# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 11:23:31 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: methyl beta-D-xylopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1OC[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
 6MJ  6MJ  'methyl beta-D-xylopyranoside'  D-saccharide  23  11  .  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_6MJ
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
 6MJ  C01  C  CH3   0  -0.412  -3.4302   0.5887   0.2065
 6MJ  O02  O  O2    0  -0.497  -2.3564  -0.1308  -0.3691
 6MJ  C03  C  CH1   0   0.299  -1.1175   0.1622   0.1563
 6MJ  C04  C  CH1   0  -0.015  -0.1546  -0.9582  -0.2467
 6MJ  C05  C  CH1   0   0.012   1.2465  -0.6161   0.2348
 6MJ  C06  C  CH1   0  -0.006   1.6343   0.7758  -0.2498
 6MJ  C07  C  CH2   0  -0.225   0.5621   1.7819   0.1573
 6MJ  O08  O  O2    0  -0.489  -0.6929   1.3985  -0.3579
 6MJ  O09  O  OH1   0  -0.671   2.8797   1.0926   0.3292
 6MJ  O10  O  OH1   0  -0.668   2.1315  -1.6013  -0.2330
 6MJ  O11  O  OH1   0  -0.664  -0.5354  -2.1790   0.3319
 6MJ  H1   H  HCH3  0   0.241  -4.3520   0.1802  -0.2029
 6MJ  H2   H  HCH3  0   0.216  -3.4492   0.4732   1.2948
 6MJ  H3   H  HCH3  0   0.221  -3.3868   1.6548  -0.0273
 6MJ  H4   H  HCH1  0   0.184  -1.1631   0.2199   1.2617
 6MJ  H5   H  HCH1  0   0.219  -0.1473  -1.0194  -1.3468
 6MJ  H6   H  HCH1  0   0.208   1.2315  -0.5926   1.3386
 6MJ  H7   H  HCH1  0   0.221   1.7036   0.7578  -1.3464
 6MJ  H8   H  HCH2  0   0.214   0.5333   1.8656   1.2537
 6MJ  H9   H  HCH2  0   0.251   0.7896   2.7708  -0.2440
 6MJ  H10  H  HOH1  0   0.461   3.2808   1.8082  -0.1732
 6MJ  H11  H  HOH1  0   0.450   3.0173  -1.3645   0.0614
 6MJ  H12  H  HOH1  0   0.452  -1.3914  -2.4281  -0.0316

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
 6MJ  O11  C04  single  1.404  0.020  1.404
 6MJ  O10  C05  single  1.405  0.020  1.405
 6MJ  C04  C05  single  1.520  0.020  1.520
 6MJ  C04  C03  single  1.531  0.020  1.531
 6MJ  O02  C01  single  1.415  0.020  1.415
 6MJ  O02  C03  single  1.377  0.020  1.377
 6MJ  C05  C06  single  1.524  0.020  1.524
 6MJ  C03  O08  single  1.405  0.020  1.405
 6MJ  C06  O09  single  1.409  0.020  1.409
 6MJ  C06  C07  single  1.526  0.020  1.526
 6MJ  O08  C07  single  1.410  0.020  1.410
 6MJ  C01  H1   single  0.970  0.020  1.090
 6MJ  C01  H2   single  0.970  0.020  1.090
 6MJ  C01  H3   single  0.970  0.020  1.090
 6MJ  C03  H4   single  0.970  0.020  1.090
 6MJ  C04  H5   single  0.970  0.020  1.090
 6MJ  C05  H6   single  0.970  0.020  1.090
 6MJ  C06  H7   single  0.970  0.020  1.090
 6MJ  C07  H8   single  0.970  0.020  1.090
 6MJ  C07  H9   single  0.970  0.020  1.090
 6MJ  O09  H10  single  0.850  0.020  0.980
 6MJ  O10  H11  single  0.850  0.020  0.980
 6MJ  O11  H12  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
 6MJ  H3   C01  H2   108.45  3.000
 6MJ  H3   C01  H1   108.64  3.000
 6MJ  H2   C01  H1   108.65  3.000
 6MJ  H3   C01  O02  112.28  3.000
 6MJ  H2   C01  O02  111.34  3.000
 6MJ  H1   C01  O02  107.39  3.000
 6MJ  C03  O02  C01  114.79  3.000
 6MJ  H4   C03  O08  109.38  3.000
 6MJ  H4   C03  C04  109.06  3.000
 6MJ  O08  C03  C04  110.95  3.000
 6MJ  H4   C03  O02  110.78  3.000
 6MJ  O08  C03  O02  108.63  3.000
 6MJ  C04  C03  O02  108.04  3.000
 6MJ  H5   C04  O11  111.41  3.000
 6MJ  H5   C04  C05  108.82  3.000
 6MJ  O11  C04  C05  108.37  3.000
 6MJ  H5   C04  C03  107.91  3.000
 6MJ  C05  C04  C03  109.36  3.000
 6MJ  O11  C04  C03  110.93  3.000
 6MJ  H6   C05  O10  110.88  3.000
 6MJ  H6   C05  C06  107.57  3.000
 6MJ  O10  C05  C06  111.99  3.000
 6MJ  H6   C05  C04  107.99  3.000
 6MJ  C06  C05  C04  109.83  3.000
 6MJ  O10  C05  C04  108.50  3.000
 6MJ  H7   C06  O09  110.97  3.000
 6MJ  H7   C06  C07  108.75  3.000
 6MJ  O09  C06  C07  111.29  3.000
 6MJ  H7   C06  C05  108.56  3.000
 6MJ  C07  C06  C05  109.79  3.000
 6MJ  O09  C06  C05  107.43  3.000
 6MJ  H9   C07  H8   107.64  3.000
 6MJ  H9   C07  O08  107.31  3.000
 6MJ  H8   C07  O08  111.20  3.000
 6MJ  H9   C07  C06  110.67  3.000
 6MJ  H8   C07  C06  109.55  3.000
 6MJ  O08  C07  C06  110.42  3.000
 6MJ  C07  O08  C03  112.00  3.000
 6MJ  H10  O09  C06  108.73  3.000
 6MJ  H11  O10  C05  107.78  3.000
 6MJ  H12  O11  C04  108.10  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
 6MJ  Var_01  C06  C07  O08  C03    62.52  30.0  1
 6MJ  Var_02  H1   C01  O02  C03  -173.08  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
 6MJ  chir_01  C03  C04  O02  O08  positiv
 6MJ  chir_02  C04  O11  C03  C05  negativ
 6MJ  chir_03  C05  O10  C04  C06  positiv
 6MJ  chir_04  C06  O09  C05  C07  negativ

