# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:06:20 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC[C@H](CC[P](O)(=O)OC)[C@H](C(C)=O)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
 9SW  9SW  'methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid'  ligand  69  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9SW
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
 9SW  C10  C  CH2   0  -0.399  -1.0932  -0.4808  -0.4527
 9SW  C13  C  C     0   0.649  -1.6534   2.6188   0.4196
 9SW  C15  C  CH3   0  -0.414  -8.5476  -1.7828   1.2440
 9SW  C20  C  CH2   0  -0.412   2.7452  -0.1190   0.0786
 9SW  C21  C  CH2   0  -0.413   3.9803  -0.8474  -0.4354
 9SW  C22  C  CH2   0  -0.412   5.2740  -0.3217   0.1740
 9SW  C24  C  CH2   0  -0.411   7.8086  -0.4860   0.2723
 9SW  C26  C  CH2   0  -0.406  10.3475  -0.6226   0.3623
 9SW  C28  C  CH3   0  -0.662  12.8832  -0.7338   0.4430
 9SW  C03  C  CH2   0  -0.766  -4.8682  -0.3706   0.4470
 9SW  C08  C  CH1   0  -0.239  -2.3710   0.1402   0.1208
 9SW  C09  C  CH1   0  -0.528  -2.6152   1.6341  -0.2148
 9SW  C11  C  CH2   0  -0.443  -3.5761  -0.7153  -0.2951
 9SW  C12  C  C     0   0.417  -2.7001   1.8969  -1.7135
 9SW  C14  C  CH3   0  -0.777  -4.0462   2.3029  -2.2339
 9SW  C16  C  CH3   0  -0.424  -0.6237   3.2550   2.4361
 9SW  C18  C  CH2   0  -0.435   0.2242   0.1335   0.0001
 9SW  C19  C  CH2   0  -0.409   1.4349  -0.6606  -0.4785
 9SW  C23  C  CH2   0  -0.412   6.5239  -1.0147  -0.3531
 9SW  C25  C  CH2   0  -0.412   9.0660  -1.1591  -0.2627
 9SW  C27  C  CH2   0  -0.419  11.6081  -1.2840  -0.1806
 9SW  O04  O  O     0  -0.378  -1.7356   1.7672  -2.4281
 9SW  O05  O  O2    0  -0.590  -7.3597  -1.0136   1.0348
 9SW  O06  O  O     0  -0.441  -1.1721   3.5655  -0.1504
 9SW  O07  O  O     0  -0.717  -5.7431  -3.0188   0.5835
 9SW  O17  O  OH1   0  -0.753  -6.5556  -1.6098  -1.3399
 9SW  P01  P  P     0   1.395  -6.1288  -1.6357   0.2137
 9SW  H1   H  HCH2  0   0.225  -1.0980  -1.5313  -0.1426
 9SW  H2   H  HCH2  0   0.223  -1.1349  -0.5010  -1.5439
 9SW  H3   H  HCH3  0   0.235  -9.0167  -2.0595   0.2990
 9SW  H4   H  HCH3  0   0.238  -8.3372  -2.6860   1.8162
 9SW  H5   H  HCH3  0   0.253  -9.2355  -1.1573   1.8067
 9SW  H6   H  HCH2  0   0.207   2.7197  -0.1787   1.1724
 9SW  H7   H  HCH2  0   0.207   2.8298   0.9468  -0.1613
 9SW  H8   H  HCH2  0   0.206   3.8878  -1.9187  -0.2250
 9SW  H9   H  HCH2  0   0.207   4.0280  -0.7568  -1.5263
 9SW  H10  H  HCH2  0   0.206   5.3517   0.7549  -0.0149
 9SW  H11  H  HCH2  0   0.206   5.2304  -0.4327   1.2633
 9SW  H12  H  HCH2  0   0.206   7.8764   0.5943   0.1011
 9SW  H13  H  HCH2  0   0.206   7.7621  -0.6154   1.3594
