# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:50:33 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (2S)-3-[(6-deoxy-beta-D-glucopyranosyl)oxy]-2-hydroxypropyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](OC[C@H](O)CO[P](O)(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
 4JA  4JA  '(2S)-3-[(6-deoxy-beta-D-glucopyranosyl)oxy]-2-hydroxypropyl dihydrogen phosphate'  D-saccharide  39  20  .  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
;

data_comp_4JA
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
 4JA  P     P  P     0   1.454   5.2558   0.0021  -0.4022
 4JA  O2    O  OH1   0  -0.669  -2.7217  -2.3850  -0.5902
 4JA  O3    O  OH1   0  -0.668  -5.4459  -1.7526  -0.1066
 4JA  O4    O  OH1   0  -0.668  -6.0922   0.9235  -0.5295
 4JA  O5    O  O2    0  -0.499  -2.5567   1.1224   0.3662
 4JA  C1    C  CH1   0   0.303  -2.1053  -0.0682  -0.2234
 4JA  C2    C  CH1   0  -0.035  -3.0962  -1.1926   0.0548
 4JA  C3    C  CH1   0   0.012  -4.4748  -0.8047  -0.4694
 4JA  C4    C  CH1   0   0.030  -4.8846   0.5500   0.0868
 4JA  C5    C  CH1   0   0.006  -3.7784   1.5803  -0.1844
 4JA  C6    C  CH3   0  -0.698  -4.0798   2.9346   0.4224
 4JA  OP1   O  O     0  -0.710   5.6149   1.3739  -0.8055
 4JA  OP2   O  OH1   0  -0.731   6.1676  -0.7171   0.6892
 4JA  O5'   O  O2    0  -0.585   3.8654  -0.1857   0.3575
 4JA  C5'   C  CH2   0  -0.187   2.6854   0.4007  -0.1957
 4JA  C3'   C  CH1   0  -0.051   1.4792  -0.2491   0.4612
 4JA  C2'   C  CH2   0  -0.169   0.2131   0.3210  -0.1563
 4JA  O1    O  O2    0  -0.498  -0.8916  -0.4056   0.3387
 4JA  O3'   O  OH1   0  -0.651   1.5006  -0.1331   1.8598
 4JA  HO3   H  HOH1  0   0.450  -5.1788  -2.6042  -0.4679
 4JA  HO4   H  HOH1  0   0.456  -6.5101   1.6073   0.0015
 4JA  H1    H  HCH1  0   0.186  -2.0048   0.0717  -1.3169
 4JA  H2    H  HCH1  0   0.224  -3.1593  -1.3303   1.1448
 4JA  H3    H  HCH1  0   0.209  -4.4060  -0.7122  -1.5667
 4JA  H4    H  HCH1  0   0.215  -5.0076   0.4581   1.1769
 4JA  H5    H  HCH1  0   0.216  -3.6756   1.6916  -1.2758
 4JA  H61   H  HCH3  0   0.249  -3.2593   3.6287   0.2411
 4JA  H62   H  HCH3  0   0.234  -4.9727   3.3710  -0.0246
 4JA  H63   H  HCH3  0   0.232  -4.2377   2.8617   1.5000
 4JA  HOP2  H  HOH1  0   0.504   7.1163  -0.6040   0.5428
 4JA  H5''  H  HCH2  0   0.245   2.6934   1.4801  -0.0170
 4JA  H5'   H  HCH2  0   0.243   2.6356   0.2417  -1.2769
 4JA  H3'   H  HCH1  0   0.246   1.5124  -1.3225   0.2484
 4JA  H2''  H  HCH2  0   0.222   0.1255   1.3884   0.0818
 4JA  H2'   H  HCH2  0   0.223   0.2649   0.2360  -1.2494
 4JA  HO3'  H  HOH1  0   0.448   1.4517   0.7993   2.0991
 4JA  OP3   O  OH1   0  -0.741   5.2040  -0.9387  -1.6940
 4JA  HOP3  H  HOH1  0   0.496   5.0233  -1.8732  -1.5251
 4JA  HO2   H  HOH1  0   0.457  -1.9689  -2.7624  -0.1249

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
 4JA  OP2  P     single  1.594  0.020  1.594
 4JA  C6   C5    single  1.514  0.020  1.514
 4JA  P    O5'   single  1.596  0.020  1.596
 4JA  P    OP1   double  1.474  0.020  1.474
 4JA  O5'  C5'   single  1.429  0.020  1.429
 4JA  C5   O5    single  1.416  0.020  1.416
 4JA  C5   C4    single  1.536  0.020  1.536
 4JA  O5   C1    single  1.403  0.020  1.403
 4JA  C5'  C3'   single  1.519  0.020  1.519
 4JA  C3'  C2'   single  1.520  0.020  1.520
 4JA  C3'  O3'   single  1.404  0.020  1.404
 4JA  C2'  O1    single  1.412  0.020  1.412
 4JA  O4   C4    single  1.406  0.020  1.406
 4JA  C4   C3    single  1.521  0.020  1.521
 4JA  C1   O1    single  1.379  0.020  1.379
 4JA  C1   C2    single  1.524  0.020  1.524
 4JA  C3   C2    single  1.525  0.020  1.525
 4JA  C3   O3    single  1.405  0.020  1.405
 4JA  C2   O2    single  1.406  0.020  1.406
 4JA  O2   HO2   single  0.850  0.020  0.980
 4JA  O3   HO3   single  0.850  0.020  0.980
 4JA  O4   HO4   single  0.850  0.020  0.980
 4JA  C1   H1    single  0.970  0.020  1.090
 4JA  C2   H2    single  0.970  0.020  1.090
 4JA  C3   H3    single  0.970  0.020  1.090
 4JA  C4   H4    single  0.970  0.020  1.090
 4JA  C5   H5    single  0.970  0.020  1.090
 4JA  C6   H61   single  0.970  0.020  1.090
 4JA  C6   H62   single  0.970  0.020  1.090
 4JA  C6   H63   single  0.970  0.020  1.090
 4JA  OP2  HOP2  single  0.850  0.020  0.980
 4JA  C5'  H5''  single  0.970  0.020  1.090
 4JA  C5'  H5'   single  0.970  0.020  1.090
 4JA  C3'  H3'   single  0.970  0.020  1.090
 4JA  C2'  H2''  single  0.970  0.020  1.090
 4JA  C2'  H2'   single  0.970  0.020  1.090
 4JA  O3'  HO3'  single  0.850  0.020  0.980
 4JA  P    OP3   single  1.599  0.020  1.599
 4JA  OP3  HOP3  single  0.850  0.020  0.980

