1864  -37.8178  -24.6926
 9PD  H26  H  HCH3  0   0.273  -11.9593  -39.5923  -25.9751
 9PD  H27  H  HCH3  0   0.264  -13.6694  -39.2693  -26.3056
 9PD  H28  H  HCH3  0   0.272  -12.5005  -37.9391  -26.2990
 9PD  H29  H  HCH3  0   0.271  -13.8404  -40.1491  -22.3580
 9PD  H30  H  HCH3  0   0.266  -14.5423  -40.5169  -23.9424
 9PD  H31  H  HCH3  0   0.276  -12.8695  -40.9764  -23.5810

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
 9PD  C14  P13  single  1.814  0.020  1.814
 9PD  C03  C02  single  1.527  0.020  1.527
 9PD  C03  C04  single  1.525  0.020  1.525
 9PD  C02  C01  single  1.524  0.020  1.524
 9PD  C12  P13  single  1.822  0.020  1.822
 9PD  C12  C11  single  1.530  0.020  1.530
 9PD  P13  O16  double  1.508  0.020  1.508
 9PD  P13  C15  single  1.813  0.020  1.813
 9PD  C04  C05  single  1.523  0.020  1.523
 9PD  C05  C06  single  1.527  0.020  1.527
 9PD  C11  C10  single  1.527  0.020  1.527
 9PD  C09  C10  single  1.525  0.020  1.525
 9PD  C09  C08  single  1.523  0.020  1.523
 9PD  C06  C07  single  1.535  0.020  1.535
 9PD  C07  C08  single  1.528  0.020  1.528
 9PD  C01  H1   single  0.970  0.020  1.090
 9PD  C01  H2   single  0.970  0.020  1.090
 9PD  C01  H3   single  0.970  0.020  1.090
 9PD  C02  H4   single  0.970  0.020  1.090
 9PD  C02  H5   single  0.970  0.020  1.090
 9PD  C03  H6   single  0.970  0.020  1.090
 9PD  C03  H7   single  0.970  0.020  1.090
 9PD  C04  H8   single  0.970  0.020  1.090
 9PD  C04  H9   single  0.970  0.020  1.090
 9PD  C05  H10  single  0.970  0.020  1.090
 9PD  C05  H11  single  0.970  0.020  1.090
 9PD  C06  H12  single  0.970  0.020  1.090
 9PD  C06  H13  single  0.970  0.020  1.090
 9PD  C07  H14  single  0.970  0.020  1.090
 9PD  C07  H15  single  0.970  0.020  1.090
 9PD  C08  H16  single  0.970  0.020  1.090
 9PD  C08  H17  single  0.970  0.020  1.090
 9PD  C09  H18  single  0.970  0.020  1.090
 9PD  C09  H19  single  0.970  0.020  1.090
 9PD  C10  H20  single  0.970  0.020  1.090
 9PD  C10  H21  single  0.970  0.020  1.090
 9PD  C11  H22  single  0.970  0.020  1.090
 9PD  C11  H23  single  0.970  0.020  1.090
 9PD  C12  H24  single  0.970  0.020  1.090
 9PD  C12  H25  single  0.970  0.020  1.090
 9PD  C14  H26  single  0.970  0.020  1.090
 9PD  C14  H27  single  0.970  0.020  1.090
 9PD  C14  H28  single  0.970  0.020  1.090
 9PD  C15  H29  single  0.970  0.020  1.090
 9PD  C15  H30  single  0.970  0.020  1.090
 9PD  C15  H31  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
 9PD  H3   C01  H2   107.54  3.000
 9PD  H3   C01  H1   107.56  3.000
 9PD  H2   C01  H1   107.23  3.000
 9PD  H3   C01  C02  111.00  3.000
 9PD  H2   C01  C02  112.06  3.000
 9PD  H1   C01  C02  111.23  3.000
 9PD  H5   C02  H4   105.98  3.000
 9PD  H5   C02  C03  109.28  3.000
 9PD  H4   C02  C03  108.79  3.000
 9PD  H5   C02  C01  109.56  3.000
 9PD  H4   C02  C01  108.98  3.000
 9PD  C03  C02  C01  113.94  3.000
 9PD  H7   C03  H6   106.02  3.000
 9PD  H7   C03  C04  109.36  3.000
 9PD  H6   C03  C04  108.71  3.000
 9PD  H7   C03  C02  109.22  3.000
 9PD  H6   C03  C02  108.89  3.000
 9PD  C04  C03  C02  114.31  3.000
 9PD  H9   C04  H8   105.99  3.000
 9PD  H9   C04  C05  109.24  3.000
