# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 12:42:07 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: methyl 6-deoxy-1-seleno-alpha-L-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se][C@@H]1O[C@@H](C)[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
 SFU  SFU  'methyl 6-deoxy-1-seleno-alpha-L-galactopyranoside'  L-saccharide  26  12  .  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_SFU
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
 SFU  C1    C   CH1   0  -0.136  -0.3330   0.1239   0.0875
 SFU  C2    C   CH1   0  -0.006   0.3210  -1.2396   0.2198
 SFU  C3    C   CH1   0  -0.035   1.8346  -1.0721   0.4554
 SFU  C4    C   CH1   0   0.040   2.4141  -0.1317  -0.5890
 SFU  C5    C   CH1   0  -0.025   1.6411   1.1935  -0.7022
 SFU  C6    C   CH3   0  -0.682   1.8591   2.2031   0.4147
 SFU  O2    O   OH1   0  -0.664   0.0545  -1.9623  -0.9571
 SFU  O3    O   OH1   0  -0.661   2.0908  -0.5617   1.7404
 SFU  O4    O   OH1   0  -0.666   3.7782   0.0651  -0.3137
 SFU  O5    O   O2    0  -0.481   0.2616   0.9027  -0.9165
 SFU  SE    SE  SE    0   0.061  -2.2155  -0.1014  -0.3772
 SFU  H1    H   HCH1  0   0.257  -0.3009   0.6256   1.0629
 SFU  H2    H   HCH1  0   0.240  -0.1093  -1.7416   1.0988
 SFU  H3    H   HCH1  0   0.234   2.3088  -2.0583   0.3314
 SFU  HA    H   HOH1  0   0.459   0.3373  -2.8733  -0.8288
 SFU  H4    H   HCH1  0   0.229   2.2852  -0.6453  -1.5516
 SFU  HB    H   HOH1  0   0.454   1.7827  -1.2041   2.3878
 SFU  H5    H   HCH1  0   0.242   1.9603   1.6670  -1.6363
 SFU  HC    H   HOH1  0   0.453   4.1838   0.4762  -1.0836
 SFU  H61C  H   HCH3  0   0.232   2.9205   2.4230   0.5218
 SFU  H62C  H   HCH3  0   0.230   1.3553   3.1377   0.1645
 SFU  H63C  H   HCH3  0   0.235   1.4938   1.8666   1.3822
 SFU  HM1   H   HCH3  0   0.263  -2.6207   1.7996   1.2784
 SFU  HM2   H   HCH3  0   0.264  -2.2725   2.4470  -0.3421
 SFU  HM3   H   HCH3  0   0.271  -3.8628   1.7568   0.0171
 SFU  CM    C   CH3   0  -0.810  -2.7945   1.6685   0.2113

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
 SFU  C1  C2    single  1.518  0.020  1.518
 SFU  C1  O5    single  1.403  0.020  1.403
 SFU  C1  SE    single  1.952  0.020  1.952
 SFU  C2  C3    single  1.541  0.020  1.541
 SFU  C2  O2    single  1.407  0.020  1.407
 SFU  C3  C4    single  1.520  0.020  1.520
 SFU  C3  O3    single  1.406  0.020  1.406
 SFU  C4  C5    single  1.538  0.020  1.538
 SFU  C4  O4    single  1.405  0.020  1.405
 SFU  C5  C6    single  1.521  0.020  1.521
 SFU  C5  O5    single  1.426  0.020  1.426
 SFU  CM  SE    single  1.953  0.020  1.953
 SFU  C1  H1    single  0.970  0.020  1.090
 SFU  C2  H2    single  0.970  0.020  1.090
 SFU  C3  H3    single  0.970  0.020  1.090
 SFU  O2  HA    single  0.850  0.020  0.980
 SFU  C4  H4    single  0.970  0.020  1.090
 SFU  O3  HB    single  0.850  0.020  0.980
 SFU  C5  H5    single  0.970  0.020  1.090
 SFU  O4  HC    single  0.850  0.020  0.980
 SFU  C6  H61C  single  0.970  0.020  1.090
 SFU  C6  H62C  single  0.970  0.020  1.090
 SFU  C6  H63C  single  0.970  0.020  1.090
 SFU  CM  HM1   single  0.970  0.020  1.090
 SFU  CM  HM2   single  0.970  0.020  1.090
 SFU  CM  HM3   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
 SFU  H1    C1  SE    107.01  3.000
 SFU  H1    C1  O5    111.71  3.000
 SFU  SE    C1  O5    107.60  3.000
 SFU  H1    C1  C2    108.70  3.000
 SFU  SE    C1  C2    109.43  3.000
 SFU  O5    C1  C2    112.23  3.000
 SFU  H2    C2  O2    111.10  3.000
 SFU  H2    C2  C3    108.16  3.000
 SFU  O2    C2  C3    111.70  3.000
 SFU  H2    C2  C1    108.13  3.000
 SFU  O2    C2  C1    107.88  3.000
 SFU  C3    C2  C1    109.81  3.000
 SFU  H3    C3  O3    110.45  3.000
 SFU  H3    C3  C4    108.21  3.000
 SFU  O3    C3  C4    109.50  3.000
 SFU  H3    C3  C2    107.96  3.000
 SFU  O3    C3  C2    110.98  3.000
 SFU  C4    C3  C2    109.67  3.000
 SFU  H4    C4  O4    110.54  3.000
 SFU  H4    C4  C5    106.22  3.000
 SFU  O4    C4  C5    112.43  3.000
 SFU  H4    C4  C3    105.55  3.000
 SFU  O4    C4  C3    108.79  3.000
 SFU  C5    C4  C3    113.07  3.000
 SFU  H5    C5  O5    104.01  3.000
 SFU  H5    C5  C6    107.31  3.000
 SFU  O5    C5  C6    112.60  3.000
 SFU  H5    C5  C4    106.79  3.000
 SFU  O5    C5  C4    108.76  3.000
 SFU  C6    C5  C4    116.47  3.000
 SFU  H63C  C6  H62C  108.31  3.000
 SFU  H63C  C6  H61C  107.59  3.000
 SFU  H62C  C6  H61C  107.44  3.000
 SFU  H63C  C6  C5    113.55  3.000
 SFU  H62C  C6  C5    109.52  3.000
 SFU  H61C  C6  C5    110.23  3.000
 SFU  HA    O2  C2    108.62  3.000
 SFU  HB    O3  C3    108.30  3.000
 SFU  HC    O4  C4    108.19  3.000
 SFU  C5    O5  C1    114.56  3.000
 SFU  CM    SE  C1     96.29  3.000
 SFU  HM3   CM  HM2   108.77  3.000
 SFU  HM3   CM  HM1   108.74  3.000
 SFU  HM2   CM  HM1   109.61  3.000
 SFU  HM3   CM  SE    108.09  3.000
 SFU  HM2   CM  SE    110.66  3.000
 SFU  HM1   CM  SE    110.92  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
 SFU  Var_01  HM1  CM  SE  C1  -61.70  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
 SFU  chir_01  C1  C2  O5  SE  negativ
 SFU  chir_02  C2  O2  C1  C3  positiv
 SFU  chir_03  C3  O3  C2  C4  negativ
 SFU  chir_04  C4  O4  C5  C3  positiv
 SFU  chir_05  C5  O5  C4  C6  positiv

