# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:01:20 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(NO)C(=O)N[C@H]1[C@H](O)O[C@H](CO)[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
 YX1  YX1  2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose  D-saccharide  35  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_YX1
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
 YX1  O3    O  OH1   0  -0.663   0.4583   2.4160   1.0290
 YX1  C3    C  CH1   0   0.038   0.9256   1.3995   0.1832
 YX1  C4    C  CH1   0  -0.003   2.3943   1.0790   0.4425
 YX1  O4    O  OH1   0  -0.674   3.1320   2.2333   0.1046
 YX1  C5    C  CH1   0  -0.021   2.8188  -0.1370  -0.3875
 YX1  C6    C  CH2   0  -0.160   4.2412  -0.5580  -0.0910
 YX1  O6    O  OH1   0  -0.669   4.5965  -1.6104  -0.9541
 YX1  O5    O  O2    0  -0.496   1.9704  -1.2242  -0.0845
 YX1  C1    C  CH1   0   0.305   0.6262  -0.9970  -0.4315
 YX1  O1    O  OH1   0  -0.648  -0.0961  -2.1348  -0.1549
 YX1  C2    C  CH1   0  -0.148   0.0613   0.1613   0.3962
 YX1  N2    N  NH1   0  -0.675  -1.3040   0.4274   0.0434
 YX1  CAM   C  C     0   0.747  -2.3505   0.0146   0.7913
 YX1  OAG   O  O     0  -0.532  -2.2462  -0.4684   1.9093
 YX1  NAN   N  NT    0  -0.371  -3.5974   0.2285   0.2296
 YX1  CAH   C  CH3   0  -0.519  -4.7735  -0.3039   0.8927
 YX1  NAO   N  NH1   0  -0.252  -3.6446   0.4722  -1.1205
 YX1  OAP   O  OH1   0  -0.578  -3.9690  -0.7011  -1.8337
 YX1  H3    H  HOH1  0   0.450   1.0147   3.1902   0.8908
 YX1  HA    H  HCH1  0   0.206   0.8387   1.7020  -0.8753
 YX1  H4    H  HCH1  0   0.226   2.5126   0.8328   1.5078
 YX1  H2    H  HCH1  0   0.267   0.1000  -0.1215   1.4512
 YX1  HB    H  HOH1  0   0.463   3.9165   2.2806   0.6578
 YX1  H5    H  HCH1  0   0.221   2.7383   0.1237  -1.4564
 YX1  H6C1  H  HCH2  0   0.203   4.8943   0.3113  -0.2280
 YX1  H6C2  H  HCH2  0   0.200   4.3132  -0.8512   0.9657
 YX1  H6    H  HOH1  0   0.457   5.5129  -1.8421  -0.7796
 YX1  H1    H  HCH1  0   0.182   0.5694  -0.7334  -1.5032
 YX1  HC    H  HOH1  0   0.464   0.0256  -2.7708  -0.8674
 YX1  HD    H  HNH1  0   0.398  -1.5039   0.8094  -0.8687
 YX1  HAH1  H  HCH3  0   0.251  -4.7495  -0.0623   1.9512
 YX1  HAH2  H  HCH3  0   0.243  -5.6535   0.1717   0.4626
 YX1  HAH3  H  HCH3  0   0.235  -4.8734  -1.3855   0.7831
 YX1  HAO   H  HNH1  0   0.390  -4.4226   1.0958  -1.3016
 YX1  HAP   H  HOH1  0   0.461  -3.1473  -0.9454  -2.2727

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
 YX1  O3   C3    single  1.402  0.020  1.402
 YX1  C3   C4    single  1.525  0.020  1.525
 YX1  C3   C2    single  1.525  0.020  1.525
 YX1  C4   O4    single  1.411  0.020  1.411
 YX1  C4   C5    single  1.532  0.020  1.532
 YX1  C5   C6    single  1.513  0.020  1.513
 YX1  C5   O5    single  1.412  0.020  1.412
 YX1  C6   O6    single  1.407  0.020  1.407
 YX1  O5   C1    single  1.407  0.020  1.407
 YX1  C1   O1    single  1.376  0.020  1.376
 YX1  C1   C2    single  1.532  0.020  1.532
 YX1  C2   N2    single  1.435  0.020  1.435
 YX1  N2   CAM   single  1.351  0.020  1.351
 YX1  CAM  OAG   double  1.222  0.020  1.222
 YX1  CAM  NAN   single  1.384  0.020  1.384
 YX1  NAN  CAH   single  1.451  0.020  1.451
 YX1  NAN  NAO   single  1.373  0.020  1.373
 YX1  NAO  OAP   single  1.411  0.020  1.411
 YX1  O3   H3    single  0.850  0.020  0.980
 YX1  C3   HA    single  0.970  0.020  1.090
 YX1  C4   H4    single  0.970  0.020  1.090
 YX1  C2   H2    single  0.970  0.020  1.090
 YX1  O4   HB    single  0.850  0.020  0.980
 YX1  C5   H5    single  0.970  0.020  1.090
 YX1  C6   H6C1  single  0.970  0.020  1.090