 9PD  H8   C04  C05  109.09  3.000
 9PD  H9   C04  C03  109.19  3.000
 9PD  H8   C04  C03  110.08  3.000
 9PD  C05  C04  C03  113.01  3.000
 9PD  H11  C05  H10  105.83  3.000
 9PD  H11  C05  C06  108.88  3.000
 9PD  H10  C05  C06  110.30  3.000
 9PD  H11  C05  C04  109.38  3.000
 9PD  H10  C05  C04  109.29  3.000
 9PD  C06  C05  C04  112.92  3.000
 9PD  H13  C06  H12  105.54  3.000
 9PD  H13  C06  C07  109.46  3.000
 9PD  H12  C06  C07  109.47  3.000
 9PD  H13  C06  C05  109.46  3.000
 9PD  H12  C06  C05  107.94  3.000
 9PD  C07  C06  C05  114.58  3.000
 9PD  H15  C07  H14  105.76  3.000
 9PD  H15  C07  C08  107.74  3.000
 9PD  H14  C07  C08  109.47  3.000
 9PD  H15  C07  C06  109.28  3.000
 9PD  H14  C07  C06  109.36  3.000
 9PD  C08  C07  C06  114.84  3.000
 9PD  H17  C08  H16  105.80  3.000
 9PD  H17  C08  C09  108.95  3.000
 9PD  H16  C08  C09  109.00  3.000
 9PD  H17  C08  C07  108.63  3.000
 9PD  H16  C08  C07  108.84  3.000
 9PD  C09  C08  C07  115.21  3.000
 9PD  H19  C09  H18  106.50  3.000
 9PD  H19  C09  C10  109.01  3.000
 9PD  H18  C09  C10  109.39  3.000
 9PD  H19  C09  C08  109.79  3.000
 9PD  H18  C09  C08  109.34  3.000
 9PD  C10  C09  C08  112.63  3.000
 9PD  H21  C10  H20  106.10  3.000
 9PD  H21  C10  C11  110.40  3.000
 9PD  H20  C10  C11  107.64  3.000
 9PD  H21  C10  C09  109.27  3.000
 9PD  H20  C10  C09  109.28  3.000
 9PD  C11  C10  C09  113.85  3.000
 9PD  H23  C11  H22  105.62  3.000
 9PD  H23  C11  C12  109.20  3.000
 9PD  H22  C11  C12  107.43  3.000
 9PD  H23  C11  C10  109.37  3.000
 9PD  H22  C11  C10  108.65  3.000
 9PD  C12  C11  C10  116.06  3.000
 9PD  H25  C12  H24  106.24  3.000
 9PD  H25  C12  P13  107.52  3.000
 9PD  H24  C12  P13  106.55  3.000
 9PD  H25  C12  C11  109.19  3.000
 9PD  H24  C12  C11  111.18  3.000
 9PD  P13  C12  C11  115.67  3.000
 9PD  O16  P13  C15  113.30  3.000
 9PD  C15  P13  C14  104.82  3.000
 9PD  O16  P13  C14  112.84  3.000
 9PD  C15  P13  C12  105.69  3.000
 9PD  O16  P13  C12  114.76  3.000
 9PD  C14  P13  C12  104.48  3.000
 9PD  H28  C14  H27  108.65  3.000
 9PD  H28  C14  H26  108.50  3.000
 9PD  H27  C14  H26  108.72  3.000
 9PD  H28  C14  P13  109.71  3.000
 9PD  H27  C14  P13  111.59  3.000
 9PD  H26  C14  P13  109.61  3.000
 9PD  H31  C15  H30  108.78  3.000
 9PD  H31  C15  H29  108.33  3.000
 9PD  H30  C15  H29  108.74  3.000
 9PD  H31  C15  P13  109.48  3.000
 9PD  H30  C15  P13  111.11  3.000
 9PD  H29  C15  P13  110.33  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
 9PD  Var_01  C04  C03  C02  C01    65.82  30.0  1
 9PD  Var_02  C05  C04  C03  C02   177.21  30.0  3
 9PD  Var_03  C06  C05  C04  C03   178.77  30.0  3
 9PD  Var_04  C07  C06  C05  C04   177.76  30.0  3
 9PD  Var_05  C08  C07  C06  C05   -94.76  30.0  3
 9PD  Var_06  C09  C08  C07  C06    60.55  30.0  3
 9PD  Var_07  C10  C09  C08  C07   176.01  30.0  1
 9PD  Var_08  C11  C10  C09  C08   168.36  30.0  3
 9PD  Var_09  C12  C11  C10  C09    56.61  30.0  2
 9PD  Var_10  P13  C12  C11  C10    59.19  30.0  1
 9PD  Var_11  C14  P13  C12  C11   164.44  30.0  3
 9PD  Var_12  H1   C01  C02  C03   176.62  30.0  3
 9PD  Var_13  H26  C14  P13  C12  -177.46  30.0  3
 9PD  Var_14  H29  C15  P13  C12   -68.59  30.0  3