 9SW  H14  H  HCH2  0   0.205  10.4067   0.4590   0.1963
 9SW  H15  H  HCH2  0   0.206  10.3064  -0.7576   1.4491
 9SW  H16  H  HCH3  0   0.216  12.9792   0.3387   0.2626
 9SW  H17  H  HCH3  0   0.216  12.8917  -0.8851   1.5241
 9SW  H18  H  HCH3  0   0.225  13.7712  -1.2180   0.0350
 9SW  H19  H  HCH2  0   0.296  -4.6765  -0.3035   1.5215
 9SW  H20  H  HCH1  0   0.255  -2.3055   0.0769   1.2113
 9SW  H21  H  HCH1  0   0.314  -3.5807   1.8989   0.2337
 9SW  H22  H  HCH2  0   0.261  -3.3187  -1.7557  -0.0832
 9SW  H23  H  HCH3  0   0.269  -4.0215   2.5162  -3.3000
 9SW  H24  H  HCH3  0   0.257  -4.7704   1.5054  -2.0496
 9SW  H25  H  HCH3  0   0.274  -4.4079   3.1777  -1.6904
 9SW  H26  H  HCH3  0   0.254  -0.6103   2.8807   3.4550
 9SW  H27  H  HCH3  0   0.239   0.3900   3.2521   2.0358
 9SW  H28  H  HCH3  0   0.243  -1.0113   4.2731   2.4277
 9SW  H29  H  HCH2  0   0.215   0.3247   1.1570  -0.3712
 9SW  H30  H  HCH2  0   0.213   0.2468   0.1907   1.0929
 9SW  H31  H  HCH2  0   0.209   1.4677  -0.6499  -1.5734
 9SW  H32  H  HCH2  0   0.209   1.3225  -1.7111  -0.1886
 9SW  H33  H  HCH2  0   0.206   6.4474  -2.0926  -0.1714
 9SW  H34  H  HCH2  0   0.206   6.5737  -0.8951  -1.4411
 9SW  H35  H  HCH2  0   0.206   9.0018  -2.2394  -0.0907
 9SW  H36  H  HCH2  0   0.206   9.1117  -1.0296  -1.3499
 9SW  H37  H  HCH2  0   0.210  11.5523  -2.3636  -0.0101
 9SW  H38  H  HCH2  0   0.210  11.6453  -1.1520  -1.2665
 9SW  H39  H  HOH1  0   0.488  -6.8771  -0.7616  -1.6717
 9SW  H40  H  HCH2  0   0.282  -5.2866   0.5926   0.1443
 9SW  H41  H  HCH2  0   0.242  -3.7314  -0.6631  -1.3769
 9SW  O02  O  O2    0  -0.446  -1.4727   2.3686   1.7049

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
 9SW  O07  P01  double  1.483  0.020  1.483
 9SW  C15  O05  single  1.431  0.020  1.431
 9SW  O05  P01  single  1.605  0.020  1.605
 9SW  O17  P01  single  1.611  0.020  1.611
 9SW  P01  C03  single  1.801  0.020  1.801
 9SW  C03  C11  single  1.529  0.020  1.529
 9SW  C14  C12  single  1.499  0.020  1.499
 9SW  C11  C08  single  1.535  0.020  1.535
 9SW  C12  O04  double  1.207  0.020  1.207
 9SW  C12  C09  single  1.524  0.020  1.524
 9SW  C08  C09  single  1.551  0.020  1.551
 9SW  C08  C10  single  1.532  0.020  1.532
 9SW  C09  C13  single  1.516  0.020  1.516
 9SW  C18  C10  single  1.523  0.020  1.523
 9SW  C18  C19  single  1.525  0.020  1.525
 9SW  C13  O02  single  1.322  0.020  1.322
 9SW  C13  O06  double  1.205  0.020  1.205
 9SW  O02  C16  single  1.429  0.020  1.429
 9SW  C19  C20  single  1.523  0.020  1.523
 9SW  C20  C21  single  1.523  0.020  1.523
 9SW  C21  C22  single  1.524  0.020  1.524
