# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:58:17 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-ammonio-3-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@@H]1[C@@H](O)[C@@H](O)O[C@H](CO)[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
 TOA  TOA  3-ammonio-3-deoxy-alpha-D-glucopyranose  D-saccharide  26  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TOA
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
 TOA  C1    C  CH1   0   0.226  -2.3678  5.4443  3.0092
 TOA  C2    C  CH1   0   0.032  -1.5832  4.6559  1.9527
 TOA  C3    C  CH1   0  -0.195  -1.4419  3.2152  2.4147
 TOA  C4    C  CH1   0   0.051  -0.7920  3.1492  3.7882
 TOA  C5    C  CH1   0  -0.007  -1.6301  3.9989  4.7524
 TOA  C6    C  CH2   0  -0.196  -1.0492  4.0607  6.1478
 TOA  O1    O  OH1   0  -0.656  -3.6722  4.9785  3.0148
 TOA  O2    O  OH1   0  -0.657  -2.1989  4.6436  0.6957
 TOA  N3    N  NT3   1  -0.788  -0.6244  2.4532  1.4306
 TOA  O4    O  OH1   0  -0.663  -0.7505  1.7993  4.1725
 TOA  O5    O  O2    0  -0.499  -1.7334  5.3228  4.2546
 TOA  O6    O  OH1   0  -0.666   0.2682  4.5500  6.0927
 TOA  H1    H  HCH1  0   0.246  -2.3202  6.5140  2.7737
 TOA  H2    H  HCH1  0   0.255  -0.5794  5.1008  1.9033
 TOA  H3    H  HCH1  0   0.318  -2.4156  2.7193  2.4373
 TOA  H4    H  HCH1  0   0.252   0.2161  3.5774  3.7156
 TOA  H5    H  HCH1  0   0.240  -2.6221  3.5367  4.8440
 TOA  H61   H  HCH2  0   0.222  -1.6993  4.6963  6.7631
 TOA  H62   H  HCH2  0   0.213  -1.0993  3.0534  6.5779
 TOA  HO1   H  HOH1  0   0.466  -4.2275  5.5909  3.5102
 TOA  HO2   H  HOH1  0   0.467  -1.9931  5.4625  0.2341
 TOA  HN31  H  HNT3  0   0.473  -1.0458  2.4796  0.5003
 TOA  HN32  H  HNT3  0   0.469   0.3250  2.8234  1.3429
 TOA  HN33  H  HNT3  0   0.473  -0.5415  1.4732  1.7064
 TOA  HO4   H  HOH1  0   0.468   0.0050  1.6570  4.7508
 TOA  HO6   H  HOH1  0   0.459   0.6556  4.4780  6.9693

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
 TOA  C1  C2    single  1.534  0.020  1.534
 TOA  C1  O1    single  1.385  0.020  1.385
 TOA  C1  O5    single  1.403  0.020  1.403
 TOA  C1  H1    single  0.970  0.020  1.090
 TOA  C2  C3    single  1.520  0.020  1.520
 TOA  C2  O2    single  1.400  0.020  1.400
 TOA  C2  H2    single  0.970  0.020  1.090
 TOA  C3  C4    single  1.521  0.020  1.521
 TOA  C3  N3    single  1.489  0.020  1.489
 TOA  C3  H3    single  0.970  0.020  1.090
 TOA  C4  C5    single  1.534  0.020  1.534
 TOA  C4  O4    single  1.404  0.020  1.404
 TOA  C4  H4    single  0.970  0.020  1.090
 TOA  C5  C6    single  1.513  0.020  1.513
 TOA  C5  O5    single  1.418  0.020  1.418
 TOA  C5  H5    single  0.970  0.020  1.090
 TOA  C6  O6    single  1.406  0.020  1.406
 TOA  C6  H61   single  0.970  0.020  1.090
 TOA  C6  H62   single  0.970  0.020  1.090
 TOA  O1  HO1   single  0.850  0.020  0.980
 TOA  O2  HO2   single  0.850  0.020  0.980
 TOA  N3  HN31  single  0.890  0.020  1.040
 TOA  N3  HN32  single  0.890  0.020  1.040
 TOA  N3  HN33  single  0.890  0.020  1.040
 TOA  O4  HO4   single  0.850  0.020  0.980
 TOA  O6  HO6   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
 TOA  H1    C1  O5    104.80  3.000
 TOA  H1    C1  O1    111.70  3.000
 TOA  O5    C1  O1    113.15  3.000
 TOA  H1    C1  C2    109.35  3.000
 TOA  O5    C1  C2    109.61  3.000
 TOA  O1    C1  C2    108.16  3.000
 TOA  H2    C2  O2    111.40  3.000
 TOA  H2    C2  C3    108.21  3.000
 TOA  O2    C2  C3    107.80  3.000
 TOA  H2    C2  C1    106.86  3.000
 TOA  O2    C2  C1    113.45  3.000
 TOA  C3    C2  C1    108.99  3.000
 TOA  H3    C3  N3    105.70  3.000
 TOA  H3    C3  C4    110.02  3.000
 TOA  N3    C3  C4    109.88  3.000
 TOA  H3    C3  C2    110.71  3.000
 TOA  N3    C3  C2    109.59  3.000
 TOA  C4    C3  C2    110.82  3.000
 TOA  H4    C4  O4    111.47  3.000
 TOA  H4    C4  C5    109.10  3.000
 TOA  O4    C4  C5    112.13  3.000
 TOA  H4    C4  C3    108.40  3.000
 TOA  O4    C4  C3    107.55  3.000
 TOA  C5    C4  C3    108.06  3.000
 TOA  H5    C5  O5    110.88  3.000
 TOA  H5    C5  C6    106.68  3.000
 TOA  O5    C5  C6    108.28  3.000
 TOA  H5    C5  C4    108.22  3.000
 TOA  O5    C5  C4    109.65  3.000
 TOA  C6    C5  C4    113.11  3.000
 TOA  H62   C6  H61   106.56  3.000
 TOA  H62   C6  O6    112.19  3.000
 TOA  H61   C6  O6    112.04  3.000
 TOA  H62   C6  C5    107.87  3.000
 TOA  H61   C6  C5    108.26  3.000
 TOA  O6    C6  C5    109.74  3.000
 TOA  HO1   O1  C1    109.33  3.000
 TOA  HO2   O2  C2    109.22  3.000
 TOA  HN33  N3  HN32  107.16  3.000
 TOA  HN33  N3  HN31  107.71  3.000
 TOA  HN32  N3  HN31  107.18  3.000
 TOA  HN33  N3  C3    110.92  3.000
 TOA  HN32  N3  C3    112.40  3.000
 TOA  HN31  N3  C3    111.23  3.000
 TOA  HO4   O4  C4    109.26  3.000
 TOA  C5    O5  C1    115.17  3.000
 TOA  HO6   O6  C6    108.40  3.000

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
 TOA  chir_01  C1  C2  O1  O5  negativ
 TOA  chir_02  C2  O2  C1  C3  negativ
 TOA  chir_03  C3  N3  C2  C4  positiv
 TOA  chir_04  C4  O4  C5  C3  positiv
 TOA  chir_05  C5  O5  C4  C6  negativ

