# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:42:51 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  31  16  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.261  -2.1053   1.4649   0.3264
 G7P  C2    C  CH1   0  -0.023  -3.1991   0.5601  -0.2339
 G7P  C3    C  CH1   0  -0.014  -2.9188  -0.8770   0.1837
 G7P  C4    C  CH1   0   0.044  -1.5064  -1.2861  -0.2170
 G7P  C5    C  CH1   0   0.033  -0.5048  -0.2662   0.3277
 G7P  C6    C  CH2   0  -0.466   0.9186  -0.5610  -0.1105
 G7P  O1    O  OH1   0  -0.660  -2.3143   2.7484  -0.1324
 G7P  O2    O  OH1   0  -0.670  -4.4674   0.9084   0.2632
 G7P  O3    O  OH1   0  -0.673  -3.8104  -1.7877  -0.4139
 G7P  O4    O  OH1   0  -0.673  -1.1704  -2.5473   0.3045
 G7P  O5    O  O2    0  -0.502  -0.8504   1.0222  -0.1356
 G7P  C7    C  CH2   0  -0.762   1.9209   0.4240   0.4885
 G7P  P     P  P     0   1.375   3.6119  -0.0055   0.0472
 G7P  O3P   O  OH1   0  -0.753   3.7429   0.1730  -1.5492
 G7P  O2P   O  OH1   0  -0.745   4.4326   1.2054   0.7160
 G7P  O1P   O  O     0  -0.720   4.0555  -1.3718   0.4162
 G7P  H1    H  HCH1  0   0.191  -2.1243   1.4186   1.4293
 G7P  H2    H  HCH1  0   0.221  -3.1669   0.6261  -1.3324
 G7P  HA    H  HOH1  0   0.467  -1.8731   3.3756   0.4500
 G7P  H3    H  HCH1  0   0.214  -2.9837  -0.9326   1.2832
 G7P  HB    H  HOH1  0   0.456  -4.7311   1.7460  -0.1299
 G7P  H5    H  HCH1  0   0.219  -0.5520  -0.2937   1.4298
 G7P  H4    H  HCH1  0   0.210  -1.4374  -1.2800  -1.3169
 G7P  HC    H  HOH1  0   0.456  -4.6912  -1.6337  -0.0584
 G7P  HD    H  HOH1  0   0.454  -1.8169  -3.1865  -0.0125
 G7P  H61C  H  HCH2  0   0.260   1.1692  -1.5753   0.2014
 G7P  H62C  H  HCH2  0   0.243   0.9695  -0.5416  -1.2028
 G7P  H71C  H  HCH2  0   0.290   1.7140   1.4458   0.1650
 G7P  H72C  H  HCH2  0   0.286   1.8532   0.4149   1.5798
 G7P  H2P   H  HOH1  0   0.493   5.3933   1.1040   0.6660
 G7P  H3P   H  HOH1  0   0.489   3.4886   1.0412  -1.8884

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  1.379  0.020  1.379
 G7P  C1   O5    single  1.409  0.020  1.409
 G7P  C2   C3    single  1.523  0.020  1.523
 G7P  C2   O2    single  1.406  0.020  1.406
 G7P  O5   C5    single  1.412  0.020  1.412
 G7P  C3   C4    single  1.524  0.020  1.524
 G7P  C3   O3    single  1.408  0.020  1.408
 G7P  C4   C5    single  1.530  0.020  1.530
 G7P  C4   O4    single  1.405  0.020  1.405
 G7P  C5   C6    single  1.518  0.020  1.518
 G7P  C6   C7    single  1.528  0.020  1.528
 G7P  C7   P     single  1.800  0.020  1.800
 G7P  P    O1P   double  1.483  0.020  1.483
 G7P  P    O2P   single  1.608  0.020  1.608
 G7P  P    O3P   single  1.612  0.020  1.612
 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
 G7P  O2P  H2P   single  0.850  0.020  0.980
 G7P  O3P  H3P   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
 G7P  H1    C1   O5    109.26  3.000
 G7P  H1    C1   O1    111.64  3.000
 G7P  O5    C1   O1    108.57  3.000
 G7P  H1    C1   C2    109.25  3.000
 G7P  O5    C1   C2    109.38  3.000
 G7P  O1    C1   C2    108.73  3.000
 G7P  H2    C2   O2    111.37  3.000
 G7P  H2    C2   C3    108.95  3.000
 G7P  O2    C2   C3    107.63  3.000
 G7P  H2    C2   C1    108.05  3.000
 G7P  O2    C2   C1    111.71  3.000
 G7P  C3    C2   C1    109.09  3.000
 G7P  H3    C3   O3    110.69  3.000
 G7P  H3    C3   C4    107.64  3.000
 G7P  O3    C3   C4    107.56  3.000
 G7P  H3    C3   C2    108.07  3.000
 G7P  O3    C3   C2    112.19  3.000
 G7P  C4    C3   C2    110.60  3.000
 G7P  H4    C4   O4    111.12  3.000
 G7P  H4    C4   C5    108.10  3.000
 G7P  O4    C4   C5    108.04  3.000
 G7P  H4    C4   C3    108.60  3.000
 G7P  O4    C4   C3    111.40  3.000
 G7P  C5    C4   C3    109.52  3.000
 G7P  H5    C5   O5    109.87  3.000
 G7P  H5    C5   C6    108.88  3.000
 G7P  O5    C5   C6    108.17  3.000
 G7P  H5    C5   C4    108.12  3.000
 G7P  C6    C5   C4    112.43  3.000
 G7P  O5    C5   C4    109.35  3.000
 G7P  H62C  C6   H61C  106.95  3.000
 G7P  H62C  C6   C7    110.47  3.000
 G7P  H61C  C6   C7    109.68  3.000
 G7P  H62C  C6   C5    109.17  3.000
 G7P  H61C  C6   C5    108.27  3.000
 G7P  C7    C6   C5    112.13  3.000
 G7P  HA    O1   C1    109.61  3.000
 G7P  HB    O2   C2    108.56  3.000
 G7P  HC    O3   C3    108.63  3.000
 G7P  HD    O4   C4    108.25  3.000
 G7P  C5    O5   C1    113.40  3.000
 G7P  H72C  C7   H71C  106.97  3.000
 G7P  H72C  C7   P     107.51  3.000
 G7P  H71C  C7   P     109.19  3.000
 G7P  H72C  C7   C6    110.20  3.000
 G7P  H71C  C7   C6    111.28  3.000
 G7P  P     C7   C6    111.50  3.000
 G7P  O1P   P    O2P   115.95  3.000
 G7P  O2P   P    O3P   106.68  3.000
 G7P  O1P   P    O3P   108.91  3.000
 G7P  O3P   P    C7    107.03  3.000
 G7P  O2P   P    C7    101.41  3.000
 G7P  O1P   P    C7    116.09  3.000
 G7P  H3P   O3P  P     115.20  3.000
 G7P  H2P   O2P  P     113.98  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  176.22  30.0  3
 G7P  Var_02  O1P  P   C7  C6  -56.48  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

