# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:55:27 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2R)-2,3-bis(hexyloxy)propyl hydrogen (S)-pentylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCOC[C@H](CO[P](O)(=O)CCCCC)OCCCCCC
#
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
 C63  C63  '(2R)-2,3-bis(hexyloxy)propyl hydrogen (S)-pentylphosphonate'  ligand  69  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C63
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
 C63  P5   P  P     0   1.391    3.3241  -1.5576   0.4273
 C63  O11  O  O     0  -0.720    3.4755  -1.7613   1.8888
 C63  C6   C  CH2   0  -0.744    4.0771  -0.0734  -0.2555
 C63  C7   C  CH2   0  -0.431    5.5828  -0.0069  -0.0014
 C63  C8   C  CH2   0  -0.402    6.1833   1.2968  -0.5125
 C63  C9   C  CH2   0  -0.420    7.6873   1.3866  -0.2862
 C63  C10  C  CH3   0  -0.663    8.2778   2.6960  -0.7902
 C63  O4   O  O2    0  -0.592    1.8144  -1.4180  -0.1008
 C63  C3   C  CH2   0  -0.154    0.7556  -2.2322   0.4024
 C63  C2   C  CH1   0  -0.033   -0.5500  -1.5816  -0.0149
 C63  O13  O  O2    0  -0.499   -0.6322  -0.3029   0.5678
 C63  C14  C  CH2   0  -0.122   -0.6774   0.7814  -0.3330
 C63  C15  C  CH2   0  -0.464   -0.5592   2.0723   0.4504
 C63  C16  C  CH2   0  -0.424   -0.6001   3.2981  -0.4540
 C63  C17  C  CH2   0  -0.405   -0.4726   4.6046   0.3188
 C63  C1   C  CH2   0  -0.129   -1.7352  -2.4206   0.4256
 C63  O20  O  O2    0  -0.486   -2.8953  -1.8659  -0.1317
 C63  C21  C  CH2   0  -0.122   -4.0813  -2.4594   0.3418
 C63  C22  C  CH2   0  -0.461   -5.2698  -1.8054  -0.3327
 C63  C23  C  CH2   0  -0.424   -6.5958  -2.3677   0.1638
 C63  C24  C  CH2   0  -0.406   -7.7989  -1.7238  -0.5133
 C63  C25  C  CH2   0  -0.419   -9.1326  -2.2654  -0.0151
 C63  C26  C  CH3   0  -0.663  -10.3274  -1.6149  -0.6981
 C63  H2   H  HCH2  0   0.282    3.8635  -0.0206  -1.3264
 C63  H3   H  HCH2  0   0.280    3.5785   0.7833   0.2066
 C63  H4   H  HCH2  0   0.233    5.7804  -0.1025   1.0698
 C63  H5   H  HCH2  0   0.231    6.0799  -0.8510  -0.4866
 C63  H6   H  HCH2  0   0.214    5.9696   1.4014  -1.5817
 C63  H7   H  HCH2  0   0.215    5.6891   2.1405  -0.0189
 C63  H8   H  HCH2  0   0.213    7.9001   1.2739   0.7813
 C63  H9   H  HCH2  0   0.213    8.1784   0.5453  -0.7845
 C63  H10  H  HCH3  0   0.217    8.1135   2.8153  -1.8628
 C63  H11  H  HCH3  0   0.217    7.8207   3.5521  -0.2906
 C63  H12  H  HCH3  0   0.228    9.3528   2.7455  -0.6144
 C63  H13  H  HCH2  0   0.235    0.8279  -3.2414  -0.0114
 C63  H14  H  HCH2  0   0.234    0.8144  -2.3059   1.4919
 C63  H15  H  HCH1  0   0.229   -0.5655  -1.5166  -1.1117
 C63  H16  H  HCH2  0   0.195    0.1410   0.7200  -1.0617
 C63  H17  H  HCH2  0   0.193   -1.6159   0.7736  -0.9043
 C63  H18  H  HCH2  0   0.220   -1.3694   2.1320   1.1838
 C63  H19  H  HCH2  0   0.218    0.3791   2.0651   1.0146
 C63  H20  H  HCH2  0   0.212    0.2061   3.2338  -1.1929
 C63  H21  H  HCH2  0   0.212   -1.5357   3.3027  -1.0241
 C63  H22  H  HCH2  0   0.208   -1.2799   4.6714   1.0567
 C63  H23  H  HCH2  0   0.208    0.4613   4.5974   0.8922
 C63  H25  H  HCH2  0   0.201   -1.5976  -3.4621   0.1006
 C63  H26  H  HCH2  0   0.202   -1.7911  -2.4340   1.5241
 C63  H27  H  HCH2  0   0.192   -4.0825  -3.5408   0.1400
 C63  H28  H  HCH2  0   0.194   -4.1567  -2.3448   1.4334
