# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:07:09 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 6,7-dideoxy-7-phosphono-beta-D-gluco-heptopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1O[C@H](CC[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
 G7P  G7P  6,7-dideoxy-7-phosphono-beta-D-gluco-heptopyranose  D-saccharide  29  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G7P
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
 G7P  C1    C  CH1    0   0.262  -2.1740   1.4485   0.2861
 G7P  C2    C  CH1    0  -0.021  -3.2490   0.5215  -0.2733
 G7P  C3    C  CH1    0  -0.016  -2.9328  -0.9071   0.1444
 G7P  C4    C  CH1    0   0.048  -1.5096  -1.2827  -0.2530
 G7P  C5    C  CH1    0   0.032  -0.5270  -0.2433   0.2916
 G7P  C6    C  CH2    0  -0.436   0.9105  -0.4911  -0.1293
 G7P  O1    O  OH1    0  -0.663  -2.4173   2.7293  -0.1707
 G7P  O2    O  OH1    0  -0.672  -4.5256   0.8409   0.2240
 G7P  O3    O  OH1    0  -0.675  -3.8040  -1.8410  -0.4513
 G7P  O4    O  OH1    0  -0.674  -1.1562  -2.5403   0.2696
 G7P  O5    O  O2     0  -0.501  -0.9127   1.0379  -0.1740
 G7P  C7    C  CH2    0  -0.719   1.9244   0.4424   0.5160
 G7P  P     P  P      0   1.167   3.6770   0.0734   0.0092
 G7P  O3P   O  OP    -1  -0.918   3.7162   0.3153  -1.5078
 G7P  O2P   O  OP    -1  -0.916   4.5368   1.0625   0.8118
 G7P  O1P   O  O      0  -0.918   3.9080  -1.3953   0.3983
 G7P  H1    H  HCH1   0   0.183  -2.1953   1.4022   1.3898
 G7P  H2    H  HCH1   0   0.217  -3.2187   0.5884  -1.3721
 G7P  HA    H  HOH1   0   0.465  -1.9742   3.3643   0.4016
 G7P  H3    H  HCH1   0   0.210  -2.9972  -0.9632   1.2441
 G7P  HB    H  HOH1   0   0.455  -4.7945   1.6867  -0.1480
 G7P  H5    H  HCH1   0   0.197  -0.5848  -0.2680   1.3942
 G7P  H4    H  HCH1   0   0.201  -1.4389  -1.2782  -1.3531
 G7P  HC    H  HOH1   0   0.455  -4.6795  -1.7338  -0.0671
 G7P  HD    H  HOH1   0   0.451  -1.8114  -3.1809  -0.0261
 G7P  H61C  H  HCH2   0   0.217   1.1730  -1.5191   0.1270
 G7P  H62C  H  HCH2   0   0.201   0.9826  -0.4194  -1.2199
 G7P  H71C  H  HCH2   0   0.189   1.6899   1.4829   0.2687
 G7P  H72C  H  HCH2   0   0.180   1.8365   0.3652   1.6070

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
 G7P  C1  C2    single  1.526  0.020  1.526
 G7P  C1  O1    single  1.381  0.020  1.381
 G7P  C1  O5    single  1.404  0.020  1.404
 G7P  C2  C3    single  1.522  0.020  1.522
 G7P  C2  O2    single  1.407  0.020  1.407
 G7P  O5  C5    single  1.417  0.020  1.417
 G7P  C3  C4    single  1.525  0.020  1.525
 G7P  C3  O3    single  1.409  0.020  1.409
 G7P  C4  C5    single  1.531  0.020  1.531
 G7P  C4  O4    single  1.407  0.020  1.407
 G7P  C5  C6    single  1.518  0.020  1.518
 G7P  C6  C7    single  1.522  0.020  1.522
 G7P  C7  P     single  1.861  0.020  1.861
 G7P  P   O1P   deloc   1.537  0.020  1.537
 G7P  P   O2P   deloc   1.537  0.020  1.537
