# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 12:38:08 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: heptyl 1-seleno-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC[Se][C@@H]1O[C@H](CO)[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
 05L  05L  'heptyl 1-seleno-beta-D-glucopyranoside'  D-saccharide  45  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_05L
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
 05L  SE    SE  SE    0   0.059  -0.0178  -0.8464   1.0728
 05L  C1    C   CH1   0  -0.165  -1.5290  -0.1171   0.0735
 05L  C2    C   CH1   0   0.015  -2.6513  -1.1528  -0.0460
 05L  O2    O   OH1   0  -0.665  -2.2687  -2.2690  -0.8053
 05L  C3    C   CH1   0  -0.002  -3.8248  -0.5043  -0.7738
 05L  O3    O   OH1   0  -0.671  -4.9579  -1.3383  -0.7959
 05L  C4    C   CH1   0   0.031  -4.2328   0.8008  -0.1008
 05L  O4    O   OH1   0  -0.671  -5.2025   1.4830  -0.8562
 05L  C5    C   CH1   0  -0.011  -3.0125   1.7105   0.0394
 05L  O5    O   O2    0  -0.474  -1.9882   1.0269   0.7392
 05L  C6    C   CH2   0  -0.156  -3.3330   2.9706   0.8143
 05L  O6    O   OH1   0  -0.669  -2.1967   3.8010   0.8262
 05L  C1'   C   CH2   0  -0.580   1.4218   0.0542   0.0858
 05L  C2'   C   CH2   0  -0.429   2.7849  -0.4401   0.5450
 05L  C3'   C   CH2   0  -0.410   3.9119   0.2550  -0.2133
 05L  C4'   C   CH2   0  -0.414   5.2943  -0.2175   0.2191
 05L  C5'   C   CH2   0  -0.407   6.4234   0.4749  -0.5331
 05L  C6'   C   CH2   0  -0.419   7.8090   0.0082  -0.1040
 05L  C7'   C   CH3   0  -0.663   8.9291   0.7097  -0.8596
 05L  H1    H   HCH1  0   0.252  -1.1582   0.1328  -0.9339
 05L  H2    H   HCH1  0   0.227  -2.9823  -1.4399   0.9638
 05L  HO2   H   HOH1  0   0.457  -1.6437  -2.7976  -0.2975
 05L  H3    H   HCH1  0   0.215  -3.4932  -0.2676  -1.7980
 05L  HO3   H   HOH1  0   0.457  -4.7718  -2.0929  -1.3631
 05L  H4    H   HCH1  0   0.213  -4.6091   0.5678   0.9084
 05L  HO4   H   HOH1  0   0.455  -5.9664   0.9054  -0.9551
 05L  H5    H   HCH1  0   0.223  -2.6611   1.9834  -0.9692
 05L  H6    H   HCH2  0   0.213  -4.1884   3.4614   0.3383
 05L  H6A   H   HCH2  0   0.197  -3.6455   2.6912   1.8301
 05L  HO6   H   HOH1  0   0.457  -2.4284   4.6106   1.2897
 05L  H1'   H   HCH2  0   0.265   1.2794  -0.1464  -0.9780
 05L  H1'A  H   HCH2  0   0.265   1.3303   1.1303   0.2436
 05L  H2'   H   HCH2  0   0.230   2.9089  -0.2617   1.6175
 05L  H2'A  H   HCH2  0   0.230   2.8619  -1.5212   0.3951
 05L  H3'   H   HCH2  0   0.216   3.7884   0.0824  -1.2876
 05L  H3'A  H   HCH2  0   0.216   3.8343   1.3374  -0.0665
 05L  H4'   H   HCH2  0   0.210   5.4150  -0.0473   1.2945
 05L  H4'A  H   HCH2  0   0.210   5.3705  -1.3006   0.0729
 05L  H5'   H   HCH2  0   0.207   6.3021   0.3056  -1.6088
 05L  H5'A  H   HCH2  0   0.207   6.3450   1.5582  -0.3878
 05L  H6'   H   HCH2  0   0.210   7.9289   0.1750   0.9709
 05L  H6'A  H   HCH2  0   0.210   7.8878  -1.0732  -0.2531
 05L  H7'   H   HCH3  0   0.226   9.9110   0.3615  -0.5376
