# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 07:42:55 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S,3R,4S,5S,6R)-2-[(R)-amino(hydroxy)methyl]-2-azido-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](O)[C@]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)N=[N+]=[N-]
#
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
 CGF  CGF  '(2S,3R,4S,5S,6R)-2-[(R)-amino(hydroxy)methyl]-2-azido-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol (non-preferred name)'  D-saccharide  31  17  .  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_CGF
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
 CGF  O5    O  O2     0  -0.497   0.1321  -0.8395  -0.4628
 CGF  C1    C  CT     0   0.349   0.6882   0.3971  -0.1052
 CGF  C7    C  CH1    0   0.139   1.0785   0.3929   1.4002
 CGF  N7    N  NH2    0  -0.791   1.6687   1.6219   1.7970
 CGF  O7    O  OH1    0  -0.662   1.8662  -0.7623   1.6360
 CGF  N1    N  N      0  -0.399   1.9085   0.5597  -0.8906
 CGF  N2    N  N      1   0.379   2.5043  -0.4695  -1.1637
 CGF  N3    N  N     -1  -0.212   3.1219  -1.3456  -1.4932
 CGF  C2    C  CH1    0   0.043  -0.2859   1.4903  -0.5713
 CGF  O2    O  OH1    0  -0.658   0.2379   2.7670  -0.3614
 CGF  C3    C  CH1    0  -0.014  -1.6411   1.2868   0.0981
 CGF  O3    O  OH1    0  -0.672  -2.5011   2.2808  -0.4035
 CGF  C4    C  CH1    0  -0.001  -2.1653  -0.1092  -0.2180
 CGF  O4    O  OH1    0  -0.671  -3.3480  -0.3017   0.5250
 CGF  C5    C  CH1    0  -0.032  -1.1165  -1.1758   0.1199
 CGF  C6    C  CH2    0  -0.151  -1.5182  -2.5272  -0.4312
 CGF  O6    O  OH1    0  -0.663  -0.6098  -3.5026   0.0122
 CGF  H7    H  HCH1   0   0.226   0.1732   0.2593   1.9989
 CGF  HN71  H  HNH2   0   0.361   1.9642   1.5845   2.7634
 CGF  HN72  H  HNH2   0   0.351   2.4627   1.8789   1.2249
 CGF  HO7   H  HOH1   0   0.439   2.7891  -0.4918   1.6774
 CGF  H2    H  HCH1   0   0.227  -0.4225   1.3060  -1.6495
 CGF  HO2   H  HOH1   0   0.453  -0.3523   3.3950  -0.7905
 CGF  H3    H  HCH1   0   0.221  -1.5322   1.3898   1.1885
 CGF  HO3   H  HOH1   0   0.456  -3.3348   2.2297   0.0750
 CGF  H4    H  HCH1   0   0.226  -2.3679  -0.1527  -1.2980
 CGF  HO4   H  HOH1   0   0.462  -3.9592  -0.8402   0.0157
 CGF  H5    H  HCH1   0   0.233  -1.0327  -1.2580   1.2122
 CGF  H61   H  HCH2   0   0.201  -2.5375  -2.7419  -0.0874
 CGF  H62   H  HCH2   0   0.200  -1.5543  -2.4654  -1.5278
 CGF  HO6   H  HOH1   0   0.456  -0.9041  -4.3544  -0.3229

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
 CGF  O5  C1    single  1.402  0.020  1.402
 CGF  O5  C5    single  1.418  0.020  1.418
 CGF  C1  C7    single  1.555  0.020  1.555
 CGF  C1  N1    single  1.460  0.020  1.460
 CGF  C1  C2    single  1.537  0.020  1.537
 CGF  C7  N7    single  1.420  0.020  1.420
 CGF  C7  O7    single  1.418  0.020  1.418
 CGF  C7  H7    single  0.970  0.020  1.090
 CGF  N7  HN71  single  0.890  0.020  1.040
 CGF  N7  HN72  single  0.890  0.020  1.040
 CGF  O7  HO7   single  0.850  0.020  0.980
 CGF  N1  N2    double  1.220  0.020  1.220
 CGF  N2  N3    double  1.121  0.020  1.121
 CGF  C2  O2    single  1.396  0.020  1.396
 CGF  C2  C3    single  1.525  0.020  1.525
