# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 21:46:31 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-azidoethyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1OCCN=[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
 Z3Q  Z3Q  '2-azidoethyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranoside'  D-saccharide  38  20  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z3Q
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
 Z3Q  C1    C  CH1    0   0.354   -7.4980   -6.4061  53.1041
 Z3Q  C11   C  CH2    0  -0.160   -7.2225   -7.0449  55.3603
 Z3Q  C12   C  CH2    0  -0.350   -7.0209   -8.3211  56.1479
 Z3Q  C2    C  CH1    0  -0.168   -7.6294   -7.0536  51.7225
 Z3Q  C7    C  C      0   0.494   -6.6512   -9.3621  51.6160
 Z3Q  C8    C  CH3    0  -0.809   -8.0074   -9.9705  51.8701
 Z3Q  C3    C  CH1    0   0.044   -7.5830   -5.9643  50.6564
 Z3Q  C4    C  CH1    0  -0.001   -8.5849   -4.8533  50.9630
 Z3Q  C5    C  CH1    0  -0.020   -8.3899   -4.3509  52.3976
 Z3Q  C6    C  CH2    0  -0.159   -9.4273   -3.3225  52.7924
 Z3Q  N1A   N  N      0  -0.360   -8.2398   -9.1328  56.2471
 Z3Q  N1B   N  N      1   0.358   -9.0710   -8.7629  57.0552
 Z3Q  N1C   N  N     -1  -0.220   -9.8962   -8.5070  57.7750
 Z3Q  N2    N  NH1    0  -0.610   -6.5824   -8.0172  51.5025
 Z3Q  O1    O  O2     0  -0.484   -7.6427   -7.3865  54.0563
 Z3Q  O7    O  O      0  -0.489   -5.6488  -10.0515  51.4952
 Z3Q  O3    O  OH1    0  -0.657   -7.8297   -6.5614  49.4132
 Z3Q  O4    O  OH1    0  -0.668   -8.3612   -3.8322  50.0161
 Z3Q  O5    O  O2     0  -0.494   -8.5004   -5.4443  53.2865
 Z3Q  O6    O  OH1    0  -0.664   -9.1249   -2.8392  54.0787
 Z3Q  H1    H  HCH1   0   0.186   -6.5043   -5.9230  53.1837
 Z3Q  H111  H  HCH2   0   0.229   -6.2687   -6.5032  55.3360
 Z3Q  H112  H  HCH2   0   0.227   -7.9541   -6.3982  55.8572
 Z3Q  H121  H  HCH2   0   0.266   -6.2832   -8.9515  55.6545
 Z3Q  H122  H  HCH2   0   0.264   -6.6306   -8.0689  57.1375
 Z3Q  H2    H  HCH1   0   0.280   -8.6008   -7.5518  51.6720
 Z3Q  H82   H  HCH3   0   0.264   -8.4226   -9.6381  52.8213
 Z3Q  H83   H  HCH3   0   0.264   -8.7204   -9.7000  51.0897
 Z3Q  H81   H  HCH3   0   0.265   -7.9153  -11.0531  51.8907
 Z3Q  HN2   H  HNH1   0   0.387   -5.6531   -7.6479  51.3496
 Z3Q  H3    H  HCH1   0   0.212   -6.5768   -5.5095  50.6818
 Z3Q  HO3   H  HOH1   0   0.450   -7.7602   -5.8780  48.7381
 Z3Q  H4    H  HCH1   0   0.227   -9.6001   -5.2657  50.8713
 Z3Q  HO4   H  HOH1   0   0.461   -9.1950   -3.4010  49.8098
 Z3Q  H5    H  HCH1   0   0.223   -7.3881   -3.8967  52.4756
 Z3Q  H62   H  HCH2   0   0.200  -10.4221   -3.7878  52.7513
