# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 20:38:20 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-3-fluoro-D-glycero-D-galacto-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](NC(N)=N)C(=C(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)F
#
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
 ZGE  ZGE  '5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-3-fluoro-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  43  24  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZGE
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
 ZGE  O10   O  O     0  -0.513  27.9881  15.1583  62.7679
 ZGE  C10   C  C     0   0.553  27.3919  15.1209  61.6936
 ZGE  C11   C  CH3   0  -0.773  27.8290  14.2069  60.5838
 ZGE  N5    N  NH1   0  -0.628  26.3234  15.8926  61.4298
 ZGE  C5    C  CH1   0  -0.129  25.6756  16.7474  62.3934
 ZGE  C4    C  CH1   0  -0.238  24.1586  16.6632  62.1633
 ZGE  N4    N  NH1   0  -0.649  23.6177  15.3993  62.5692
 ZGE  C12   C  C     0   0.554  23.3982  14.3569  61.6932
 ZGE  N7    N  NH2   0  -0.825  23.3108  13.1437  62.3282
 ZGE  N6    N  N     0  -0.705  23.2108  14.4306  60.4286
 ZGE  C3    C  C     0   0.500  23.4693  17.7987  62.8526
 ZGE  F1    F  F     0  -0.277  22.1422  17.7152  62.8446
 ZGE  C6    C  CH1   0   0.028  26.1241  18.2099  62.3235
 ZGE  O6    O  O2    0  -0.482  25.4559  18.9372  63.3484
 ZGE  C2    C  C     0   0.027  24.1083  18.8417  63.3870
 ZGE  C1    C  C     0   0.516  23.4259  19.9761  64.0552
 ZGE  O1B   O  OH1   0  -0.584  24.2827  20.9297  64.3787
 ZGE  O1A   O  O     0  -0.424  22.2421  20.0219  64.2769
 ZGE  C7    C  CH1   0  -0.030  27.6234  18.4070  62.5365
 ZGE  O7    O  OH1   0  -0.698  28.0785  17.7769  63.7060
 ZGE  C8    C  CH1   0   0.011  27.9937  19.8964  62.6652
 ZGE  O8    O  OH1   0  -0.672  27.3553  20.6836  61.6829
 ZGE  C9    C  CH2   0  -0.174  29.4907  20.1163  62.5545
 ZGE  O9    O  OH1   0  -0.675  29.9333  19.7309  61.2733
 ZGE  H1    H  HCH3  0   0.275  27.9639  13.2017  60.9802
 ZGE  H2    H  HCH3  0   0.255  27.1262  14.1639  59.7546
 ZGE  H3    H  HCH3  0   0.278  28.7946  14.5402  60.2027
 ZGE  H4    H  HNH1  0   0.408  25.9162  15.8339  60.5090
 ZGE  H5    H  HCH1  0   0.292  25.8879  16.3628  63.3948
 ZGE  H6    H  HCH1  0   0.297  23.9666  16.7911  61.0927
 ZGE  H7    H  HNH1  0   0.396  23.7650  15.1538  63.5369
 ZGE  H8    H  HNH2  0   0.385  23.9296  12.9835  63.1075
 ZGE  H9    H  HNH2  0   0.384  23.2648  12.3578  61.7001
 ZGE  H10   H  H     0   0.326  23.1524  15.3839  60.0949
 ZGE  H11   H  HCH1  0   0.261  25.8419  18.6198  61.3443
 ZGE  H13   H  HCH1  0   0.229  28.1156  18.0050  61.6408
 ZGE  H14   H  HOH1  0   0.460  28.1273  16.8205  63.5331
 ZGE  H15   H  HCH1  0   0.227  27.7124  20.2234  63.6742
 ZGE  H16   H  HOH1  0   0.452  26.4818  20.9228  62.0059
 ZGE  H17   H  HCH2  0   0.206  29.9836  19.5451  63.3485
 ZGE  H18   H  HCH2  0   0.208  29.6950  21.1775  62.7491
 ZGE  H19   H  HOH1  0   0.457  30.8913  19.8022  61.2537