 9SW  C22  C23  single  1.523  0.020  1.523
 9SW  C23  C24  single  1.524  0.020  1.524
 9SW  C24  C25  single  1.523  0.020  1.523
 9SW  C25  C26  single  1.523  0.020  1.523
 9SW  C26  C27  single  1.524  0.020  1.524
 9SW  C27  C28  single  1.522  0.020  1.522
 9SW  C10  H1   single  0.970  0.020  1.090
 9SW  C10  H2   single  0.970  0.020  1.090
 9SW  C15  H3   single  0.970  0.020  1.090
 9SW  C15  H4   single  0.970  0.020  1.090
 9SW  C15  H5   single  0.970  0.020  1.090
 9SW  C20  H6   single  0.970  0.020  1.090
 9SW  C20  H7   single  0.970  0.020  1.090
 9SW  C21  H8   single  0.970  0.020  1.090
 9SW  C21  H9   single  0.970  0.020  1.090
 9SW  C22  H10  single  0.970  0.020  1.090
 9SW  C22  H11  single  0.970  0.020  1.090
 9SW  C24  H12  single  0.970  0.020  1.090
 9SW  C24  H13  single  0.970  0.020  1.090
 9SW  C26  H14  single  0.970  0.020  1.090
 9SW  C26  H15  single  0.970  0.020  1.090
 9SW  C28  H16  single  0.970  0.020  1.090
 9SW  C28  H17  single  0.970  0.020  1.090
 9SW  C28  H18  single  0.970  0.020  1.090
 9SW  C03  H19  single  0.970  0.020  1.090
 9SW  C08  H20  single  0.970  0.020  1.090
 9SW  C09  H21  single  0.970  0.020  1.090
 9SW  C11  H22  single  0.970  0.020  1.090
 9SW  C14  H23  single  0.970  0.020  1.090
 9SW  C14  H24  single  0.970  0.020  1.090
 9SW  C14  H25  single  0.970  0.020  1.090
 9SW  C16  H26  single  0.970  0.020  1.090
 9SW  C16  H27  single  0.970  0.020  1.090
 9SW  C16  H28  single  0.970  0.020  1.090
 9SW  C18  H29  single  0.970  0.020  1.090
 9SW  C18  H30  single  0.970  0.020  1.090
 9SW  C19  H31  single  0.970  0.020  1.090
 9SW  C19  H32  single  0.970  0.020  1.090
 9SW  C23  H33  single  0.970  0.020  1.090
 9SW  C23  H34  single  0.970  0.020  1.090
 9SW  C25  H35  single  0.970  0.020  1.090
 9SW  C25  H36  single  0.970  0.020  1.090
 9SW  C27  H37  single  0.970  0.020  1.090
 9SW  C27  H38  single  0.970  0.020  1.090
 9SW  O17  H39  single  0.850  0.020  0.980
 9SW  C03  H40  single  0.970  0.020  1.090
 9SW  C11  H41  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
 9SW  H2   C10  H1   105.36  3.000
 9SW  H2   C10  C18  109.73  3.000
 9SW  H1   C10  C18  107.85  3.000
 9SW  H2   C10  C08  110.47  3.000
 9SW  H1   C10  C08  106.21  3.000
 9SW  C18  C10  C08  116.54  3.000
 9SW  O06  C13  O02  123.64  3.000
 9SW  O06  C13  C09  124.46  3.000
 9SW  O02  C13  C09  111.76  3.000
 9SW  H5   C15  H4   109.11  3.000
 9SW  H5   C15  H3   108.81  3.000
 9SW  H4   C15  H3   109.13  3.000
 9SW  H5   C15  O05  106.97  3.000
 9SW  H4   C15  O05  111.23  3.000
 9SW  H3   C15  O05  111.52  3.000
 9SW  H7   C20  H6   105.87  3.000