 Z3Q  H61   H  HCH2   0   0.203   -9.4183   -2.5171  52.0484
 Z3Q  HO6   H  HOH1   0   0.454   -9.7831   -2.1779  54.3108

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
 Z3Q  C1   O1    single  1.374  0.020  1.374
 Z3Q  C1   C2    single  1.531  0.020  1.531
 Z3Q  C1   O5    single  1.401  0.020  1.401
 Z3Q  C1   H1    single  0.970  0.020  1.090
 Z3Q  C11  O1    single  1.412  0.020  1.412
 Z3Q  C11  C12   single  1.513  0.020  1.513
 Z3Q  C11  H111  single  0.970  0.020  1.090
 Z3Q  C11  H112  single  0.970  0.020  1.090
 Z3Q  C12  H121  single  0.970  0.020  1.090
 Z3Q  C12  H122  single  0.970  0.020  1.090
 Z3Q  C12  N1A   single  1.468  0.020  1.468
 Z3Q  C2   N2    single  1.440  0.020  1.440
 Z3Q  C2   H2    single  0.970  0.020  1.090
 Z3Q  C2   C3    single  1.525  0.020  1.525
 Z3Q  C7   N2    single  1.351  0.020  1.351
 Z3Q  C7   O7    double  1.223  0.020  1.223
 Z3Q  C7   C8    single  1.508  0.020  1.508
 Z3Q  C8   H81   single  0.970  0.020  1.090
 Z3Q  C8   H82   single  0.970  0.020  1.090
 Z3Q  C8   H83   single  0.970  0.020  1.090
 Z3Q  C3   C4    single  1.527  0.020  1.527
 Z3Q  C3   O3    single  1.401  0.020  1.401
 Z3Q  C3   H3    single  0.970  0.020  1.090
 Z3Q  C4   H4    single  0.970  0.020  1.090
 Z3Q  C4   C5    single  1.532  0.020  1.532
 Z3Q  C4   O4    single  1.410  0.020  1.410
 Z3Q  C5   H5    single  0.970  0.020  1.090
 Z3Q  C5   C6    single  1.513  0.020  1.513
 Z3Q  C5   O5    single  1.413  0.020  1.413
 Z3Q  C6   O6    single  1.407  0.020  1.407
 Z3Q  C6   H61   single  0.970  0.020  1.090
 Z3Q  C6   H62   single  0.970  0.020  1.090
 Z3Q  N1A  N1B   double  1.217  0.020  1.217
 Z3Q  N1B  N1C   double  1.125  0.020  1.125
 Z3Q  N2   HN2   single  0.860  0.020  1.020
 Z3Q  O3   HO3   single  0.850  0.020  0.980
 Z3Q  O4   HO4   single  0.850  0.020  0.980
 Z3Q  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
 Z3Q  H1    C1   O5    109.46  3.000
 Z3Q  H1    C1   O1    110.84  3.000
 Z3Q  O5    C1   O1    108.92  3.000
 Z3Q  H1    C1   C2    109.03  3.000
 Z3Q  O5    C1   C2    110.26  3.000
 Z3Q  O1    C1   C2    108.32  3.000
 Z3Q  H112  C11  H111  107.41  3.000
 Z3Q  H112  C11  O1    111.28  3.000
 Z3Q  H111  C11  O1    110.96  3.000
 Z3Q  H112  C11  C12   110.53  3.000
 Z3Q  H111  C11  C12   108.19  3.000
 Z3Q  O1    C11  C12   108.44  3.000
 Z3Q  H122  C12  H121  107.58  3.000
 Z3Q  H122  C12  N1A   111.27  3.000
 Z3Q  H121  C12  N1A   105.85  3.000
 Z3Q  N1A   C12  C11   113.01  3.000
 Z3Q  H122  C12  C11   108.91  3.000
 Z3Q  H121  C12  C11   110.05  3.000
 Z3Q  H2    C2   N2    109.52  3.000
 Z3Q  H2    C2   C3    108.69  3.000
 Z3Q  N2    C2   C3    110.44  3.000
