# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 15:18:38 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [(3E)-3-(1-hydroxyethylidene)-2,3-dihydroisoxazol-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](OCC2=C\C(NO2)=C(C)/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
 YX0  YX0  '[(3E)-3-(1-hydroxyethylidene)-2,3-dihydroisoxazol-5-yl]methyl 6-deoxy-alpha-L-galactopyranoside'  L-saccharide  39  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_YX0
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
 YX0  C1    C  CH1   0   0.259  -1.7849  -0.3870  -1.2265
 YX0  C2    C  CH1   0  -0.029  -2.6891  -1.3500  -0.4507
 YX0  C3    C  CH1   0   0.025  -2.9124  -0.8356   0.9678
 YX0  C4    C  CH1   0  -0.005  -3.4536   0.5863   0.9258
 YX0  C5    C  CH1   0   0.015  -2.4950   1.4539   0.1065
 YX0  C6    C  CH3   0  -0.710  -2.9844   2.8764  -0.0710
 YX0  O1    O  O2    0  -0.499  -0.5049  -0.4578  -0.6769
 YX0  O2    O  OH1   0  -0.671  -2.1378  -2.6416  -0.3693
 YX0  O3    O  OH1   0  -0.672  -3.8077  -1.6487   1.6824
 YX0  O4    O  OH1   0  -0.672  -4.7518   0.5538   0.3829
 YX0  O5    O  O2    0  -0.501  -2.3061   0.9092  -1.1965
 YX0  O5'   O  OH1   0  -0.635   5.9713  -0.5987  -0.7804
 YX0  C6'   C  CH3   0  -0.732   5.9763   0.4231   1.3626
 YX0  C4'   C  CR5   0   0.140   3.8565   0.0329   0.0948
 YX0  C3'   C  CR15  0  -0.499   2.9564  -0.2990  -0.9953
 YX0  C2'   C  CR5   0   0.384   1.7555   0.1695  -0.6556
 YX0  C1'   C  CH2   0  -0.229   0.4843   0.2293  -1.4140
 YX0  O     O  O     0  -0.399   1.7444   0.7535   0.5718
 YX0  N     N  NR15  0  -0.405   3.0340   0.5697   1.1440
 YX0  H1    H  HCH1  0   0.232  -1.7603  -0.6640  -2.2899
 YX0  H2    H  HCH1  0   0.236  -3.6541  -1.3685  -0.9719
 YX0  H3    H  HCH1  0   0.219  -1.9406  -0.7893   1.4817
 YX0  HA    H  HOH1  0   0.460  -2.3715  -3.1289  -1.1642
 YX0  H4    H  HCH1  0   0.233  -3.4651   0.9846   1.9509
 YX0  HB    H  HOH1  0   0.448  -3.4468  -2.5413   1.6901
 YX0  H5    H  HCH1  0   0.223  -1.5388   1.4802   0.6457
 YX0  HC    H  HOH1  0   0.456  -5.1591   1.4147   0.5147
 YX0  H6C1  H  HCH3  0   0.238  -3.1799   3.3336   0.8996
 YX0  H6C2  H  HCH3  0   0.250  -2.2326   3.4829  -0.5755
 YX0  H6C3  H  HCH3  0   0.229  -3.9003   2.9201  -0.6623
 YX0  H1'1  H  HCH2  0   0.249   0.6368  -0.2248  -2.3998
 YX0  H1'2  H  HCH2  0   0.243   0.2083   1.2782  -1.5755
 YX0  H5'   H  HOH1  0   0.469   5.4411  -0.9114  -1.5210
 YX0  H6'1  H  HCH3  0   0.246   6.8241   1.0328   1.0421
 YX0  H6'2  H  HCH3  0   0.251   5.3620   1.0204   2.0336
 YX0  H6'3  H  HCH3  0   0.249   6.3812  -0.4128   1.9388
 YX0  H     H  HNR5  0   0.388   2.8776  -0.1300   1.8656