 G7P  P   O3P   deloc   1.537  0.020  1.537
 G7P  C1  H1    single  0.970  0.020  1.090
 G7P  C2  H2    single  0.970  0.020  1.090
 G7P  O1  HA    single  0.850  0.020  0.980
 G7P  C3  H3    single  0.970  0.020  1.090
 G7P  O2  HB    single  0.850  0.020  0.980
 G7P  C5  H5    single  0.970  0.020  1.090
 G7P  C4  H4    single  0.970  0.020  1.090
 G7P  O3  HC    single  0.850  0.020  0.980
 G7P  O4  HD    single  0.850  0.020  0.980
 G7P  C6  H61C  single  0.970  0.020  1.090
 G7P  C6  H62C  single  0.970  0.020  1.090
 G7P  C7  H71C  single  0.970  0.020  1.090
 G7P  C7  H72C  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
 G7P  H1    C1  O5    109.42  3.000
 G7P  H1    C1  O1    111.46  3.000
 G7P  O5    C1  O1    108.73  3.000
 G7P  H1    C1  C2    109.10  3.000
 G7P  O5    C1  C2    109.57  3.000
 G7P  O1    C1  C2    108.54  3.000
 G7P  H2    C2  O2    111.33  3.000
 G7P  H2    C2  C3    108.98  3.000
 G7P  O2    C2  C3    107.74  3.000
 G7P  H2    C2  C1    108.04  3.000
 G7P  O2    C2  C1    111.83  3.000
 G7P  C3    C2  C1    108.87  3.000
 G7P  H3    C3  O3    110.58  3.000
 G7P  H3    C3  C4    107.56  3.000
 G7P  O3    C3  C4    107.68  3.000
 G7P  H3    C3  C2    108.02  3.000
 G7P  O3    C3  C2    112.19  3.000
 G7P  C4    C3  C2    110.72  3.000
 G7P  H4    C4  O4    110.99  3.000
 G7P  H4    C4  C5    108.12  3.000
 G7P  O4    C4  C5    108.28  3.000
 G7P  H4    C4  C3    108.60  3.000
 G7P  O4    C4  C3    110.97  3.000
 G7P  C5    C4  C3    109.83  3.000
 G7P  H5    C5  O5    109.52  3.000
 G7P  H5    C5  C6    108.82  3.000
 G7P  O5    C5  C6    108.32  3.000
 G7P  H5    C5  C4    107.85  3.000
 G7P  C6    C5  C4    113.48  3.000
 G7P  O5    C5  C4    108.81  3.000
 G7P  H62C  C6  H61C  106.24  3.000
 G7P  H62C  C6  C7    109.76  3.000
 G7P  H61C  C6  C7    108.54  3.000
 G7P  H62C  C6  C5    109.13  3.000
 G7P  H61C  C6  C5    108.44  3.000
 G7P  C7    C6  C5    114.40  3.000
 G7P  HA    O1  C1    109.50  3.000
 G7P  HB    O2  C2    108.45  3.000
 G7P  HC    O3  C3    108.66  3.000
 G7P  HD    O4  C4    108.05  3.000
 G7P  C5    O5  C1    113.66  3.000
 G7P  H72C  C7  H71C  105.92  3.000
 G7P  H72C  C7  P     109.40  3.000
 G7P  H71C  C7  P     109.18  3.000
 G7P  H72C  C7  C6    108.97  3.000
 G7P  H71C  C7  C6    110.15  3.000
 G7P  P     C7  C6    112.97  3.000
 G7P  O1P   P   O2P   113.50  3.000
 G7P  O2P   P   O3P   113.58  3.000
 G7P  O1P   P   O3P   113.36  3.000
 G7P  O3P   P   C7    105.17  3.000
 G7P  O2P   P   C7    104.89  3.000
 G7P  O1P   P   C7    105.19  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
 G7P  Var_01  P    C7  C6  C5  178.40  30.0  3
 G7P  Var_02  O1P  P   C7  C6  -57.23  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
 G7P  chir_01  C1  C2  O1  O5  positiv
 G7P  chir_02  C2  O2  C1  C3  negativ
 G7P  chir_03  C3  O3  C2  C4  positiv
 G7P  chir_04  C4  O4  C3  C5  negativ
 G7P  chir_05  C5  O5  C6  C4  positiv

