# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 16:42:10 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-nitrophenyl beta-D-glucopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]([C@H]1O)C(O)=O)Oc2ccc(cc2)[N+]([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
 C3G  C3G  '4-nitrophenyl beta-D-glucopyranosiduronic acid'  D-saccharide  35  22  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C3G
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
 C3G  C10  C  C      0   0.504   2.4065   2.4772  -0.4963
 C3G  C15  C  CR16   0  -0.339  -2.4977  -1.5712  -0.9095
 C3G  C17  C  CR6    0   0.234  -4.0818  -0.1368   0.1561
 C3G  C02  C  CH1    0   0.011   3.3070  -1.1413   0.4761
 C3G  C03  C  CH1    0  -0.030   2.0451  -1.7307  -0.1480
 C3G  C05  C  CH1    0   0.254   0.8876  -0.7608   0.0533
 C3G  C07  C  CH1    0  -0.083   2.2796   1.1032   0.1287
 C3G  C08  C  CH1    0   0.013   3.5706   0.2645  -0.0515
 C3G  C14  C  CR6    0   0.408  -1.4563  -0.8388  -0.3366
 C3G  C16  C  CR16   0  -0.253  -3.8083  -1.2239  -0.6669
 C3G  C18  C  CR16   0  -0.255  -3.0556   0.6028   0.7248
 C3G  C19  C  CR16   0  -0.349  -1.7398   0.2587   0.4752
 C3G  O01  O  OH1    0  -0.662   4.4304  -1.9283   0.1903
 C3G  O04  O  OH1    0  -0.663   1.8005  -2.9599   0.4820
 C3G  O06  O  O2     0  -0.487   1.1958   0.4807  -0.5102
 C3G  O09  O  OH1    0  -0.655   4.6445   0.7939   0.6699
 C3G  O11  O  O      0  -0.417   1.8834   2.7987  -1.5283
 C3G  O12  O  OH1    0  -0.587   3.1814   3.2671   0.2302
 C3G  O13  O  O2     0  -0.484  -0.2151  -1.2684  -0.6308
 C3G  O21  O  O      0  -0.386  -6.3310  -0.4379  -0.0829
 C3G  O22  O  O     -1  -0.386  -5.6667   1.1878   1.1282
 C3G  H1   H  HCR6   0   0.289  -2.2709  -2.4191  -1.5419
 C3G  H2   H  HCH1   0   0.223   3.1432  -1.0653   1.5643
 C3G  H3   H  HCH1   0   0.243   2.2071  -1.8510  -1.2288
 C3G  H4   H  HCH1   0   0.231   0.6636  -0.6585   1.1286
 C3G  H5   H  HCH1   0   0.276   2.0927   1.2216   1.2069
 C3G  H6   H  HCH1   0   0.245   3.7904   0.2022  -1.1267
 C3G  H7   H  HCR6   0   0.301  -4.6024  -1.8041  -1.1133
 C3G  H8   H  HCR6   0   0.303  -3.2627   1.4539   1.3569
 C3G  H9   H  HCR6   0   0.301  -0.9608   0.8660   0.9119
 C3G  H10  H  HOH1   0   0.454   4.2798  -2.8085   0.5509
 C3G  H11  H  HOH1   0   0.464   1.2184  -3.4892  -0.0720
 C3G  H12  H  HOH1   0   0.461   5.0507   1.5053   0.1670
 C3G  H13  H  HOH1   0   0.491   3.2822   4.1293  -0.2023
 C3G  N20  N  N      1   0.329  -5.4558   0.2304   0.4188

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
 C3G  O01  C02  single    1.401  0.020  1.401
 C3G  O04  C03  single    1.403  0.020  1.403
 C3G  C03  C02  single    1.526  0.020  1.526
 C3G  C03  C05  single    1.523  0.020  1.523
