# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 05:36:34 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-amino-1-beta-D-glucopyranosylpyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O
#
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
 C3B  C3B  4-amino-1-beta-D-glucopyranosylpyrimidin-2(1H)-one  D-saccharide  34  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C3B
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
 C3B  C1'   C  CH1   0   0.217   0.0973  -0.2146   0.4835
 C3B  C2'   C  CH1   0   0.002   0.6510  -1.4869  -0.1540
 C3B  O2'   O  OH1   0  -0.670  -0.0663  -2.5631   0.3917
 C3B  C3'   C  CH1   0  -0.017   2.1357  -1.5487   0.1810
 C3B  O3'   O  OH1   0  -0.674   2.6701  -2.6889  -0.4531
 C3B  C4'   C  CH1   0   0.014   2.8371  -0.2677  -0.2694
 C3B  O4'   O  OH1   0  -0.673   4.1833  -0.2607   0.1472
 C3B  C5'   C  CH1   0  -0.019   2.1364   0.9460   0.3455
 C3B  O5'   O  O2    0  -0.481   0.7586   0.9214   0.0194
 C3B  C6'   C  CH2   0  -0.158   2.7016   2.2510  -0.1710
 C3B  O6'   O  OH1   0  -0.670   2.0748   3.3165   0.5021
 C3B  N1    N  NR6   0  -0.569  -1.3283  -0.0325   0.3001
 C3B  C2    C  CR6   0   0.600  -1.8921   0.0958  -0.9853
 C3B  O2    O  O     0  -0.509  -1.1686   0.0540  -1.9683
 C3B  N3    N  N     0  -0.541  -3.2275   0.2633  -1.0765
 C3B  C4    C  CR6   0   0.515  -3.9898   0.3116  -0.0027
 C3B  N4    N  NH2   0  -0.808  -5.3002   0.4842  -0.1643
 C3B  C5    C  CR16  0  -0.475  -3.4521   0.1869   1.3154
 C3B  C6    C  CR16  0   0.094  -2.1198   0.0185   1.4011
 C3B  H1'   H  HCH1  0   0.242   0.2389  -0.3156   1.5698
 C3B  H2'   H  HCH1  0   0.241   0.5389  -1.4367  -1.2419
 C3B  HO2'  H  HOH1  0   0.455   0.3141  -3.3789   0.0496
 C3B  H3'   H  HCH1  0   0.218   2.2405  -1.6311   1.2741
 C3B  HO3'  H  HOH1  0   0.460   3.4425  -2.9842   0.0375
 C3B  H4'   H  HCH1  0   0.225   2.7616  -0.1916  -1.3640
 C3B  HO4'  H  HOH1  0   0.460   4.7150  -0.7052  -0.5186
 C3B  H5'   H  HCH1  0   0.225   2.2617   0.9095   1.4407
 C3B  H6'   H  HCH2  0   0.214   3.7833   2.2454  -0.0044
 C3B  H6'A  H  HCH2  0   0.198   2.5416   2.3019  -1.2572
 C3B  HO6'  H  HOH1  0   0.457   2.5052   4.1322   0.2315
 C3B  HN4   H  HNH2  0   0.403  -5.6881   0.5820  -1.0871
 C3B  HN4A  H  HNH2  0   0.414  -5.9253   0.5349   0.6202
 C3B  H5    H  HCR6  0   0.290  -4.0707   0.2251   2.1989
 C3B  H6    H  HCR6  0   0.319  -1.6224  -0.0822   2.3559

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
 C3B  C1'  C2'   single  1.527  0.020  1.527
 C3B  C1'  O5'   single  1.394  0.020  1.394
 C3B  C1'  N1    single  1.449  0.020  1.449
 C3B  C2'  O2'   single  1.404  0.020  1.404
 C3B  C2'  C3'   single  1.523  0.020  1.523
 C3B  C3'  O3'   single  1.410  0.020  1.410
 C3B  C3'  C4'   single  1.528  0.020  1.528
 C3B  C4'  O4'   single  1.409  0.020  1.409
 C3B  C4'  C5'   single  1.530  0.020  1.530
 C3B  C5'  O5'   single  1.416  0.020  1.416
 C3B  C5'  C6'   single  1.513  0.020  1.513
 C3B  C6'  O6'   single  1.408  0.020  1.408
 C3B  N1   C2    single  1.409  0.020  1.409
 C3B  N1   C6    single  1.357  0.020  1.357
 C3B  C2   O2    double  1.221  0.020  1.221
 C3B  C2   N3    single  1.349  0.020  1.349
 C3B  N3   C4    double  1.318  0.020  1.318
 C3B  C4   N4    single  1.332  0.020  1.332
 C3B  C4   C5    single  1.429  0.020  1.429
 C3B  C5   C6    double  1.346  0.020  1.346
 C3B  C1'  H1'   single  0.970  0.020  1.090
 C3B  C2'  H2'   single  0.970  0.020  1.090
 C3B  O2'  HO2'  single  0.850  0.020  0.980
 C3B  C3'  H3'   single  0.970  0.020  1.090
 C3B  O3'  HO3'  single  0.850  0.020  0.980
 C3B  C4'  H4'   single  0.970  0.020  1.090
 C3B  O4'  HO4'  single  0.850  0.020  0.980
 C3B  C5'  H5'   single  0.970  0.020  1.090
 C3B  C6'  H6'   single  0.970  0.020  1.090
 C3B  C6'  H6'A  single  0.970  0.020  1.090
 C3B  O6'  HO6'  single  0.850  0.020  0.980
 C3B  N4   HN4   single  0.860  0.020  1.020
 C3B  N4   HN4A  single  0.860  0.020  1.020
 C3B  C5   H5    single  0.930  0.020  1.080
 C3B  C6   H6    single  0.930  0.020  1.080