 05L  H7'A  H   HCH3  0   0.216   8.8514   0.5312  -1.9338
 05L  H7'B  H   HCH3  0   0.216   8.8934   1.7896  -0.7041

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
 05L  C1   SE    single  1.953  0.020  1.953
 05L  C1'  SE    single  1.964  0.020  1.964
 05L  C1   C2    single  1.532  0.020  1.532
 05L  C1   O5    single  1.401  0.020  1.401
 05L  C1   H1    single  0.970  0.020  1.090
 05L  O2   C2    single  1.403  0.020  1.403
 05L  C3   C2    single  1.526  0.020  1.526
 05L  C2   H2    single  0.970  0.020  1.090
 05L  O2   HO2   single  0.850  0.020  0.980
 05L  C3   O3    single  1.407  0.020  1.407
 05L  C3   C4    single  1.524  0.020  1.524
 05L  C3   H3    single  0.970  0.020  1.090
 05L  O3   HO3   single  0.850  0.020  0.980
 05L  C5   C4    single  1.529  0.020  1.529
 05L  O4   C4    single  1.406  0.020  1.406
 05L  C4   H4    single  0.970  0.020  1.090
 05L  O4   HO4   single  0.850  0.020  0.980
 05L  C5   O5    single  1.416  0.020  1.416
 05L  C5   C6    single  1.514  0.020  1.514
 05L  C5   H5    single  0.970  0.020  1.090
 05L  C6   O6    single  1.407  0.020  1.407
 05L  C6   H6    single  0.970  0.020  1.090
 05L  C6   H6A   single  0.970  0.020  1.090
 05L  O6   HO6   single  0.850  0.020  0.980
 05L  C1'  C2'   single  1.521  0.020  1.521
 05L  C1'  H1'   single  0.970  0.020  1.090
 05L  C1'  H1'A  single  0.970  0.020  1.090
 05L  C2'  C3'   single  1.526  0.020  1.526
 05L  C2'  H2'   single  0.970  0.020  1.090
 05L  C2'  H2'A  single  0.970  0.020  1.090
 05L  C3'  C4'   single  1.524  0.020  1.524
 05L  C3'  H3'   single  0.970  0.020  1.090
 05L  C3'  H3'A  single  0.970  0.020  1.090
 05L  C4'  C5'   single  1.523  0.020  1.523
 05L  C4'  H4'   single  0.970  0.020  1.090
 05L  C4'  H4'A  single  0.970  0.020  1.090
 05L  C5'  C6'   single  1.524  0.020  1.524
 05L  C5'  H5'   single  0.970  0.020  1.090
 05L  C5'  H5'A  single  0.970  0.020  1.090
 05L  C6'  C7'   single  1.522  0.020  1.522
 05L  C6'  H6'   single  0.970  0.020  1.090
 05L  C6'  H6'A  single  0.970  0.020  1.090
 05L  C7'  H7'   single  0.970  0.020  1.090
 05L  C7'  H7'A  single  0.970  0.020  1.090
 05L  C7'  H7'B  single  0.970  0.020  1.090

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
 05L  C1'   SE   C1     97.98  3.000
 05L  H1    C1   O5    111.06  3.000
 05L  H1    C1   C2    109.17  3.000
 05L  O5    C1   C2    110.42  3.000
 05L  H1    C1   SE    106.98  3.000
 05L  O5    C1   SE    108.39  3.000
 05L  C2    C1   SE    110.76  3.000
 05L  H2    C2   C3    108.49  3.000
 05L  H2    C2   O2    111.77  3.000
 05L  C3    C2   O2    106.84  3.000
 05L  H2    C2   C1    108.97  3.000
 05L  C3    C2   C1    108.27  3.000
 05L  O2    C2   C1    112.35  3.000
 05L  HO2   O2   C2    109.16  3.000
 05L  H3    C3   C4    107.88  3.000
 05L  H3    C3   O3    110.78  3.000
 05L  C4    C3   O3    107.40  3.000
 05L  H3    C3   C2    107.64  3.000
 05L  C4    C3   C2    111.06  3.000
 05L  O3    C3   C2    112.02  3.000