 9SW  H7   C20  C19  109.40  3.000
 9SW  H6   C20  C19  109.01  3.000
 9SW  H7   C20  C21  109.18  3.000
 9SW  H6   C20  C21  109.25  3.000
 9SW  C19  C20  C21  113.83  3.000
 9SW  H9   C21  H8   106.01  3.000
 9SW  H9   C21  C22  109.44  3.000
 9SW  H8   C21  C22  109.40  3.000
 9SW  H9   C21  C20  109.37  3.000
 9SW  H8   C21  C20  109.53  3.000
 9SW  C22  C21  C20  112.86  3.000
 9SW  H11  C22  H10  105.88  3.000
 9SW  H11  C22  C23  109.30  3.000
 9SW  H10  C22  C23  109.22  3.000
 9SW  H11  C22  C21  109.20  3.000
 9SW  H10  C22  C21  109.28  3.000
 9SW  C23  C22  C21  113.66  3.000
 9SW  H13  C24  H12  105.91  3.000
 9SW  H13  C24  C25  109.35  3.000
 9SW  H12  C24  C25  109.25  3.000
 9SW  H13  C24  C23  109.30  3.000
 9SW  H12  C24  C23  109.28  3.000
 9SW  C25  C24  C23  113.48  3.000
 9SW  H15  C26  H14  105.90  3.000
 9SW  H15  C26  C27  109.33  3.000
 9SW  H14  C26  C27  109.25  3.000
 9SW  H15  C26  C25  109.39  3.000
 9SW  H14  C26  C25  109.32  3.000
 9SW  C27  C26  C25  113.38  3.000
 9SW  H18  C28  H17  107.61  3.000
 9SW  H18  C28  H16  107.63  3.000
 9SW  H17  C28  H16  107.41  3.000
 9SW  H18  C28  C27  111.61  3.000
 9SW  H17  C28  C27  111.23  3.000
 9SW  H16  C28  C27  111.16  3.000
 9SW  H40  C03  H19  106.57  3.000
 9SW  H40  C03  P01  108.37  3.000
 9SW  H19  C03  P01  107.04  3.000
 9SW  H40  C03  C11  112.81  3.000
 9SW  H19  C03  C11  110.03  3.000
 9SW  P01  C03  C11  111.73  3.000
 9SW  H20  C08  C11  106.54  3.000
 9SW  H20  C08  C09  106.31  3.000
 9SW  C11  C08  C09  110.77  3.000
 9SW  H20  C08  C10  107.44  3.000
 9SW  C09  C08  C10  116.16  3.000
 9SW  C11  C08  C10  109.11  3.000
 9SW  H21  C09  C12  108.14  3.000
 9SW  H21  C09  C08  106.42  3.000
 9SW  C12  C09  C08  112.82  3.000
 9SW  H21  C09  C13  103.33  3.000
 9SW  C08  C09  C13  115.81  3.000
 9SW  C12  C09  C13  109.57  3.000
 9SW  H41  C11  H22  105.70  3.000
 9SW  H41  C11  C08  110.65  3.000
 9SW  H22  C11  C08  107.05  3.000
 9SW  H41  C11  C03  110.43  3.000
 9SW  H22  C11  C03  108.64  3.000
 9SW  C08  C11  C03  113.96  3.000
 9SW  O04  C12  C14  122.75  3.000
 9SW  O04  C12  C09  121.27  3.000
 9SW  C14  C12  C09  115.98  3.000
 9SW  H25  C14  H24  106.34  3.000
 9SW  H25  C14  H23  109.78  3.000
 9SW  H24  C14  H23  108.87  3.000
 9SW  H25  C14  C12  109.98  3.000
 9SW  H24  C14  C12  109.81  3.000
 9SW  H23  C14  C12  111.90  3.000
 9SW  H28  C16  H27  109.31  3.000
 9SW  H28  C16  H26  109.50  3.000
 9SW  H27  C16  H26  109.41  3.000
 9SW  H28  C16  O02  111.37  3.000
 9SW  H27  C16  O02  111.29  3.000
 9SW  H26  C16  O02  105.89  3.000
 9SW  H30  C18  H29  106.76  3.000
