# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 10:41:39 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-alpha-L-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](OCc2cnnn2CC=O)[C@@H](O)[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
 LZ0  LZ0  '[1-(2-oxoethyl)-1H-1,2,3-triazol-5-yl]methyl 6-deoxy-alpha-L-galactopyranoside'  L-saccharide  37  20  .  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_LZ0
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
 LZ0  C1    C  CH1   0   0.246  39.2818  4.5095  -3.3446
 LZ0  C2    C  CH1   0  -0.013  37.8768  4.4366  -2.7331
 LZ0  C3    C  CH1   0   0.007  36.9674  3.5718  -3.6030
 LZ0  C4    C  CH1   0  -0.032  37.6281  2.2131  -3.8427
 LZ0  C5    C  CH1   0   0.024  39.0371  2.3939  -4.4027
 LZ0  C6    C  CH3   0  -0.701  39.7905  1.0883  -4.5466
 LZ0  O1    O  O2    0  -0.491  39.1928  5.2490  -4.5295
 LZ0  O2    O  OH1   0  -0.659  37.3038  5.7108  -2.5945
 LZ0  O3    O  OH1   0  -0.667  35.6826  3.4325  -3.0547
 LZ0  O4    O  OH1   0  -0.681  37.6264  1.5302  -2.6047
 LZ0  O5    O  O2    0  -0.498  39.8135  3.2397  -3.5592
 LZ0  O1'   O  O     0  -0.359  39.9399  8.8991  -6.3387
 LZ0  C5'   C  C1    0   0.176  39.0558  8.9180  -5.5252
 LZ0  N1'   N  NR5   0  -0.290  40.4940  7.8752  -3.8356
 LZ0  C1'   C  CR5   0   0.299  41.0778  6.7277  -4.2400
 LZ0  C3'   C  CH2   0  -0.259  40.4236  5.6757  -5.0705
 LZ0  C2'   C  CR15  0  -0.221  42.3380  6.8082  -3.7072
 LZ0  N3'   N  N     0  -0.292  42.4490  7.9756  -3.0406
 LZ0  N2'   N  N     0  -0.091  41.3342  8.6105  -3.1224
 LZ0  H1    H  HCH1  0   0.242  39.9672  4.9926  -2.6341
 LZ0  H2    H  HCH1  0   0.233  37.9907  3.9528  -1.7535
 LZ0  H3    H  HCH1  0   0.246  36.8347  4.0593  -4.5741
 LZ0  HA    H  HOH1  0   0.457  37.6884  6.1384  -1.8231
 LZ0  H4    H  HCH1  0   0.244  37.0383  1.6671  -4.5906
 LZ0  HB    H  HOH1  0   0.440  35.7485  2.8272  -2.3066
 LZ0  H5    H  HCH1  0   0.225  38.9329  2.8456  -5.3980
 LZ0  HC    H  HOH1  0   0.464  37.6030  0.5833  -2.7674
 LZ0  H6C1  H  HCH3  0   0.246  40.7658  1.2525  -5.0048
 LZ0  H6C2  H  HCH3  0   0.230  39.9464  0.6036  -3.5824
 LZ0  H6C3  H  HCH3  0   0.236  39.2356  0.4028  -5.1879
 LZ0  H3'1  H  HCH2  0   0.258  41.1311  4.8509  -5.1966
 LZ0  H3'2  H  HCH2  0   0.273  40.2024  6.0592  -6.0680
 LZ0  H4'1  H  HCH2  0   0.327  38.9403  9.1709  -3.4225
 LZ0  H4'2  H  HCH2  0   0.316  38.4267  7.5942  -3.9819
 LZ0  H2'   H  HCR5  0   0.283  43.1451  6.0966  -3.7736
 LZ0  H1A   H  H     0   0.226  38.0624  9.3414  -5.7435
 LZ0  C4'   C  CH2   0  -0.444  39.1777  8.3734  -4.1294

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
 LZ0  C1   C2    single    1.534  0.020  1.534
 LZ0  C1   O1    single    1.400  0.020  1.400