 YX0  H3'   H  HCR5  0   0.280   3.1975  -0.7813  -1.9292
 YX0  C5'   C  C     0   0.241   5.1905  -0.0452   0.1879

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
 YX0  C1   C2    single  1.532  0.020  1.532
 YX0  C1   O1    single  1.395  0.020  1.395
 YX0  C1   O5    single  1.397  0.020  1.397
 YX0  C2   C3    single  1.525  0.020  1.525
 YX0  C2   O2    single  1.407  0.020  1.407
 YX0  C3   C4    single  1.522  0.020  1.522
 YX0  C3   O3    single  1.405  0.020  1.405
 YX0  C4   C5    single  1.531  0.020  1.531
 YX0  C4   O4    single  1.408  0.020  1.408
 YX0  C5   C6    single  1.515  0.020  1.515
 YX0  C5   O5    single  1.425  0.020  1.425
 YX0  O1   C1'   single  1.412  0.020  1.412
 YX0  O5'  C5'   single  1.361  0.020  1.361
 YX0  C5'  C6'   single  1.489  0.020  1.489
 YX0  C5'  C4'   double  1.339  0.020  1.339
 YX0  C4'  C3'   single  1.452  0.020  1.452
 YX0  C4'  N     single  1.437  0.020  1.437
 YX0  C3'  C2'   double  1.333  0.020  1.333
 YX0  C2'  C1'   single  1.482  0.020  1.482
 YX0  C2'  O     single  1.359  0.020  1.359
 YX0  O    N     single  1.423  0.020  1.423
 YX0  C1   H1    single  0.970  0.020  1.090
 YX0  C2   H2    single  0.970  0.020  1.090
 YX0  C3   H3    single  0.970  0.020  1.090
 YX0  O2   HA    single  0.850  0.020  0.980
 YX0  C4   H4    single  0.970  0.020  1.090
 YX0  O3   HB    single  0.850  0.020  0.980
 YX0  C5   H5    single  0.970  0.020  1.090
 YX0  O4   HC    single  0.850  0.020  0.980
 YX0  C6   H6C1  single  0.970  0.020  1.090
 YX0  C6   H6C2  single  0.970  0.020  1.090
 YX0  C6   H6C3  single  0.970  0.020  1.090
 YX0  C1'  H1'1  single  0.970  0.020  1.090
 YX0  C1'  H1'2  single  0.970  0.020  1.090
 YX0  O5'  H5'   single  0.850  0.020  0.980
 YX0  C6'  H6'1  single  0.970  0.020  1.090
 YX0  C6'  H6'2  single  0.970  0.020  1.090
 YX0  C6'  H6'3  single  0.970  0.020  1.090
 YX0  C3'  H3'   single  0.930  0.020  1.080
 YX0  N    H     single  0.860  0.020  1.020

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
 YX0  H1    C1   O5    105.24  3.000
 YX0  H1    C1   O1    110.36  3.000
 YX0  O5    C1   O1    112.39  3.000
 YX0  H1    C1   C2    110.16  3.000
 YX0  O5    C1   C2    110.62  3.000
 YX0  O1    C1   C2    108.07  3.000
 YX0  H2    C2   O2    110.90  3.000
 YX0  H2    C2   C3    108.58  3.000
 YX0  O2    C2   C3    108.25  3.000
 YX0  H2    C2   C1    106.82  3.000
 YX0  O2    C2   C1    112.04  3.000
 YX0  C3    C2   C1    110.20  3.000
 YX0  H3    C3   O3    110.47  3.000
 YX0  H3    C3   C4    106.72  3.000
 YX0  O3    C3   C4    109.16  3.000
 YX0  H3    C3   C2    108.61  3.000
 YX0  O3    C3   C2    111.79  3.000
 YX0  C4    C3   C2    109.97  3.000
