# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 21:55:56 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](CCO[PH](O)=O)[C@@H](O)[C@H](O)[C@@H]1O
#
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
 61J  61J  (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol  D-saccharide  33  16  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_61J
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
 61J  C01  C  CH1   0  -0.021  -2.3567   1.0831   0.8728
 61J  C02  C  CH1   0   0.022  -3.4997   0.0799   0.6405
 61J  C03  C  CH1   0  -0.034  -3.2962  -0.7836  -0.6005
 61J  C04  C  CH1   0   0.012  -1.8949  -1.4045  -0.5807
 61J  C05  C  CH1   0   0.030  -0.8468  -0.3266  -0.3307
 61J  O01  O  O2    0  -0.502  -1.1224   0.3854   0.8592
 61J  C06  C  CH3   0  -0.693  -2.3464   2.3080  -0.0321
 61J  O02  O  OH1   0  -0.673  -4.7542   0.7080   0.5109
 61J  O03  O  OH1   0  -0.670  -3.4287  -0.0635  -1.8030
 61J  O04  O  OH1   0  -0.673  -1.7952  -2.3733   0.4353
 61J  C07  C  CH2   0  -0.485   0.5592  -0.8928  -0.2098
 61J  C08  C  CH2   0  -0.156   1.6003   0.2064  -0.1843
 61J  O05  O  O2    0  -0.588   2.8948  -0.4098  -0.1102
 61J  P01  P  P     0   1.131   4.1639   0.4951   0.2505
 61J  O06  O  O     0  -0.709   4.5602   1.5241  -0.7378
 61J  O07  O  OH1   0  -0.734   5.1990  -0.6996   0.4992
 61J  H1   H  HCH1  0   0.238  -2.4525   1.4450   1.9025
 61J  H2   H  HCH1  0   0.225  -3.4973  -0.6054   1.4989
 61J  H3   H  HCH1  0   0.226  -4.0364  -1.5998  -0.5677
 61J  H4   H  HCH1  0   0.232  -1.6970  -1.8419  -1.5699
 61J  H5   H  HCH1  0   0.225  -0.8706   0.3443  -1.2018
 61J  H6   H  HCH3  0   0.231  -3.2703   2.8754   0.0789
 61J  H7   H  HCH3  0   0.233  -1.5276   2.9682   0.2570
 61J  H8   H  HCH3  0   0.234  -2.2342   2.0693  -1.0876
 61J  H9   H  HOH1  0   0.458  -4.9285   1.2265   1.3028
 61J  H10  H  HOH1  0   0.453  -4.2174   0.4856  -1.7405
 61J  H11  H  HOH1  0   0.455  -2.3731  -3.1096   0.2116
 61J  H12  H  HCH2  0   0.247   0.6426  -1.5079   0.6882
 61J  H13  H  HCH2  0   0.246   0.7440  -1.5434  -1.0687
 61J  H14  H  HCH2  0   0.235   1.5371   0.8169  -1.0892
 61J  H15  H  HCH2  0   0.234   1.4469   0.8646   0.6760
 61J  H17  H  HOH1  0   0.500   6.1241  -0.4243   0.4619
 61J  H16  H  H     0   0.070   3.8625   1.0271   1.5141

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
 61J  O04  C04  single  1.407  0.020  1.407
 61J  O07  P01  single  1.600  0.020  1.600
 61J  C04  C05  single  1.524  0.020  1.524
 61J  C04  C03  single  1.533  0.020  1.533
 61J  O06  P01  double  1.481  0.020  1.481
 61J  C05  O01  single  1.414  0.020  1.414
 61J  C05  C07  single  1.521  0.020  1.521
 61J  O03  C03  single  1.408  0.020  1.408
 61J  P01  O05  single  1.600  0.020  1.600
 61J  C08  O05  single  1.436  0.020  1.436
 61J  C08  C07  single  1.514  0.020  1.514
 61J  O01  C01  single  1.418  0.020  1.418
 61J  C03  C02  single  1.525  0.020  1.525
 61J  O02  C02  single  1.409  0.020  1.409
 61J  C02  C01  single  1.538  0.020  1.538
 61J  C01  C06  single  1.523  0.020  1.523
 61J  C01  H1   single  0.939  0.020  1.096
 61J  C02  H2   single  0.939  0.020  1.096
 61J  C03  H3   single  0.939  0.020  1.096
 61J  C04  H4   single  0.939  0.020  1.096
 61J  C05  H5   single  0.939  0.020  1.096
 61J  C06  H6   single  0.939  0.020  1.096
 61J  C06  H7   single  0.939  0.020  1.096
 61J  C06  H8   single  0.939  0.020  1.096
 61J  O02  H9   single  0.832  0.020  0.971
 61J  O03  H10  single  0.832  0.020  0.971
 61J  O04  H11  single  0.832  0.020  0.971
 61J  C07  H12  single  0.939  0.020  1.096
 61J  C07  H13  single  0.939  0.020  1.096
 61J  C08  H14  single  0.939  0.020  1.096
 61J  C08  H15  single  0.939  0.020  1.096
 61J  O07  H17  single  0.832  0.020  0.971
 61J  P01  H16  single  1.209  0.020  1.412