 C63  H29  H  HCH2  0   0.221   -5.2393  -0.7266  -0.1506
 C63  H30  H  HCH2  0   0.221   -5.1952  -1.9443  -1.4157
 C63  H31  H  HCH2  0   0.213   -6.6231  -3.4501  -0.0023
 C63  H32  H  HCH2  0   0.213   -6.6709  -2.2256   1.2473
 C63  H33  H  HCH2  0   0.208   -7.7659  -0.6400  -0.3557
 C63  H34  H  HCH2  0   0.209   -7.7283  -1.8725  -1.5965
 C63  H35  H  HCH2  0   0.211   -9.1651  -3.3480  -0.1722
 C63  H36  H  HCH2  0   0.211   -9.2018  -2.1155   1.0669
 C63  H37  H  HCH3  0   0.216  -10.3384  -0.5361  -0.5307
 C63  H38  H  HCH3  0   0.216  -10.3017  -1.7779  -1.7773
 C63  H39  H  HCH3  0   0.226  -11.2703  -2.0166  -0.3257
 C63  O12  O  OH1   0  -0.754    3.9574  -2.8232  -0.3441
 C63  H1   H  HOH1  0   0.488    3.8901  -2.7954  -1.3075
 C63  C18  C  CH2   0  -0.419   -0.5049   5.8390  -0.5741
 C63  C19  C  CH3   0  -0.662   -0.3694   7.1358   0.2120
 C63  H24  H  HCH2  0   0.211    0.2998   5.7713  -1.3125
 C63  H40  H  HCH2  0   0.211   -1.4394   5.8490  -1.1438
 C63  H41  H  HCH3  0   0.216   -1.1770   7.2426   0.9390
 C63  H42  H  HCH3  0   0.216    0.5730   7.1642   0.7628
 C63  H43  H  HCH3  0   0.226   -0.3960   8.0087  -0.4412

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
 C63  C26  C25  single  1.522  0.020  1.522
 C63  C25  C24  single  1.523  0.020  1.523
 C63  C16  C17  single  1.523  0.020  1.523
 C63  C16  C15  single  1.524  0.020  1.524
 C63  C24  C23  single  1.523  0.020  1.523
 C63  C10  C9   single  1.522  0.020  1.522
 C63  C15  C14  single  1.515  0.020  1.515
 C63  C23  C22  single  1.523  0.020  1.523
 C63  C14  O13  single  1.410  0.020  1.410
 C63  C9   C8   single  1.524  0.020  1.524
 C63  O13  C2   single  1.408  0.020  1.408
 C63  C22  C21  single  1.515  0.020  1.515
 C63  O20  C21  single  1.408  0.020  1.408
 C63  O20  C1   single  1.401  0.020  1.401
 C63  C8   C7   single  1.524  0.020  1.524
 C63  C2   C1   single  1.517  0.020  1.517
 C63  C2   C3   single  1.517  0.020  1.517
 C63  C7   C6   single  1.528  0.020  1.528
 C63  C6   P5   single  1.799  0.020  1.799
 C63  C3   O4   single  1.427  0.020  1.427
 C63  P5   O4   single  1.605  0.020  1.605
 C63  P5   O11  double  1.483  0.020  1.483
 C63  C6   H2   single  0.970  0.020  1.090
 C63  C6   H3   single  0.970  0.020  1.090
 C63  C7   H4   single  0.970  0.020  1.090
 C63  C7   H5   single  0.970  0.020  1.090
 C63  C8   H6   single  0.970  0.020  1.090
 C63  C8   H7   single  0.970  0.020  1.090
 C63  C9   H8   single  0.970  0.020  1.090
 C63  C9   H9   single  0.970  0.020  1.090
 C63  C10  H10  single  0.970  0.020  1.090
 C63  C10  H11  single  0.970  0.020  1.090
 C63  C10  H12  single  0.970  0.020  1.090
 C63  C3   H13  single  0.970  0.020  1.090
 C63  C3   H14  single  0.970  0.020  1.090
 C63  C2   H15  single  0.970  0.020  1.090
 C63  C14  H16  single  0.970  0.020  1.090
 C63  C14  H17  single  0.970  0.020  1.090
 C63  C15  H18  single  0.970  0.020  1.090
 C63  C15  H19  single  0.970  0.020  1.090
 C63  C16  H20  single  0.970  0.020  1.090
 C63  C16  H21  single  0.970  0.020  1.090
 C63  C17  H22  single  0.970  0.020  1.090
 C63  C17  H23  single  0.970  0.020  1.090
 C63  C1   H25  single  0.970  0.020  1.090
 C63  C1   H26  single  0.970  0.020  1.090
 C63  C21  H27  single  0.970  0.020  1.090