 LZ0  C1   O5    single    1.393  0.020  1.393
 LZ0  C2   C3    single    1.527  0.020  1.527
 LZ0  C2   O2    single    1.404  0.020  1.404
 LZ0  C3   C4    single    1.530  0.020  1.530
 LZ0  C3   O3    single    1.404  0.020  1.404
 LZ0  C4   C5    single    1.527  0.020  1.527
 LZ0  C4   O4    single    1.414  0.020  1.414
 LZ0  C5   C6    single    1.514  0.020  1.514
 LZ0  C5   O5    single    1.425  0.020  1.425
 LZ0  O1   C3'   single    1.411  0.020  1.411
 LZ0  O1'  C5'   double    1.202  0.020  1.202
 LZ0  C5'  C4'   single    1.503  0.020  1.503
 LZ0  C4'  N1'   single    1.438  0.020  1.438
 LZ0  N1'  C1'   aromatic  1.350  0.020  1.350
 LZ0  N1'  N2'   aromatic  1.325  0.020  1.325
 LZ0  C1'  C3'   single    1.491  0.020  1.491
 LZ0  C1'  C2'   aromatic  1.371  0.020  1.371
 LZ0  C2'  N3'   aromatic  1.349  0.020  1.349
 LZ0  N3'  N2'   aromatic  1.285  0.020  1.285
 LZ0  C1   H1    single    0.970  0.020  1.090
 LZ0  C2   H2    single    0.970  0.020  1.090
 LZ0  C3   H3    single    0.970  0.020  1.090
 LZ0  O2   HA    single    0.850  0.020  0.980
 LZ0  C4   H4    single    0.970  0.020  1.090
 LZ0  O3   HB    single    0.850  0.020  0.980
 LZ0  C5   H5    single    0.970  0.020  1.090
 LZ0  O4   HC    single    0.850  0.020  0.980
 LZ0  C6   H6C1  single    0.970  0.020  1.090
 LZ0  C6   H6C2  single    0.970  0.020  1.090
 LZ0  C6   H6C3  single    0.970  0.020  1.090
 LZ0  C3'  H3'1  single    0.970  0.020  1.090
 LZ0  C3'  H3'2  single    0.970  0.020  1.090
 LZ0  C4'  H4'1  single    0.970  0.020  1.090
 LZ0  C4'  H4'2  single    0.970  0.020  1.090
 LZ0  C2'  H2'   single    0.930  0.020  1.080
 LZ0  C5'  H1A   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
 LZ0  H1    C1   O5    105.20  3.000
 LZ0  H1    C1   O1    110.78  3.000
 LZ0  O5    C1   O1    112.06  3.000
 LZ0  H1    C1   C2    109.53  3.000
 LZ0  O5    C1   C2    111.57  3.000
 LZ0  O1    C1   C2    107.72  3.000
 LZ0  H2    C2   O2    110.74  3.000
 LZ0  H2    C2   C3    108.68  3.000
 LZ0  O2    C2   C3    109.10  3.000
 LZ0  H2    C2   C1    106.35  3.000
 LZ0  O2    C2   C1    111.72  3.000
 LZ0  C3    C2   C1    110.20  3.000
 LZ0  H3    C3   O3    106.25  3.000
 LZ0  H3    C3   C4    108.00  3.000
 LZ0  O3    C3   C4    111.61  3.000
 LZ0  H3    C3   C2    108.99  3.000
 LZ0  O3    C3   C2    112.25  3.000
 LZ0  C4    C3   C2    109.57  3.000
 LZ0  H4    C4   O4    110.83  3.000
 LZ0  H4    C4   C5    107.74  3.000
 LZ0  O4    C4   C5    112.30  3.000
 LZ0  H4    C4   C3    108.44  3.000
 LZ0  O4    C4   C3    106.94  3.000
 LZ0  C5    C4   C3    110.54  3.000
 LZ0  H5    C5   O5    110.13  3.000
 LZ0  H5    C5   C6    108.40  3.000
 LZ0  O5    C5   C6    107.27  3.000
 LZ0  H5    C5   C4    107.08  3.000
 LZ0  O5    C5   C4    110.86  3.000