 YX1  C6   H6C2  single  0.970  0.020  1.090
 YX1  O6   H6    single  0.850  0.020  0.980
 YX1  C1   H1    single  0.970  0.020  1.090
 YX1  O1   HC    single  0.850  0.020  0.980
 YX1  N2   HD    single  0.860  0.020  1.020
 YX1  CAH  HAH1  single  0.970  0.020  1.090
 YX1  CAH  HAH2  single  0.970  0.020  1.090
 YX1  CAH  HAH3  single  0.970  0.020  1.090
 YX1  NAO  HAO   single  0.890  0.020  1.040
 YX1  OAP  HAP   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
 YX1  H3    O3   C3    107.67  3.000
 YX1  HA    C3   C2    108.16  3.000
 YX1  HA    C3   C4    107.23  3.000
 YX1  C2    C3   C4    110.57  3.000
 YX1  HA    C3   O3    110.68  3.000
 YX1  C2    C3   O3    108.39  3.000
 YX1  C4    C3   O3    111.75  3.000
 YX1  H4    C4   C5    108.50  3.000
 YX1  H4    C4   O4    111.03  3.000
 YX1  C5    C4   O4    112.00  3.000
 YX1  H4    C4   C3    108.38  3.000
 YX1  C5    C4   C3    109.96  3.000
 YX1  O4    C4   C3    106.91  3.000
 YX1  HB    O4   C4    109.22  3.000
 YX1  H5    C5   O5    110.25  3.000
 YX1  H5    C5   C6    108.92  3.000
 YX1  O5    C5   C6    107.97  3.000
 YX1  H5    C5   C4    108.49  3.000
 YX1  O5    C5   C4    109.17  3.000
 YX1  C6    C5   C4    112.04  3.000
 YX1  H6C2  C6   H6C1  107.02  3.000
 YX1  H6C2  C6   O6    111.95  3.000
 YX1  H6C1  C6   O6    111.48  3.000
 YX1  H6C2  C6   C5    108.93  3.000
 YX1  H6C1  C6   C5    108.37  3.000
 YX1  O6    C6   C5    108.99  3.000
 YX1  H6    O6   C6    108.05  3.000
 YX1  C1    O5   C5    113.38  3.000
 YX1  H1    C1   C2    108.95  3.000
 YX1  H1    C1   O1    111.42  3.000
 YX1  C2    C1   O1    108.85  3.000
 YX1  H1    C1   O5    109.08  3.000
 YX1  C2    C1   O5    109.96  3.000
 YX1  O1    C1   O5    108.57  3.000
 YX1  HC    O1   C1    109.33  3.000
 YX1  H2    C2   N2    108.61  3.000
 YX1  H2    C2   C1    108.23  3.000
 YX1  N2    C2   C1    111.00  3.000
 YX1  H2    C2   C3    108.95  3.000
 YX1  N2    C2   C3    110.75  3.000
 YX1  C1    C2   C3    109.24  3.000
 YX1  HD    N2   CAM   117.57  3.000
 YX1  HD    N2   C2    118.75  3.000
 YX1  CAM   N2   C2    122.97  3.000
 YX1  NAN   CAM  OAG   120.61  3.000
 YX1  NAN   CAM  N2    115.21  3.000
 YX1  OAG   CAM  N2    124.13  3.000
 YX1  NAO   NAN  CAH   119.12  3.000
 YX1  NAO   NAN  CAM   117.23  3.000
 YX1  CAH   NAN  CAM   119.20  3.000
 YX1  HAH3  CAH  HAH2  108.61  3.000
 YX1  HAH3  CAH  HAH1  108.68  3.000
 YX1  HAH2  CAH  HAH1  107.81  3.000
 YX1  HAH3  CAH  NAN   113.06  3.000
 YX1  HAH2  CAH  NAN   108.31  3.000
 YX1  HAH1  CAH  NAN   110.23  3.000
 YX1  HAO   NAO  OAP   104.18  3.000
 YX1  HAO   NAO  NAN   108.14  3.000
 YX1  OAP   NAO  NAN   110.94  3.000
 YX1  HAP   OAP  NAO   104.19  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
 YX1  CONST_01  OAG   CAM  N2   C2     0.00   0.0  0
 YX1  CONST_02  NAN   CAM  N2   C2   180.00   0.0  0
 YX1  CONST_03  CAH   NAN  CAM  OAG    0.00   0.0  0
 YX1  CONST_04  NAO   NAN  CAM  OAG  180.00   0.0  0
 YX1  CONST_05  CAH   NAN  CAM  N2   180.00   0.0  0
 YX1  CONST_07  HD    N2   CAM  OAG  180.00   0.0  0
 YX1  Var_01    OAP   NAO  NAN  CAM   98.32  30.0  2
 YX1  Var_02    HAH1  CAH  NAN  CAM   47.84  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
 YX1  chir_01  C3  O3  C4  C2  negativ
 YX1  chir_02  C4  O4  C3  C5  negativ
 YX1  chir_03  C5  O5  C4  C6  negativ
 YX1  chir_04  C1  O5  O1  C2  negativ
 YX1  chir_05  C2  N2  C3  C1  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
 YX1  plan-1  C2   0.020
 YX1  plan-1  N2   0.020
 YX1  plan-1  CAM  0.020
 YX1  plan-1  OAG  0.020
 YX1  plan-1  NAN  0.020
 YX1  plan-1  CAH  0.020
 YX1  plan-1  NAO  0.020
 YX1  plan-1  HD   0.020