 05L  HO3   O3   C3    108.57  3.000
 05L  H4    C4   C5    108.33  3.000
 05L  H4    C4   O4    111.05  3.000
 05L  C5    C4   O4    108.13  3.000
 05L  H4    C4   C3    108.35  3.000
 05L  O4    C4   C3    111.28  3.000
 05L  C5    C4   C3    109.66  3.000
 05L  HO4   O4   C4    108.13  3.000
 05L  H5    C5   C6    109.26  3.000
 05L  H5    C5   O5    109.94  3.000
 05L  C6    C5   O5    107.58  3.000
 05L  H5    C5   C4    108.54  3.000
 05L  C6    C5   C4    111.92  3.000
 05L  O5    C5   C4    109.60  3.000
 05L  C5    O5   C1    113.35  3.000
 05L  H6A   C6   H6    107.07  3.000
 05L  H6A   C6   O6    111.82  3.000
 05L  H6    C6   O6    111.71  3.000
 05L  H6A   C6   C5    108.77  3.000
 05L  H6    C6   C5    108.42  3.000
 05L  O6    C6   C5    108.94  3.000
 05L  HO6   O6   C6    107.84  3.000
 05L  H1'A  C1'  H1'   108.12  3.000
 05L  H1'A  C1'  C2'   110.61  3.000
 05L  H1'   C1'  C2'   110.57  3.000
 05L  H1'A  C1'  SE    108.54  3.000
 05L  H1'   C1'  SE    108.05  3.000
 05L  C2'   C1'  SE    110.86  3.000
 05L  H2'A  C2'  H2'   106.70  3.000
 05L  H2'A  C2'  C3'   109.27  3.000
 05L  H2'   C2'  C3'   109.22  3.000
 05L  H2'A  C2'  C1'   110.05  3.000
 05L  H2'   C2'  C1'   110.15  3.000
 05L  C3'   C2'  C1'   111.34  3.000
 05L  H3'A  C3'  H3'   106.22  3.000
 05L  H3'A  C3'  C4'   109.44  3.000
 05L  H3'   C3'  C4'   109.38  3.000
 05L  H3'A  C3'  C2'   109.35  3.000
 05L  H3'   C3'  C2'   109.42  3.000
 05L  C4'   C3'  C2'   112.82  3.000
 05L  H4'A  C4'  H4'   106.08  3.000
 05L  H4'A  C4'  C5'   109.38  3.000
 05L  H4'   C4'  C5'   109.42  3.000
 05L  H4'A  C4'  C3'   109.38  3.000
 05L  H4'   C4'  C3'   109.29  3.000
 05L  C5'   C4'  C3'   113.04  3.000
 05L  H5'A  C5'  H5'   105.97  3.000
 05L  H5'A  C5'  C6'   109.30  3.000
 05L  H5'   C5'  C6'   109.26  3.000
 05L  H5'A  C5'  C4'   109.32  3.000
 05L  H5'   C5'  C4'   109.42  3.000
 05L  C6'   C5'  C4'   113.31  3.000
 05L  H6'A  C6'  H6'   106.05  3.000
 05L  H6'A  C6'  C7'   109.56  3.000
 05L  H6'   C6'  C7'   109.67  3.000
 05L  H6'A  C6'  C5'   109.26  3.000
 05L  H6'   C6'  C5'   109.24  3.000
 05L  C7'   C6'  C5'   112.84  3.000
 05L  H7'B  C7'  H7'A  107.43  3.000
 05L  H7'B  C7'  H7'   107.65  3.000
 05L  H7'A  C7'  H7'   107.60  3.000
 05L  H7'B  C7'  C6'   111.17  3.000
 05L  H7'A  C7'  C6'   111.14  3.000
 05L  H7'   C7'  C6'   111.64  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
 05L  Var_01  C2'  C1'  SE   C1   -173.76  30.0  1
 05L  Var_02  C3'  C2'  C1'  SE   -179.89  30.0  3
 05L  Var_03  C4'  C3'  C2'  C1'  -179.90  30.0  3
 05L  Var_04  C5'  C4'  C3'  C2'  -179.90  30.0  3
 05L  Var_05  C6'  C5'  C4'  C3'   179.92  30.0  3
 05L  Var_06  C7'  C6'  C5'  C4'  -179.84  30.0  3
 05L  Var_07  H7'  C7'  C6'  C5'   180.00  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
 05L  chir_01  C1  SE  C2  O5  negativ
 05L  chir_02  C2  O2  C1  C3  negativ
 05L  chir_03  C3  O3  C2  C4  positiv
 05L  chir_04  C4  O4  C5  C3  positiv
 05L  chir_05  C5  O5  C4  C6  negativ