 Z3Q  C3    C2   C1    109.03  3.000
 Z3Q  H2    C2   C1    108.10  3.000
 Z3Q  N2    C2   C1    111.00  3.000
 Z3Q  O7    C7   N2    120.74  3.000
 Z3Q  O7    C7   C8    121.77  3.000
 Z3Q  N2    C7   C8    117.48  3.000
 Z3Q  H81   C8   H83   108.41  3.000
 Z3Q  H83   C8   H82   107.44  3.000
 Z3Q  H81   C8   H82   108.64  3.000
 Z3Q  H83   C8   C7    111.54  3.000
 Z3Q  H82   C8   C7    111.51  3.000
 Z3Q  H81   C8   C7    109.20  3.000
 Z3Q  H3    C3   O3    110.88  3.000
 Z3Q  H3    C3   C4    107.07  3.000
 Z3Q  O3    C3   C4    111.88  3.000
 Z3Q  H3    C3   C2    107.81  3.000
 Z3Q  O3    C3   C2    108.09  3.000
 Z3Q  C4    C3   C2    111.06  3.000
 Z3Q  H4    C4   O4    111.22  3.000
 Z3Q  O4    C4   C5    111.77  3.000
 Z3Q  H4    C4   C5    108.57  3.000
 Z3Q  O4    C4   C3    106.73  3.000
 Z3Q  C5    C4   C3    110.05  3.000
 Z3Q  H4    C4   C3    108.43  3.000
 Z3Q  H5    C5   O5    110.19  3.000
 Z3Q  O5    C5   C6    107.94  3.000
 Z3Q  H5    C5   C6    108.93  3.000
 Z3Q  O5    C5   C4    108.98  3.000
 Z3Q  C6    C5   C4    112.32  3.000
 Z3Q  H5    C5   C4    108.48  3.000
 Z3Q  H61   C6   H62   107.04  3.000
 Z3Q  H62   C6   O6    111.98  3.000
 Z3Q  H61   C6   O6    111.48  3.000
 Z3Q  H62   C6   C5    108.85  3.000
 Z3Q  H61   C6   C5    108.45  3.000
 Z3Q  O6    C6   C5    108.95  3.000
 Z3Q  N1B   N1A  C12   116.36  3.000
 Z3Q  N1C   N1B  N1A   174.56  3.000
 Z3Q  HN2   N2   C7    115.01  3.000
 Z3Q  HN2   N2   C2    116.53  3.000
 Z3Q  C7    N2   C2    128.04  3.000
 Z3Q  C11   O1   C1    115.84  3.000
 Z3Q  HO3   O3   C3    107.87  3.000
 Z3Q  HO4   O4   C4    109.35  3.000
 Z3Q  C5    O5   C1    113.15  3.000
 Z3Q  HO6   O6   C6    108.05  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
 Z3Q  CONST_01  O7    C7   N2   C2    180.00   0.0  0
 Z3Q  CONST_02  C8    C7   N2   C2      0.00   0.0  0
 Z3Q  CONST_03  HN2   N2   C7   C8    180.00   0.0  0
 Z3Q  Var_01    C12   C11  O1   C1   -161.65  30.0  1
 Z3Q  Var_02    O1    C11  C12  N1A   -59.58  30.0  2
 Z3Q  Var_03    H121  C12  N1A  N1B   161.76  30.0  2
 Z3Q  Var_04    H81   C8   C7   N2    177.34  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
 Z3Q  chir_01  C1  O1  C2  O5  negativ
 Z3Q  chir_02  C2  N2  C3  C1  positiv
 Z3Q  chir_03  C3  O3  C2  C4  positiv
 Z3Q  chir_04  C4  O4  C5  C3  positiv
 Z3Q  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
 Z3Q  plan-1  C2   0.020
 Z3Q  plan-1  C7   0.020
 Z3Q  plan-1  C8   0.020
 Z3Q  plan-1  N2   0.020
 Z3Q  plan-1  O7   0.020
 Z3Q  plan-1  HN2  0.020
 Z3Q  plan-2  C12  0.020
 Z3Q  plan-2  N1A  0.020
 Z3Q  plan-2  N1B  0.020
 Z3Q  plan-2  N1C  0.020