 C3G  C02  C08  single    1.525  0.020  1.525
 C3G  C08  O09  single    1.398  0.020  1.398
 C3G  C08  C07  single    1.550  0.020  1.550
 C3G  O13  C05  single    1.393  0.020  1.393
 C3G  O13  C14  single    1.346  0.020  1.346
 C3G  C05  O06  single    1.398  0.020  1.398
 C3G  O06  C07  single    1.404  0.020  1.404
 C3G  C14  C15  aromatic  1.396  0.020  1.396
 C3G  C14  C19  aromatic  1.394  0.020  1.394
 C3G  C07  C10  single    1.515  0.020  1.515
 C3G  C15  C16  aromatic  1.377  0.020  1.377
 C3G  C10  O11  double    1.201  0.020  1.201
 C3G  C10  O12  single    1.324  0.020  1.324
 C3G  C19  C18  aromatic  1.383  0.020  1.383
 C3G  C16  C17  aromatic  1.391  0.020  1.391
 C3G  C18  C17  aromatic  1.387  0.020  1.387
 C3G  C17  N20  single    1.446  0.020  1.446
 C3G  N20  O21  double    1.210  0.020  1.210
 C3G  N20  O22  single    1.210  0.020  1.210
 C3G  C15  H1   single    0.930  0.020  1.080
 C3G  C02  H2   single    0.970  0.020  1.090
 C3G  C03  H3   single    0.970  0.020  1.090
 C3G  C05  H4   single    0.970  0.020  1.090
 C3G  C07  H5   single    0.970  0.020  1.090
 C3G  C08  H6   single    0.970  0.020  1.090
 C3G  C16  H7   single    0.930  0.020  1.080
 C3G  C18  H8   single    0.930  0.020  1.080
 C3G  C19  H9   single    0.930  0.020  1.080
 C3G  O01  H10  single    0.850  0.020  0.980
 C3G  O04  H11  single    0.850  0.020  0.980
 C3G  O09  H12  single    0.850  0.020  0.980
 C3G  O12  H13  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
 C3G  O12  C10  O11  124.54  3.000
 C3G  O12  C10  C07  111.34  3.000
 C3G  O11  C10  C07  124.12  3.000
 C3G  H1   C15  C16  120.01  3.000
 C3G  H1   C15  C14  119.65  3.000
 C3G  C16  C15  C14  120.35  3.000
 C3G  N20  C17  C18  119.54  3.000
 C3G  N20  C17  C16  119.52  3.000
 C3G  C18  C17  C16  120.94  3.000
 C3G  H2   C02  O01  111.04  3.000
 C3G  H2   C02  C08  107.67  3.000
 C3G  O01  C02  C08  107.98  3.000
 C3G  H2   C02  C03  107.89  3.000
 C3G  C08  C02  C03  110.95  3.000
 C3G  O01  C02  C03  111.27  3.000
 C3G  H3   C03  O04  111.79  3.000
 C3G  H3   C03  C05  108.15  3.000
 C3G  O04  C03  C05  111.48  3.000
 C3G  H3   C03  C02  108.81  3.000
 C3G  C05  C03  C02  109.17  3.000
 C3G  O04  C03  C02  107.40  3.000
 C3G  H4   C05  O13  110.59  3.000
 C3G  H4   C05  O06  110.82  3.000
 C3G  O13  C05  O06  107.47  3.000
 C3G  H4   C05  C03  110.00  3.000
 C3G  O06  C05  C03  110.16  3.000
 C3G  O13  C05  C03  107.72  3.000
 C3G  H5   C07  O06  111.25  3.000
 C3G  H5   C07  C08  108.27  3.000
 C3G  O06  C07  C08  110.50  3.000
 C3G  H5   C07  C10  108.71  3.000
 C3G  O06  C07  C10  106.21  3.000
 C3G  C08  C07  C10  111.91  3.000
 C3G  H6   C08  O09  111.89  3.000
 C3G  H6   C08  C07  108.11  3.000
 C3G  O09  C08  C07  112.02  3.000
 C3G  H6   C08  C02  108.71  3.000
