# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:49:16 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-deoxy-6-O-phosphono-D-arabino-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[C@@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=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
 DG6  DG6  2-deoxy-6-O-phosphono-D-arabino-hexitol  ligand  30  15  .  2021-08-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DG6
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
 DG6  C1    C  CH2   0  -0.180   -7.7002  40.0280   9.4337
 DG6  O1    O  OH1   0  -0.679   -7.6519  39.1388   8.3307
 DG6  C2    C  CH2   0  -0.525   -8.9377  40.9126   9.4912
 DG6  C3    C  CH1   0   0.033  -10.2641  40.1653   9.6438
 DG6  O3    O  OH1   0  -0.707  -11.2808  41.0561  10.1197
 DG6  C4    C  CH1   0   0.012  -10.8217  39.3953   8.4251
 DG6  O4    O  OH1   0  -0.689  -10.2079  38.1329   8.3305
 DG6  C5    C  CH1   0  -0.029  -10.8300  40.0646   7.0391
 DG6  O5    O  OH1   0  -0.680   -9.5127  40.2645   6.5621
 DG6  C6    C  CH2   0  -0.221  -11.5585  41.3996   6.9484
 DG6  O6    O  O2    0  -0.590  -12.9163  41.2155   7.3538
 DG6  P     P  P     0   1.449  -13.7705  42.3698   8.0641
 DG6  O1P   O  OH1   0  -0.788  -12.8359  42.9424   9.2101
 DG6  O2P   O  OH1   0  -0.746  -13.9014  43.5898   7.0418
 DG6  O3P   O  O     0  -0.702  -15.1006  41.8595   8.4394
 DG6  HC11  H  HCH2  0   0.226   -6.8151  40.6728   9.4408
 DG6  HC12  H  HCH2  0   0.226   -7.6513  39.4093  10.3328
 DG6  HO1   H  HOH1  0   0.461   -7.8810  39.6397   7.5345
 DG6  HC21  H  HCH2  0   0.247   -8.9597  41.5992   8.6419
 DG6  HC22  H  HCH2  0   0.252   -8.8104  41.5394  10.3798
 DG6  HC3   H  HCH1  0   0.242  -10.1293  39.3958  10.4141
 DG6  HO3   H  HOH1  0   0.481  -11.0563  41.3047  11.0240
 DG6  HC4   H  HCH1  0   0.252  -11.8705  39.1978   8.6654
 DG6  HO4   H  HOH1  0   0.444   -9.2444  38.2717   8.2753
 DG6  HC5   H  HCH1  0   0.250  -11.3554  39.3543   6.3883
 DG6  HO5   H  HOH1  0   0.473   -9.5070  40.1601   5.6057
 DG6  HC61  H  HCH2  0   0.261  -11.5419  41.7433   5.9109
 DG6  HC62  H  HCH2  0   0.235  -11.0489  42.1584   7.5487
 DG6  H1P   H  HOH1  0   0.500  -12.2009  42.2688   9.5807
 DG6  H2P   H  HOH1  0   0.494  -13.1075  44.1209   6.8972

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
 DG6  C1   O1    single  1.418  0.020  1.418
 DG6  C1   C2    single  1.522  0.020  1.522
 DG6  C1   HC11  single  0.970  0.020  1.090
 DG6  C1   HC12  single  0.970  0.020  1.090
 DG6  O1   HO1   single  0.850  0.020  0.980
 DG6  C2   C3    single  1.530  0.020  1.530
 DG6  C2   HC21  single  0.970  0.020  1.090
 DG6  C2   HC22  single  0.970  0.020  1.090
 DG6  C3   O3    single  1.433  0.020  1.433
 DG6  C3   C4    single  1.546  0.020  1.546
 DG6  C3   HC3   single  0.970  0.020  1.090
 DG6  O3   HO3   single  0.850  0.020  0.980