 C63  C21  H28  single  0.970  0.020  1.090
 C63  C22  H29  single  0.970  0.020  1.090
 C63  C22  H30  single  0.970  0.020  1.090
 C63  C23  H31  single  0.970  0.020  1.090
 C63  C23  H32  single  0.970  0.020  1.090
 C63  C24  H33  single  0.970  0.020  1.090
 C63  C24  H34  single  0.970  0.020  1.090
 C63  C25  H35  single  0.970  0.020  1.090
 C63  C25  H36  single  0.970  0.020  1.090
 C63  C26  H37  single  0.970  0.020  1.090
 C63  C26  H38  single  0.970  0.020  1.090
 C63  C26  H39  single  0.970  0.020  1.090
 C63  P5   O12  single  1.612  0.020  1.612
 C63  O12  H1   single  0.850  0.020  0.980
 C63  C17  C18  single  1.524  0.020  1.524
 C63  C18  C19  single  1.522  0.020  1.522
 C63  C18  H24  single  0.970  0.020  1.090
 C63  C18  H40  single  0.970  0.020  1.090
 C63  C19  H41  single  0.970  0.020  1.090
 C63  C19  H42  single  0.970  0.020  1.090
 C63  C19  H43  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
 C63  O12  P5   O4   106.28  3.000
 C63  O12  P5   C6   107.56  3.000
 C63  O4   P5   C6   101.36  3.000
 C63  O12  P5   O11  108.88  3.000
 C63  O4   P5   O11  115.60  3.000
 C63  C6   P5   O11  116.39  3.000
 C63  H3   C6   H2   106.68  3.000
 C63  H3   C6   C7   110.17  3.000
 C63  H2   C6   C7   110.68  3.000
 C63  H3   C6   P5   107.16  3.000
 C63  H2   C6   P5   109.26  3.000
 C63  C7   C6   P5   112.65  3.000
 C63  H5   C7   H4   106.56  3.000
 C63  H5   C7   C8   109.42  3.000
 C63  H4   C7   C8   109.40  3.000
 C63  H5   C7   C6   109.92  3.000
 C63  H4   C7   C6   109.70  3.000
 C63  C8   C7   C6   111.70  3.000
 C63  H7   C8   H6   106.16  3.000
 C63  H7   C8   C9   109.45  3.000
 C63  H6   C8   C9   109.39  3.000
 C63  H7   C8   C7   109.28  3.000
 C63  H6   C8   C7   109.41  3.000
 C63  C9   C8   C7   112.93  3.000
 C63  H9   C9   H8   106.13  3.000
 C63  H9   C9   C10  109.66  3.000
 C63  H8   C9   C10  109.64  3.000
 C63  H9   C9   C8   109.27  3.000
 C63  H8   C9   C8   109.31  3.000
 C63  C10  C9   C8   112.61  3.000
 C63  H12  C10  H11  107.67  3.000
 C63  H12  C10  H10  107.57  3.000
 C63  H11  C10  H10  107.51  3.000
 C63  H12  C10  C9   111.60  3.000
 C63  H11  C10  C9   111.14  3.000
 C63  H10  C10  C9   111.16  3.000
 C63  C3   O4   P5   122.14  3.000
 C63  H14  C3   H13  108.14  3.000
 C63  H14  C3   C2   110.44  3.000
 C63  H13  C3   C2   110.41  3.000
 C63  H14  C3   O4   110.48  3.000
 C63  H13  C3   O4   110.13  3.000
 C63  C2   C3   O4   107.26  3.000
 C63  H15  C2   C1   108.14  3.000
 C63  H15  C2   O13  111.02  3.000
 C63  C1   C2   O13  109.66  3.000
 C63  H15  C2   C3   108.18  3.000
 C63  C1   C2   C3   110.80  3.000
 C63  O13  C2   C3   109.03  3.000
 C63  C14  O13  C2   115.84  3.000
 C63  H17  C14  H16  106.94  3.000
 C63  H17  C14  C15  109.97  3.000
 C63  H16  C14  C15  109.45  3.000
 C63  H17  C14  O13  110.73  3.000
 C63  H16  C14  O13  110.93  3.000
 C63  C15  C14  O13  108.80  3.000
 C63  H19  C15  H18  106.83  3.000
 C63  H19  C15  C16  109.52  3.000
 C63  H18  C15  C16  109.51  3.000
 C63  H19  C15  C14  109.13  3.000
 C63  H18  C15  C14  109.59  3.000
 C63  C16  C15  C14  112.12  3.000
 C63  H21  C16  H20  106.13  3.000
 C63  H21  C16  C17  109.38  3.000
 C63  H20  C16  C17  109.33  3.000
 C63  H21  C16  C15  109.58  3.000
 C63  H20  C16  C15  109.47  3.000
 C63  C17  C16  C15  112.74  3.000