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
 C3B  H1'   C1'  N1   105.26  3.000
 C3B  H1'   C1'  O5'  110.03  3.000
 C3B  N1    C1'  O5'  108.80  3.000
 C3B  H1'   C1'  C2'  106.80  3.000
 C3B  N1    C1'  C2'  114.12  3.000
 C3B  O5'   C1'  C2'  111.59  3.000
 C3B  H2'   C2'  C3'  108.68  3.000
 C3B  H2'   C2'  O2'  111.66  3.000
 C3B  C3'   C2'  O2'  112.43  3.000
 C3B  H2'   C2'  C1'  109.84  3.000
 C3B  C3'   C2'  C1'  107.18  3.000
 C3B  O2'   C2'  C1'  106.93  3.000
 C3B  HO2'  O2'  C2'  108.03  3.000
 C3B  H3'   C3'  C4'  108.16  3.000
 C3B  H3'   C3'  O3'  110.48  3.000
 C3B  C4'   C3'  O3'  111.80  3.000
 C3B  H3'   C3'  C2'  108.30  3.000
 C3B  C4'   C3'  C2'  110.40  3.000
 C3B  O3'   C3'  C2'  107.65  3.000
 C3B  HO3'  O3'  C3'  108.86  3.000
 C3B  H4'   C4'  C5'  108.27  3.000
 C3B  H4'   C4'  O4'  111.07  3.000
 C3B  C5'   C4'  O4'  108.34  3.000
 C3B  H4'   C4'  C3'  108.65  3.000
 C3B  C5'   C4'  C3'  109.64  3.000
 C3B  O4'   C4'  C3'  110.82  3.000
 C3B  HO4'  O4'  C4'  108.74  3.000
 C3B  H5'   C5'  C6'  108.97  3.000
 C3B  H5'   C5'  O5'  109.79  3.000
 C3B  C6'   C5'  O5'  107.45  3.000
 C3B  H5'   C5'  C4'  108.70  3.000
 C3B  C6'   C5'  C4'  112.08  3.000
 C3B  O5'   C5'  C4'  109.83  3.000
 C3B  C5'   O5'  C1'  113.53  3.000
 C3B  H6'A  C6'  H6'  107.13  3.000
 C3B  H6'A  C6'  O6'  111.88  3.000
 C3B  H6'   C6'  O6'  111.79  3.000
 C3B  H6'A  C6'  C5'  108.84  3.000
 C3B  H6'   C6'  C5'  108.23  3.000
 C3B  O6'   C6'  C5'  108.87  3.000
 C3B  HO6'  O6'  C6'  107.97  3.000
 C3B  C6    N1   C2   120.21  3.000
 C3B  C6    N1   C1'  118.42  3.000
 C3B  C2    N1   C1'  121.36  3.000
 C3B  N3    C2   O2   122.43  3.000
 C3B  N3    C2   N1   117.97  3.000
 C3B  O2    C2   N1   119.60  3.000
 C3B  C4    N3   C2   121.47  3.000
 C3B  C5    C4   N4   119.57  3.000
 C3B  C5    C4   N3   122.06  3.000
 C3B  N4    C4   N3   118.37  3.000
 C3B  HN4A  N4   HN4  118.14  3.000
 C3B  HN4A  N4   C4   121.62  3.000
 C3B  HN4   N4   C4   120.24  3.000
 C3B  H5    C5   C6   121.31  3.000
 C3B  H5    C5   C4   122.44  3.000
 C3B  C6    C5   C4   116.24  3.000
 C3B  H6    C6   C5   121.56  3.000
 C3B  H6    C6   N1   116.40  3.000
 C3B  C5    C6   N1   122.04  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
 C3B  CONST_01  N3    C2  N1  C1'  180.00  0.0  0
 C3B  CONST_02  C4    N3  C2  N1     0.00  0.0  0
 C3B  CONST_03  C5    C4  N3  C2     0.00  0.0  0
 C3B  CONST_04  C6    N1  C2  N3     0.00  0.0  0
 C3B  CONST_05  O2    C2  N1  C1'    0.00  0.0  0
 C3B  CONST_06  N4    C4  N3  C2   180.00  0.0  0
 C3B  CONST_07  C6    N1  C2  O2   180.00  0.0  0
 C3B  CONST_08  C4    N3  C2  O2   180.00  0.0  0
 C3B  CONST_09  HN4   N4  C4  N3     0.00  0.0  0
 C3B  CONST_10  HN4A  N4  C4  N3   180.00  0.0  0

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
 C3B  chir_01  C1'  C2'  O5'  N1   negativ
 C3B  chir_02  C2'  O2'  C1'  C3'  negativ
 C3B  chir_03  C3'  O3'  C2'  C4'  positiv
 C3B  chir_04  C4'  O4'  C5'  C3'  positiv
 C3B  chir_05  C5'  O5'  C4'  C6'  negativ

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
 C3B  plan-1  C1'   0.020
 C3B  plan-1  N1    0.020
 C3B  plan-1  C2    0.020
 C3B  plan-1  O2    0.020
 C3B  plan-1  N3    0.020
 C3B  plan-1  C4    0.020
 C3B  plan-1  N4    0.020
 C3B  plan-1  C5    0.020
 C3B  plan-1  C6    0.020
 C3B  plan-1  HN4   0.020
 C3B  plan-1  HN4A  0.020
 C3B  plan-1  H5    0.020
 C3B  plan-1  H6    0.020