 C3G  C07  C08  C02  108.34  3.000
 C3G  O09  C08  C02  107.67  3.000
 C3G  O13  C14  C19  124.48  3.000
 C3G  C19  C14  C15  120.01  3.000
 C3G  O13  C14  C15  115.51  3.000
 C3G  H7   C16  C17  121.33  3.000
 C3G  H7   C16  C15  119.43  3.000
 C3G  C17  C16  C15  119.24  3.000
 C3G  H8   C18  C19  118.96  3.000
 C3G  H8   C18  C17  121.22  3.000
 C3G  C19  C18  C17  119.83  3.000
 C3G  H9   C19  C18  118.26  3.000
 C3G  H9   C19  C14  122.10  3.000
 C3G  C18  C19  C14  119.64  3.000
 C3G  H10  O01  C02  108.16  3.000
 C3G  H11  O04  C03  109.21  3.000
 C3G  C07  O06  C05  112.38  3.000
 C3G  H12  O09  C08  109.56  3.000
 C3G  H13  O12  C10  110.28  3.000
 C3G  C14  O13  C05  120.41  3.000
 C3G  O22  N20  O21  123.64  3.000
 C3G  O22  N20  C17  118.22  3.000
 C3G  O21  N20  C17  118.14  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
 C3G  CONST_01  C18  C19  C14  C15    0.00   0.0  0
 C3G  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 C3G  CONST_03  C14  C15  C16  C17    0.00   0.0  0
 C3G  CONST_04  C14  C19  C18  C17    0.00   0.0  0
 C3G  CONST_05  C19  C14  C15  C16    0.00   0.0  0
 C3G  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 C3G  CONST_07  N20  C17  C16  C15  180.00   0.0  0
 C3G  CONST_08  O13  C14  C15  C16  180.00   0.0  0
 C3G  CONST_09  O13  C14  C19  C18  180.00   0.0  0
 C3G  CONST_10  N20  C17  C18  C19  180.00   0.0  0
 C3G  CONST_11  H9   C19  C14  C15  180.00   0.0  0
 C3G  CONST_12  H1   C15  C16  C17  180.00   0.0  0
 C3G  CONST_13  H7   C16  C15  C14  180.00   0.0  0
 C3G  CONST_14  H8   C18  C19  C14  180.00   0.0  0
 C3G  CONST_15  O21  N20  C17  C16    0.00   0.0  0
 C3G  CONST_16  O22  N20  C17  C16  180.00   0.0  0
 C3G  CONST_17  O21  N20  C17  C18  180.00   0.0  0
 C3G  CONST_18  O22  N20  C17  C18    0.00   0.0  0
 C3G  CONST_19  H13  O12  C10  C07  180.00   0.0  0
 C3G  Var_01    C19  C14  O13  C05   10.88  30.0  2

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
 C3G  chir_01  C02  O01  C03  C08  positiv
 C3G  chir_02  C03  O04  C02  C05  positiv
 C3G  chir_03  C05  O06  O13  C03  negativ
 C3G  chir_04  C07  O06  C08  C10  negativ
 C3G  chir_05  C08  O09  C07  C02  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 C3G  plan-1  C15  0.020
 C3G  plan-1  C17  0.020
 C3G  plan-1  C14  0.020
 C3G  plan-1  C16  0.020
 C3G  plan-1  C18  0.020
 C3G  plan-1  C19  0.020
 C3G  plan-1  O13  0.020
 C3G  plan-1  H1   0.020
 C3G  plan-1  H7   0.020
 C3G  plan-1  H8   0.020
 C3G  plan-1  H9   0.020
 C3G  plan-1  N20  0.020
 C3G  plan-2  C17  0.020
 C3G  plan-2  O21  0.020
 C3G  plan-2  O22  0.020
 C3G  plan-2  N20  0.020
 C3G  plan-3  C10  0.020
 C3G  plan-3  C07  0.020
 C3G  plan-3  O11  0.020
 C3G  plan-3  O12  0.020
 C3G  plan-3  H13  0.020