 C63  C18  C17  H23  109.26  3.000
 C63  C18  C17  H22  109.24  3.000
 C63  H23  C17  H22  106.02  3.000
 C63  C18  C17  C16  113.31  3.000
 C63  H23  C17  C16  109.34  3.000
 C63  H22  C17  C16  109.41  3.000
 C63  H26  C1   H25  106.86  3.000
 C63  H26  C1   O20  111.09  3.000
 C63  H25  C1   O20  111.15  3.000
 C63  H26  C1   C2   109.66  3.000
 C63  H25  C1   C2   109.89  3.000
 C63  O20  C1   C2   108.20  3.000
 C63  C21  O20  C1   113.37  3.000
 C63  H28  C21  H27  106.51  3.000
 C63  H28  C21  C22  110.06  3.000
 C63  H27  C21  C22  109.99  3.000
 C63  H28  C21  O20  110.33  3.000
 C63  H27  C21  O20  110.70  3.000
 C63  C22  C21  O20  109.22  3.000
 C63  H30  C22  H29  106.72  3.000
 C63  H30  C22  C23  109.57  3.000
 C63  H29  C22  C23  109.50  3.000
 C63  H30  C22  C21  109.41  3.000
 C63  H29  C22  C21  109.24  3.000
 C63  C23  C22  C21  112.24  3.000
 C63  H32  C23  H31  106.05  3.000
 C63  H32  C23  C24  109.31  3.000
 C63  H31  C23  C24  109.31  3.000
 C63  H32  C23  C22  109.52  3.000
 C63  H31  C23  C22  109.69  3.000
 C63  C24  C23  C22  112.74  3.000
 C63  H34  C24  H33  105.94  3.000
 C63  H34  C24  C25  109.36  3.000
 C63  H33  C24  C25  109.33  3.000
 C63  H34  C24  C23  109.34  3.000
 C63  H33  C24  C23  109.30  3.000
 C63  C25  C24  C23  113.32  3.000
 C63  H36  C25  H35  105.99  3.000
 C63  H36  C25  C26  109.60  3.000
 C63  H35  C25  C26  109.57  3.000
 C63  H36  C25  C24  109.27  3.000
 C63  H35  C25  C24  109.32  3.000
 C63  C26  C25  C24  112.86  3.000
 C63  H39  C26  H38  107.63  3.000
 C63  H39  C26  H37  107.63  3.000
 C63  H38  C26  H37  107.42  3.000
 C63  H39  C26  C25  111.60  3.000
 C63  H38  C26  C25  111.17  3.000
 C63  H37  C26  C25  111.19  3.000
 C63  H1   O12  P5   115.30  3.000
 C63  H40  C18  H24  106.09  3.000
 C63  H40  C18  C19  109.69  3.000
 C63  H24  C18  C19  109.62  3.000
 C63  H40  C18  C17  109.30  3.000
 C63  H24  C18  C17  109.25  3.000
 C63  C19  C18  C17  112.68  3.000
 C63  H43  C19  H42  107.60  3.000
 C63  H43  C19  H41  107.60  3.000
 C63  H42  C19  H41  107.45  3.000
 C63  H43  C19  C18  111.74  3.000
 C63  H42  C19  C18  111.07  3.000
 C63  H41  C19  C18  111.18  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
 C63  Var_01  C8   C7   C6   P5   -176.50  30.0  1
 C63  Var_02  C2   C3   O4   P5    164.46  30.0  1
 C63  Var_03  C7   C6   P5   O11    58.69  30.0  1
 C63  Var_04  C9   C8   C7   C6   -179.41  30.0  1
 C63  Var_05  C10  C9   C8   C7   -179.58  30.0  1
 C63  Var_06  C15  C14  O13  C2   -171.81  30.0  1
 C63  Var_07  C16  C15  C14  O13  -179.98  30.0  1
 C63  Var_08  C17  C16  C15  C14  -179.60  30.0  1
 C63  Var_09  C18  C17  C16  C15   179.71  30.0  3
 C63  Var_10  C19  C18  C17  C16  -179.71  30.0  3
 C63  Var_11  C22  C21  O20  C1   -179.21  30.0  3
 C63  Var_12  C23  C22  C21  O20  -178.20  30.0  1
 C63  Var_13  C24  C23  C22  C21  -179.65  30.0  1
 C63  Var_14  C25  C24  C23  C22  -179.35  30.0  1
 C63  Var_15  C26  C25  C24  C23   179.99  30.0  1
 C63  Var_16  H10  C10  C9   C8    -60.27  30.0  3
 C63  Var_17  H41  C19  C18  C17   -59.66  30.0  3
 C63  Var_18  H25  C1   O20  C21    66.78  30.0  3
 C63  Var_19  H37  C26  C25  C24   -59.76  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
 C63  chir_02  C2  O13  C1   C3   positiv
 C63  chir_03  P5  O4   O11  O12  both