 CGF  C2  H2    single  0.970  0.020  1.090
 CGF  O2  HO2   single  0.850  0.020  0.980
 CGF  C3  O3    single  1.407  0.020  1.407
 CGF  C3  C4    single  1.524  0.020  1.524
 CGF  C3  H3    single  0.970  0.020  1.090
 CGF  O3  HO3   single  0.850  0.020  0.980
 CGF  C4  O4    single  1.410  0.020  1.410
 CGF  C4  C5    single  1.534  0.020  1.534
 CGF  C4  H4    single  0.970  0.020  1.090
 CGF  O4  HO4   single  0.850  0.020  0.980
 CGF  C5  C6    single  1.514  0.020  1.514
 CGF  C5  H5    single  0.970  0.020  1.090
 CGF  C6  O6    single  1.405  0.020  1.405
 CGF  C6  H61   single  0.970  0.020  1.090
 CGF  C6  H62   single  0.970  0.020  1.090
 CGF  O6  HO6   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
 CGF  C5    O5  C1    116.97  3.000
 CGF  C2    C1  N1    106.70  3.000
 CGF  C2    C1  C7    117.04  3.000
 CGF  N1    C1  C7    108.13  3.000
 CGF  C2    C1  O5    107.38  3.000
 CGF  N1    C1  O5    107.01  3.000
 CGF  C7    C1  O5    110.12  3.000
 CGF  H7    C7  O7    105.62  3.000
 CGF  H7    C7  N7    107.27  3.000
 CGF  O7    C7  N7    115.33  3.000
 CGF  H7    C7  C1    108.81  3.000
 CGF  O7    C7  C1    107.61  3.000
 CGF  N7    C7  C1    111.87  3.000
 CGF  HN72  N7  HN71  108.69  3.000
 CGF  HN72  N7  C7    112.83  3.000
 CGF  HN71  N7  C7    110.88  3.000
 CGF  HO7   O7  C7    108.11  3.000
 CGF  N2    N1  C1    115.75  3.000
 CGF  N3    N2  N1    173.55  3.000
 CGF  H2    C2  C3    107.27  3.000
 CGF  H2    C2  O2    110.27  3.000
 CGF  C3    C2  O2    112.93  3.000
 CGF  H2    C2  C1    104.85  3.000
 CGF  C3    C2  C1    109.59  3.000
 CGF  O2    C2  C1    111.55  3.000
 CGF  HO2   O2  C2    107.43  3.000
 CGF  H3    C3  C4    108.98  3.000
 CGF  H3    C3  O3    110.34  3.000
 CGF  C4    C3  O3    111.28  3.000
 CGF  H3    C3  C2    109.53  3.000
 CGF  C4    C3  C2    109.68  3.000
 CGF  O3    C3  C2    107.00  3.000
 CGF  HO3   O3  C3    108.34  3.000
 CGF  H4    C4  C5    108.36  3.000
 CGF  H4    C4  O4    110.95  3.000
 CGF  C5    C4  O4    111.26  3.000
 CGF  H4    C4  C3    107.65  3.000
 CGF  C5    C4  C3    110.86  3.000
 CGF  O4    C4  C3    107.71  3.000
 CGF  HO4   O4  C4    109.32  3.000
 CGF  H5    C5  C6    108.38  3.000
 CGF  H5    C5  C4    108.86  3.000
 CGF  C6    C5  C4    111.05  3.000
 CGF  H5    C5  O5    111.04  3.000
 CGF  C6    C5  O5    107.20  3.000
 CGF  C4    C5  O5    110.28  3.000
 CGF  H62   C6  H61   107.05  3.000
 CGF  H62   C6  O6    112.04  3.000
 CGF  H61   C6  O6    111.47  3.000
 CGF  H62   C6  C5    108.77  3.000
 CGF  H61   C6  C5    107.89  3.000
 CGF  O6    C6  C5    109.48  3.000
 CGF  HO6   O6  C6    107.90  3.000

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
 CGF  chir_01  C1  O5  N1  C2  negativ
 CGF  chir_02  C7  O7  N7  C1  negativ
 CGF  chir_03  C2  O2  C1  C3  negativ
 CGF  chir_04  C3  O3  C2  C4  positiv
 CGF  chir_05  C4  O4  C5  C3  positiv
 CGF  chir_06  C5  O5  C6  C4  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
 CGF  plan-1  O5  0.020
 CGF  plan-1  C1  0.020
 CGF  plan-1  C7  0.020
 CGF  plan-1  N1  0.020
 CGF  plan-1  N2  0.020
 CGF  plan-1  N3  0.020
 CGF  plan-1  C2  0.020