 ZGE  HO1B  H  HOH1  0   0.491  23.8132  21.6528  64.8215

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
 ZGE  N6   C12   double  1.281  0.020  1.281
 ZGE  C11  C10   single  1.503  0.020  1.503
 ZGE  O8   C8    single  1.411  0.020  1.411
 ZGE  N5   C10   single  1.344  0.020  1.344
 ZGE  N5   C5    single  1.442  0.020  1.442
 ZGE  O9   C9    single  1.409  0.020  1.409
 ZGE  C12  N7    single  1.372  0.020  1.372
 ZGE  C12  N4    single  1.379  0.020  1.379
 ZGE  C10  O10   double  1.229  0.020  1.229
 ZGE  C8   C9    single  1.517  0.020  1.517
 ZGE  C8   C7    single  1.540  0.020  1.540
 ZGE  C4   C5    single  1.537  0.020  1.537
 ZGE  C4   N4    single  1.433  0.020  1.433
 ZGE  C4   C3    single  1.497  0.020  1.497
 ZGE  C6   C7    single  1.527  0.020  1.527
 ZGE  C6   C5    single  1.531  0.020  1.531
 ZGE  C6   O6    single  1.423  0.020  1.423
 ZGE  C7   O7    single  1.404  0.020  1.404
 ZGE  C3   F1    single  1.330  0.020  1.330
 ZGE  C3   C2    double  1.335  0.020  1.335
 ZGE  O6   C2    single  1.351  0.020  1.351
 ZGE  C2   C1    single  1.483  0.020  1.483
 ZGE  C1   O1B   single  1.322  0.020  1.322
 ZGE  C1   O1A   double  1.205  0.020  1.205
 ZGE  C11  H1    single  0.970  0.020  1.090
 ZGE  C11  H2    single  0.970  0.020  1.090
 ZGE  C11  H3    single  0.970  0.020  1.090
 ZGE  N5   H4    single  0.860  0.020  1.020
 ZGE  C5   H5    single  0.970  0.020  1.090
 ZGE  C4   H6    single  0.970  0.020  1.090
 ZGE  N4   H7    single  0.890  0.020  1.040
 ZGE  N7   H8    single  0.890  0.020  1.040
 ZGE  N7   H9    single  0.890  0.020  1.040
 ZGE  N6   H10   single  0.890  0.020  1.040
 ZGE  C6   H11   single  0.970  0.020  1.090
 ZGE  C7   H13   single  0.970  0.020  1.090
 ZGE  O7   H14   single  0.850  0.020  0.980
 ZGE  C8   H15   single  0.970  0.020  1.090
 ZGE  O8   H16   single  0.850  0.020  0.980
 ZGE  C9   H17   single  0.970  0.020  1.090
 ZGE  C9   H18   single  0.970  0.020  1.090
 ZGE  O9   H19   single  0.850  0.020  0.980
 ZGE  O1B  HO1B  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
 ZGE  N5    C10  C11  115.82  3.000
 ZGE  N5    C10  O10  122.65  3.000
 ZGE  C11   C10  O10  121.53  3.000
 ZGE  H3    C11  H2   108.53  3.000
 ZGE  H3    C11  H1   107.44  3.000
 ZGE  H2    C11  H1   108.72  3.000
 ZGE  H3    C11  C10  109.26  3.000
 ZGE  H2    C11  C10  113.52  3.000
 ZGE  H1    C11  C10  109.19  3.000
 ZGE  H4    N5   C5   117.60  3.000
 ZGE  H4    N5   C10  117.82  3.000
 ZGE  C5    N5   C10  124.50  3.000
 ZGE  H5    C5   C6   108.71  3.000
 ZGE  H5    C5   C4   108.03  3.000
 ZGE  C6    C5   C4   109.55  3.000
 ZGE  H5    C5   N5   108.44  3.000
 ZGE  C6    C5   N5   113.83  3.000
 ZGE  C4    C5   N5   108.12  3.000
 ZGE  H6    C4   C3   106.31  3.000
 ZGE  H6    C4   N4   108.28  3.000
 ZGE  C3    C4   N4   111.40  3.000
 ZGE  H6    C4   C5   108.24  3.000
 ZGE  C3    C4   C5   110.13  3.000
 ZGE  N4    C4   C5   112.24  3.000
 ZGE  H7    N4   C12  116.64  3.000
 ZGE  H7    N4   C4   115.53  3.000
 ZGE  C12   N4   C4   123.14  3.000