 YX0  H4    C4   O4    110.99  3.000
 YX0  H4    C4   C5    107.47  3.000
 YX0  O4    C4   C5    112.60  3.000
 YX0  H4    C4   C3    108.44  3.000
 YX0  O4    C4   C3    108.48  3.000
 YX0  C5    C4   C3    108.76  3.000
 YX0  H5    C5   O5    110.05  3.000
 YX0  H5    C5   C6    108.45  3.000
 YX0  O5    C5   C6    107.14  3.000
 YX0  H5    C5   C4    107.22  3.000
 YX0  O5    C5   C4    110.85  3.000
 YX0  C6    C5   C4    113.12  3.000
 YX0  H6C3  C6   H6C2  107.81  3.000
 YX0  H6C3  C6   H6C1  108.36  3.000
 YX0  H6C2  C6   H6C1  107.60  3.000
 YX0  H6C3  C6   C5    111.86  3.000
 YX0  H6C2  C6   C5    110.74  3.000
 YX0  H6C1  C6   C5    110.32  3.000
 YX0  C1'   O1   C1    114.36  3.000
 YX0  HA    O2   C2    108.80  3.000
 YX0  HB    O3   C3    107.57  3.000
 YX0  HC    O4   C4    108.49  3.000
 YX0  C5    O5   C1    115.06  3.000
 YX0  H5'   O5'  C5'   111.30  3.000
 YX0  H6'3  C6'  H6'2  107.69  3.000
 YX0  H6'3  C6'  H6'1  107.10  3.000
 YX0  H6'2  C6'  H6'1  108.22  3.000
 YX0  H6'3  C6'  C5'   111.77  3.000
 YX0  H6'2  C6'  C5'   111.17  3.000
 YX0  H6'1  C6'  C5'   110.71  3.000
 YX0  N     C4'  C3'   106.18  3.000
 YX0  N     C4'  C5'   122.75  3.000
 YX0  C3'   C4'  C5'   131.01  3.000
 YX0  H3'   C3'  C2'   125.40  3.000
 YX0  H3'   C3'  C4'   127.86  3.000
 YX0  C2'   C3'  C4'   106.66  3.000
 YX0  O     C2'  C1'   115.97  3.000
 YX0  O     C2'  C3'   112.86  3.000
 YX0  C1'   C2'  C3'   131.05  3.000
 YX0  H1'2  C1'  H1'1  107.39  3.000
 YX0  H1'2  C1'  C2'   109.27  3.000
 YX0  H1'1  C1'  C2'   108.92  3.000
 YX0  H1'2  C1'  O1    111.47  3.000
 YX0  H1'1  C1'  O1    111.43  3.000
 YX0  C2'   C1'  O1    108.32  3.000
 YX0  N     O    C2'   107.48  3.000
 YX0  H     N    O     103.58  3.000
 YX0  H     N    C4'   110.42  3.000
 YX0  O     N    C4'   105.86  3.000
 YX0  C4'   C5'  C6'   124.21  3.000
 YX0  C4'   C5'  O5'   123.05  3.000
 YX0  C6'   C5'  O5'   112.73  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
 YX0  Var_01  C2'   C1'  O1   C1    175.06  30.0  3
 YX0  Var_02  C3'   C2'  C1'  O1    122.69  30.0  1
 YX0  Var_03  C3'   C4'  C5'  O5'    -5.86  30.0  2
 YX0  Var_04  H6'1  C6'  C5'  C4'  -132.35  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
 YX0  chir_01  C1  C2  O1  O5  positiv
 YX0  chir_02  C2  O2  C1  C3  positiv
 YX0  chir_03  C3  O3  C2  C4  negativ
 YX0  chir_04  C4  O4  C3  C5  negativ
 YX0  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
 YX0  plan-1  C4'  0.020
 YX0  plan-1  C3'  0.020
 YX0  plan-1  C2'  0.020
 YX0  plan-1  C1'  0.020
 YX0  plan-1  O    0.020
 YX0  plan-1  N    0.020
 YX0  plan-1  H    0.020
 YX0  plan-1  H3'  0.020
 YX0  plan-1  C5'  0.020