 LZ0  C6    C5   C4    113.07  3.000
 LZ0  H6C3  C6   H6C2  108.26  3.000
 LZ0  H6C3  C6   H6C1  107.62  3.000
 LZ0  H6C2  C6   H6C1  108.11  3.000
 LZ0  H6C3  C6   C5    110.17  3.000
 LZ0  H6C2  C6   C5    111.74  3.000
 LZ0  H6C1  C6   C5    110.81  3.000
 LZ0  C3'   O1   C1    115.41  3.000
 LZ0  HA    O2   C2    108.62  3.000
 LZ0  HB    O3   C3    107.62  3.000
 LZ0  HC    O4   C4    109.13  3.000
 LZ0  C5    O5   C1    115.10  3.000
 LZ0  H1A   C5'  C4'   113.35  3.000
 LZ0  H1A   C5'  O1'   122.37  3.000
 LZ0  C4'   C5'  O1'   124.28  3.000
 LZ0  N2'   N1'  C1'   111.03  3.000
 LZ0  N2'   N1'  C4'   119.89  3.000
 LZ0  C1'   N1'  C4'   129.01  3.000
 LZ0  C2'   C1'  C3'   131.39  3.000
 LZ0  C2'   C1'  N1'   103.38  3.000
 LZ0  C3'   C1'  N1'   125.23  3.000
 LZ0  H3'2  C3'  H3'1  106.90  3.000
 LZ0  H3'2  C3'  C1'   110.49  3.000
 LZ0  H3'1  C3'  C1'   108.20  3.000
 LZ0  H3'2  C3'  O1    106.26  3.000
 LZ0  H3'1  C3'  O1    112.36  3.000
 LZ0  C1'   C3'  O1    112.49  3.000
 LZ0  H2'   C2'  N3'   122.69  3.000
 LZ0  H2'   C2'  C1'   128.73  3.000
 LZ0  N3'   C2'  C1'   108.58  3.000
 LZ0  N2'   N3'  C2'   108.95  3.000
 LZ0  N3'   N2'  N1'   108.06  3.000
 LZ0  H4'2  C4'  H4'1  106.51  3.000
 LZ0  H4'2  C4'  N1'   110.77  3.000
 LZ0  H4'1  C4'  N1'   108.65  3.000
 LZ0  H4'2  C4'  C5'   109.16  3.000
 LZ0  H4'1  C4'  C5'   108.59  3.000
 LZ0  N1'   C4'  C5'   112.93  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
 LZ0  CONST_01  N3'  C2'  C1'  N1'    0.00   0.0  0
 LZ0  CONST_02  C2'  N3'  N2'  N1'    0.00   0.0  0
 LZ0  CONST_03  N3'  N2'  N1'  C1'    0.00   0.0  0
 LZ0  CONST_04  N2'  N3'  C2'  C1'    0.00   0.0  0
 LZ0  CONST_05  N2'  N1'  C1'  C2'    0.00   0.0  0
 LZ0  CONST_06  C2'  C1'  N1'  C4'  180.00   0.0  0
 LZ0  CONST_07  N3'  N2'  N1'  C4'  180.00   0.0  0
 LZ0  CONST_08  N2'  N1'  C1'  C3'  180.00   0.0  0
 LZ0  CONST_09  N3'  C2'  C1'  C3'  180.00   0.0  0
 LZ0  CONST_10  H2'  C2'  C1'  N1'  180.00   0.0  0
 LZ0  Var_01    C1'  C3'  O1   C1   -69.61  30.0  3
 LZ0  Var_02    N1'  C1'  C3'  O1   -52.84  30.0  2
 LZ0  Var_03    C1'  N1'  C4'  C5'  -75.41  30.0  2
 LZ0  Var_04    N1'  C4'  C5'  O1'    2.75  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
 LZ0  chir_01  C1  C2  O1  O5  positiv
 LZ0  chir_02  C2  O2  C1  C3  positiv
 LZ0  chir_03  C3  O3  C2  C4  negativ
 LZ0  chir_04  C4  O4  C3  C5  negativ
 LZ0  chir_05  C5  O5  C4  C6  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
 LZ0  plan-1  N1'  0.020
 LZ0  plan-1  C1'  0.020
 LZ0  plan-1  C3'  0.020
 LZ0  plan-1  C2'  0.020
 LZ0  plan-1  N3'  0.020
 LZ0  plan-1  N2'  0.020
 LZ0  plan-1  H2'  0.020
 LZ0  plan-1  C4'  0.020
 LZ0  plan-2  O1'  0.020
 LZ0  plan-2  C5'  0.020
 LZ0  plan-2  H1A  0.020
 LZ0  plan-2  C4'  0.020