 ZGE  N6    C12  N7   119.91  3.000
 ZGE  N7    C12  N4   112.61  3.000
 ZGE  N6    C12  N4   127.37  3.000
 ZGE  H9    N7   H8   112.72  3.000
 ZGE  H9    N7   C12  113.84  3.000
 ZGE  H8    N7   C12  117.33  3.000
 ZGE  H10   N6   C12  112.86  3.000
 ZGE  C2    C3   F1   121.96  3.000
 ZGE  C2    C3   C4   123.84  3.000
 ZGE  F1    C3   C4   114.15  3.000
 ZGE  H11   C6   C7   109.17  3.000
 ZGE  H11   C6   O6   109.31  3.000
 ZGE  C7    C6   O6   107.13  3.000
 ZGE  H11   C6   C5   108.78  3.000
 ZGE  O6    C6   C5   108.52  3.000
 ZGE  C7    C6   C5   113.86  3.000
 ZGE  C2    O6   C6   116.91  3.000
 ZGE  C1    C2   O6   114.69  3.000
 ZGE  C1    C2   C3   123.90  3.000
 ZGE  O6    C2   C3   121.40  3.000
 ZGE  O1A   C1   O1B  124.33  3.000
 ZGE  O1A   C1   C2   124.34  3.000
 ZGE  O1B   C1   C2   111.33  3.000
 ZGE  HO1B  O1B  C1   109.63  3.000
 ZGE  H13   C7   C8   108.32  3.000
 ZGE  H13   C7   O7   111.70  3.000
 ZGE  C8    C7   O7   106.65  3.000
 ZGE  H13   C7   C6   106.20  3.000
 ZGE  O7    C7   C6   112.11  3.000
 ZGE  C8    C7   C6   111.87  3.000
 ZGE  H14   O7   C7   108.01  3.000
 ZGE  H15   C8   C9   106.07  3.000
 ZGE  H15   C8   O8   110.96  3.000
 ZGE  C9    C8   O8   108.34  3.000
 ZGE  H15   C8   C7   107.66  3.000
 ZGE  C9    C8   C7   111.80  3.000
 ZGE  O8    C8   C7   111.87  3.000
 ZGE  H16   O8   C8   108.42  3.000
 ZGE  H18   C9   H17  106.97  3.000
 ZGE  H18   C9   O9   111.53  3.000
 ZGE  H17   C9   O9   112.03  3.000
 ZGE  H18   C9   C8   108.11  3.000
 ZGE  H17   C9   C8   108.39  3.000
 ZGE  O9    C9   C8   109.67  3.000
 ZGE  H19   O9   C9   108.15  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
 ZGE  CONST_01  C5    N5   C10  O10     0.00   0.0  0
 ZGE  CONST_02  C5    N5   C10  C11   180.00   0.0  0
 ZGE  CONST_05  HO1B  O1B  C1   C2    180.00   0.0  0
 ZGE  CONST_06  H4    N5   C10  O10   180.00   0.0  0
 ZGE  CONST_07  H10   N6   C12  N4      0.00   0.0  0
 ZGE  CONST_09  H9    N7   C12  N4    180.00   0.0  0
 ZGE  CONST_10  H7    N4   C12  N7      0.00   0.0  0
 ZGE  Var_01    O6    C2   C3   C4     -0.54  30.0  1
 ZGE  Var_02    O1B   C1   C2   C3   -173.97  30.0  2
 ZGE  Var_03    H1    C11  C10  O10    49.57  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
 ZGE  chir_01  C5  N5  C4  C6  positiv
 ZGE  chir_02  C4  N4  C3  C5  negativ
 ZGE  chir_03  C6  O6  C5  C7  positiv
 ZGE  chir_04  C7  O7  C8  C6  positiv
 ZGE  chir_05  C8  O8  C7  C9  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
 ZGE  plan-1  O10   0.020
 ZGE  plan-1  C10   0.020
 ZGE  plan-1  C11   0.020
 ZGE  plan-1  N5    0.020
 ZGE  plan-1  C5    0.020
 ZGE  plan-1  H4    0.020
 ZGE  plan-2  C4    0.020
 ZGE  plan-2  N4    0.020
 ZGE  plan-2  C12   0.020
 ZGE  plan-2  N7    0.020
 ZGE  plan-2  N6    0.020
 ZGE  plan-2  H7    0.020
 ZGE  plan-2  H8    0.020
 ZGE  plan-2  H9    0.020
 ZGE  plan-2  H10   0.020
 ZGE  plan-3  C2    0.020
 ZGE  plan-3  C1    0.020
 ZGE  plan-3  O1B   0.020
 ZGE  plan-3  O1A   0.020
 ZGE  plan-3  HO1B  0.020