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
 61J  H1   C01  C06  107.05  3.000
 61J  H1   C01  O01  104.34  3.000
 61J  C06  C01  O01  112.59  3.000
 61J  H1   C01  C02  107.00  3.000
 61J  C06  C01  C02  116.09  3.000
 61J  O01  C01  C02  108.93  3.000
 61J  H2   C02  O02  110.60  3.000
 61J  H2   C02  C03  106.40  3.000
 61J  O02  C02  C03  107.24  3.000
 61J  H2   C02  C01  106.69  3.000
 61J  O02  C02  C01  112.63  3.000
 61J  C03  C02  C01  113.13  3.000
 61J  H3   C03  O03  109.93  3.000
 61J  H3   C03  C04  108.27  3.000
 61J  O03  C03  C04  107.72  3.000
 61J  H3   C03  C02  107.78  3.000
 61J  O03  C03  C02  113.12  3.000
 61J  C04  C03  C02  109.92  3.000
 61J  H4   C04  O04  111.28  3.000
 61J  H4   C04  C05  107.77  3.000
 61J  O04  C04  C05  108.65  3.000
 61J  H4   C04  C03  108.30  3.000
 61J  C05  C04  C03  110.14  3.000
 61J  O04  C04  C03  110.67  3.000
 61J  H5   C05  C07  108.07  3.000
 61J  H5   C05  O01  110.81  3.000
 61J  C07  C05  O01  107.51  3.000
 61J  H5   C05  C04  106.65  3.000
 61J  C07  C05  C04  112.68  3.000
 61J  O01  C05  C04  111.11  3.000
 61J  C05  O01  C01  115.19  3.000
 61J  H8   C06  H7   108.21  3.000
 61J  H8   C06  H6   107.49  3.000
 61J  H7   C06  H6   107.11  3.000
 61J  H8   C06  C01  113.62  3.000
 61J  H7   C06  C01  109.53  3.000
 61J  H6   C06  C01  110.64  3.000
 61J  H9   O02  C02  109.01  3.000
 61J  H10  O03  C03  108.26  3.000
 61J  H11  O04  C04  108.44  3.000
 61J  H13  C07  H12  107.34  3.000
 61J  H13  C07  C08  109.21  3.000
 61J  H12  C07  C08  110.04  3.000
 61J  H13  C07  C05  108.38  3.000
 61J  H12  C07  C05  110.23  3.000
 61J  C08  C07  C05  111.52  3.000
 61J  H15  C08  H14  107.87  3.000
 61J  H15  C08  O05  110.12  3.000
 61J  H14  C08  O05  109.54  3.000
 61J  H15  C08  C07  110.70  3.000
 61J  H14  C08  C07  110.59  3.000
 61J  O05  C08  C07  108.01  3.000
 61J  P01  O05  C08  118.96  3.000
 61J  H16  P01  O07  106.37  3.000
 61J  H16  P01  O06  113.26  3.000
 61J  O07  P01  O06  116.71  3.000
 61J  H16  P01  O05  104.30  3.000
 61J  O06  P01  O05  117.06  3.000
 61J  O07  P01  O05   97.23  3.000
 61J  H17  O07  P01  113.63  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
 61J  Var_01  O05  C08  C07  C05  -178.28  30.0  1
 61J  Var_02  O07  P01  O05  C08   168.58  30.0  1
 61J  Var_03  H14  C08  O05  P01    72.69  30.0  1

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
 61J  chir_01  C01  O01  C02  C06  positiv
 61J  chir_02  C02  O02  C01  C03  positiv
 61J  chir_03  C03  O03  C02  C04  positiv
 61J  chir_04  C04  O04  C05  C03  positiv
 61J  chir_05  C05  O01  C04  C07  positiv
 61J  chir_06  P01  O07  O06  O05  both