 DG6  C4   O4    single  1.407  0.020  1.407
 DG6  C4   C5    single  1.539  0.020  1.539
 DG6  C4   HC4   single  0.970  0.020  1.090
 DG6  O4   HO4   single  0.850  0.020  0.980
 DG6  C5   O5    single  1.415  0.020  1.415
 DG6  C5   C6    single  1.524  0.020  1.524
 DG6  C5   HC5   single  0.970  0.020  1.090
 DG6  O5   HO5   single  0.850  0.020  0.980
 DG6  C6   O6    single  1.429  0.020  1.429
 DG6  C6   HC61  single  0.970  0.020  1.090
 DG6  C6   HC62  single  0.970  0.020  1.090
 DG6  O6   P     single  1.602  0.020  1.602
 DG6  P    O1P   single  1.586  0.020  1.586
 DG6  P    O2P   single  1.597  0.020  1.597
 DG6  P    O3P   double  1.473  0.020  1.473
 DG6  O1P  H1P   single  0.850  0.020  0.980
 DG6  O2P  H2P   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
 DG6  HC12  C1   HC11  106.97  3.000
 DG6  HC12  C1   C2    109.54  3.000
 DG6  HC11  C1   C2    108.34  3.000
 DG6  HC12  C1   O1    106.47  3.000
 DG6  HC11  C1   O1    110.29  3.000
 DG6  C2    C1   O1    114.94  3.000
 DG6  HO1   O1   C1    107.90  3.000
 DG6  HC22  C2   HC21  105.88  3.000
 DG6  HC22  C2   C3    107.42  3.000
 DG6  HC21  C2   C3    111.53  3.000
 DG6  HC22  C2   C1    105.60  3.000
 DG6  HC21  C2   C1    110.63  3.000
 DG6  C3    C2   C1    115.13  3.000
 DG6  HC3   C3   C4    104.39  3.000
 DG6  HC3   C3   O3    106.86  3.000
 DG6  C4    C3   O3    108.40  3.000
 DG6  HC3   C3   C2    107.82  3.000
 DG6  C4    C3   C2    118.51  3.000
 DG6  O3    C3   C2    110.16  3.000
 DG6  HO3   O3   C3    107.85  3.000
 DG6  HC4   C4   C5    105.73  3.000
 DG6  HC4   C4   O4    105.73  3.000
 DG6  C5    C4   O4    109.39  3.000
 DG6  HC4   C4   C3    105.22  3.000
 DG6  C5    C4   C3    119.69  3.000
 DG6  O4    C4   C3    110.04  3.000
 DG6  HO4   O4   C4    107.89  3.000
 DG6  HC5   C5   C6    107.64  3.000
 DG6  HC5   C5   O5    109.71  3.000
 DG6  C6    C5   O5    107.53  3.000
 DG6  HC5   C5   C4    104.79  3.000
 DG6  C6    C5   C4    115.92  3.000
 DG6  O5    C5   C4    111.09  3.000
 DG6  HO5   O5   C5    108.98  3.000
 DG6  HC62  C6   HC61  107.21  3.000
 DG6  HC62  C6   O6    112.11  3.000
 DG6  HC61  C6   O6    108.92  3.000
 DG6  HC62  C6   C5    110.64  3.000
 DG6  HC61  C6   C5    108.95  3.000
 DG6  O6    C6   C5    108.94  3.000
 DG6  P     O6   C6    122.65  3.000
 DG6  O3P   P    O2P   110.71  3.000
 DG6  O3P   P    O1P   118.24  3.000
 DG6  O2P   P    O1P   103.60  3.000
 DG6  O3P   P    O6    110.16  3.000
 DG6  O2P   P    O6    108.08  3.000
 DG6  O1P   P    O6    105.45  3.000
 DG6  H1P   O1P  P     113.58  3.000
 DG6  H2P   O2P  P     116.64  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
 DG6  Var_01  C3   C2  C1  O1   62.56  30.0  3
 DG6  Var_02  O1P  P   O6  C6  -47.79  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
 DG6  chir_01  C3  C2  O3  C4  negativ
 DG6  chir_02  C4  O4  C3  C5  negativ
 DG6  chir_03  C5  O5  C4  C6  negativ