 9SW  H30  C18  C19  108.92  3.000
 9SW  H29  C18  C19  107.93  3.000
 9SW  H30  C18  C10  109.63  3.000
 9SW  H29  C18  C10  110.87  3.000
 9SW  C19  C18  C10  112.55  3.000
 9SW  H32  C19  H31  106.08  3.000
 9SW  H32  C19  C18  109.56  3.000
 9SW  H31  C19  C18  109.41  3.000
 9SW  H32  C19  C20  109.42  3.000
 9SW  H31  C19  C20  109.65  3.000
 9SW  C18  C19  C20  112.52  3.000
 9SW  H34  C23  H33  105.97  3.000
 9SW  H34  C23  C24  109.35  3.000
 9SW  H33  C23  C24  109.41  3.000
 9SW  H34  C23  C22  109.34  3.000
 9SW  H33  C23  C22  109.45  3.000
 9SW  C24  C23  C22  113.08  3.000
 9SW  H36  C25  H35  105.95  3.000
 9SW  H36  C25  C26  109.29  3.000
 9SW  H35  C25  C26  109.39  3.000
 9SW  H36  C25  C24  109.31  3.000
 9SW  H35  C25  C24  109.40  3.000
 9SW  C26  C25  C24  113.24  3.000
 9SW  H38  C27  H37  105.98  3.000
 9SW  H38  C27  C28  109.53  3.000
 9SW  H37  C27  C28  109.60  3.000
 9SW  H38  C27  C26  109.23  3.000
 9SW  H37  C27  C26  109.30  3.000
 9SW  C28  C27  C26  112.96  3.000
 9SW  P01  O05  C15  120.21  3.000
 9SW  H39  O17  P01  115.69  3.000
 9SW  O17  P01  O07  108.93  3.000
 9SW  O17  P01  O05  106.49  3.000
 9SW  O07  P01  O05  115.68  3.000
 9SW  O17  P01  C03  107.40  3.000
 9SW  O05  P01  C03  101.43  3.000
 9SW  O07  P01  C03  116.16  3.000
 9SW  C16  O02  C13  117.48  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
 9SW  Var_01  C20  C19  C18  C10  -174.81  30.0  3
 9SW  Var_02  O07  P01  O05  C15   -46.09  30.0  3
 9SW  Var_03  C23  C22  C21  C20  -178.59  30.0  3
 9SW  Var_04  C18  C19  C20  C21  -177.12  30.0  1
 9SW  Var_05  C24  C23  C22  C21  -179.58  30.0  3
 9SW  Var_06  C19  C20  C21  C22  -177.91  30.0  1
 9SW  Var_07  C25  C24  C23  C22  -179.18  30.0  3
 9SW  Var_08  C27  C26  C25  C24  -179.42  30.0  3
 9SW  Var_09  C23  C24  C25  C26   179.78  30.0  1
 9SW  Var_10  C25  C26  C27  C28   179.58  30.0  1
 9SW  Var_11  P01  C03  C11  C08  -166.52  30.0  1
 9SW  Var_12  C19  C18  C10  C08   172.60  30.0  1
 9SW  Var_13  O06  C13  O02  C16    -2.02  30.0  1
 9SW  Var_14  H26  C16  O02  C13   179.91  30.0  3
 9SW  Var_15  H16  C28  C27  C26   -59.51  30.0  3
 9SW  Var_16  H23  C14  C12  C09   177.45  30.0  3
 9SW  Var_17  H3   C15  O05  P01   -60.46  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
 9SW  chir_01  C08  C11  C09  C10  positiv
 9SW  chir_02  C09  C12  C08  C13  negativ
 9SW  chir_03  P01  O05  O17  C03  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
 9SW  plan-1  C09  0.020
 9SW  plan-1  C12  0.020
 9SW  plan-1  C14  0.020
 9SW  plan-1  O04  0.020
 9SW  plan-2  C13  0.020
 9SW  plan-2  C09  0.020
 9SW  plan-2  O06  0.020
 9SW  plan-2  O02  0.020