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
 4JA  OP3   P    O5'   106.69  3.000
 4JA  OP3   P    OP2   107.83  3.000
 4JA  O5'   P    OP2    96.86  3.000
 4JA  OP3   P    OP1   109.53  3.000
 4JA  O5'   P    OP1   116.88  3.000
 4JA  OP2   P    OP1   117.90  3.000
 4JA  HO2   O2   C2    108.61  3.000
 4JA  HO3   O3   C3    107.95  3.000
 4JA  HO4   O4   C4    108.67  3.000
 4JA  C5    O5   C1    112.86  3.000
 4JA  H1    C1   O1    110.70  3.000
 4JA  H1    C1   C2    109.42  3.000
 4JA  O1    C1   C2    108.49  3.000
 4JA  H1    C1   O5    109.69  3.000
 4JA  C2    C1   O5    109.88  3.000
 4JA  O1    C1   O5    108.63  3.000
 4JA  H2    C2   C3    108.69  3.000
 4JA  H2    C2   C1    108.08  3.000
 4JA  C3    C2   C1    109.72  3.000
 4JA  H2    C2   O2    111.30  3.000
 4JA  C3    C2   O2    107.38  3.000
 4JA  C1    C2   O2    111.63  3.000
 4JA  H3    C3   C4    107.81  3.000
 4JA  H3    C3   C2    107.86  3.000
 4JA  C4    C3   C2    110.15  3.000
 4JA  H3    C3   O3    110.89  3.000
 4JA  C2    C3   O3    111.38  3.000
 4JA  C4    C3   O3    108.69  3.000
 4JA  H4    C4   C5    108.14  3.000
 4JA  H4    C4   C3    108.53  3.000
 4JA  C5    C4   C3    109.81  3.000
 4JA  H4    C4   O4    111.12  3.000
 4JA  C3    C4   O4    107.92  3.000
 4JA  C5    C4   O4    111.28  3.000
 4JA  H5    C5   C6    108.97  3.000
 4JA  H5    C5   C4    108.05  3.000
 4JA  C6    C5   C4    112.69  3.000
 4JA  H5    C5   O5    109.71  3.000
 4JA  C4    C5   O5    109.62  3.000
 4JA  C6    C5   O5    107.76  3.000
 4JA  H63   C6   H62   108.25  3.000
 4JA  H63   C6   H61   108.40  3.000
 4JA  H62   C6   H61   107.07  3.000
 4JA  H63   C6   C5    111.39  3.000
 4JA  H62   C6   C5    110.91  3.000
 4JA  H61   C6   C5    110.67  3.000
 4JA  HOP2  OP2  P     113.89  3.000
 4JA  C5'   O5'  P     119.14  3.000
 4JA  H5'   C5'  H5''  107.76  3.000
 4JA  H5'   C5'  C3'   109.21  3.000
 4JA  H5''  C5'  C3'   110.92  3.000
 4JA  H5'   C5'  O5'   111.14  3.000
 4JA  H5''  C5'  O5'   109.61  3.000
 4JA  C3'   C5'  O5'   108.22  3.000
 4JA  H3'   C3'  O3'   105.92  3.000
 4JA  H3'   C3'  C2'   108.31  3.000
 4JA  O3'   C3'  C2'   112.74  3.000
 4JA  H3'   C3'  C5'   108.13  3.000
 4JA  O3'   C3'  C5'   112.54  3.000
 4JA  C2'   C3'  C5'   108.98  3.000
 4JA  H2'   C2'  H2''  107.17  3.000
 4JA  H2'   C2'  O1    110.25  3.000
 4JA  H2''  C2'  O1    111.23  3.000
 4JA  H2'   C2'  C3'   109.65  3.000
 4JA  H2''  C2'  C3'   110.09  3.000
 4JA  O1    C2'  C3'   108.44  3.000
 4JA  C2'   O1   C1    114.82  3.000
 4JA  HO3'  O3'  C3'   109.06  3.000
 4JA  HOP3  OP3  P     115.71  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
 4JA  Var_01  C3'  C2'  O1   C1   -174.88  30.0  1
 4JA  Var_02  C3'  C5'  O5'  P     163.57  30.0  3
 4JA  Var_03  OP3  P    O5'  C5'   -73.48  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
 4JA  chir_01  C1   O5   O1   C2   negativ
 4JA  chir_02  C2   O2   C1   C3   negativ
 4JA  chir_03  C3   O3   C2   C4   positiv
 4JA  chir_04  C4   O4   C5   C3   positiv
 4JA  chir_05  C5   O5   C4   C6   negativ
 4JA  chir_06  C3'  O3'  C5'  C2'  positiv

