# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 20:36:14 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: 2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)[C@H]1[C@H](O)O[C@H](CO)[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
 TMX  TMX  2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose  D-saccharide  35  15  .  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_TMX
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
 TMX  C1   C  CH1   0   0.231  39.4130  -1.5860  12.1308
 TMX  O1   O  OH1   0  -0.653  38.9620  -0.2718  12.1442
 TMX  C2   C  CH1   0  -0.131  40.3030  -1.7004  10.8719
 TMX  N2   N  NT    1  -0.410  40.1337  -3.0488  10.1796
 TMX  C3   C  CH1   0   0.046  41.7651  -1.3685  11.1967
 TMX  O3   O  OH1   0  -0.657  42.3290  -0.7281  10.0854
 TMX  C4   C  CH1   0  -0.063  41.8582  -0.4798  12.4380
 TMX  O4   O  OH1   0  -0.664  43.2286  -0.2346  12.6581
 TMX  C5   C  CH1   0  -0.003  41.2568  -1.2122  13.6370
 TMX  O5   O  O2    0  -0.492  40.0935  -1.9582  13.2857
 TMX  C6   C  CH2   0  -0.150  40.9799  -0.2785  14.7990
 TMX  O6   O  OH1   0  -0.665  40.5993  -1.0461  15.9149
 TMX  C7   C  CH3   0  -0.556  40.3603  -4.2087  11.0922
 TMX  C8   C  CH3   0  -0.543  41.0843  -3.1693   9.0286
 TMX  C9   C  CH3   0  -0.556  38.7554  -3.1394   9.6053
 TMX  H1   H  HCH1  0   0.262  38.5663  -2.2775  12.0963
 TMX  HO1  H  HOH1  0   0.469  38.3109  -0.1670  12.8485
 TMX  H2   H  HCH1  0   0.331  39.9463  -0.9770  10.1357
 TMX  H3   H  HCH1  0   0.240  42.3121  -2.2923  11.4423
 TMX  HO3  H  HOH1  0   0.455  43.2371  -0.4953  10.3126
 TMX  H4   H  HCH1  0   0.250  41.3280   0.4596  12.2464
 TMX  HO4  H  HOH1  0   0.466  43.3477   0.6814  12.9237
 TMX  H5   H  HCH1  0   0.244  41.9933  -1.9574  13.9594
 TMX  H61  H  HCH2  0   0.200  41.8950   0.2953  14.9983
 TMX  H62  H  HCH2  0   0.200  40.2057   0.4457  14.5150
 TMX  HO6  H  HOH1  0   0.455  40.4133  -0.4452  16.6420
 TMX  H17  H  HCH3  0   0.299  39.6076  -4.2367  11.8732
 TMX  H27  H  HCH3  0   0.299  40.2900  -5.1185  10.5021
 TMX  H37  H  HCH3  0   0.300  41.3513  -4.1478  11.5319
 TMX  H18  H  HCH3  0   0.300  42.1057  -3.2283   9.3879
 TMX  H28  H  HCH3  0   0.295  40.8427  -4.0831   8.4930
 TMX  H38  H  HCH3  0   0.299  40.9629  -2.3134   8.3718
 TMX  H19  H  HCH3  0   0.300  38.0049  -3.0824  10.3859
 TMX  H29  H  HCH3  0   0.301  38.6135  -2.3265   8.8977
 TMX  H39  H  HCH3  0   0.301  38.6575  -4.0924   9.0923

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
 TMX  C8  N2   single  1.498  0.020  1.498
 TMX  C9  N2   single  1.496  0.020  1.496
 TMX  O3  C3   single  1.401  0.020  1.401
 TMX  N2  C2   single  1.525  0.020  1.525
 TMX  N2  C7   single  1.493  0.020  1.493
 TMX  C2  C3   single  1.534  0.020  1.534
 TMX  C2  C1   single  1.546  0.020  1.546
 TMX  C3  C4   single  1.530  0.020  1.530
 TMX  O1  C1   single  1.389  0.020  1.389
 TMX  C1  O5   single  1.391  0.020  1.391
 TMX  C4  O4   single  1.409  0.020  1.409
 TMX  C4  C5   single  1.528  0.020  1.528
 TMX  O5  C5   single  1.426  0.020  1.426
 TMX  C5  C6   single  1.516  0.020  1.516
 TMX  C6  O6   single  1.407  0.020  1.407
 TMX  C1  H1   single  0.970  0.020  1.090
 TMX  O1  HO1  single  0.850  0.020  0.980
 TMX  C2  H2   single  0.970  0.020  1.090
 TMX  C3  H3   single  0.970  0.020  1.090
 TMX  O3  HO3  single  0.850  0.020  0.980
 TMX  C4  H4   single  0.970  0.020  1.090
 TMX  O4  HO4  single  0.850  0.020  0.980
 TMX  C5  H5   single  0.970  0.020  1.090
 TMX  C6  H61  single  0.970  0.020  1.090
 TMX  C6  H62  single  0.970  0.020  1.090
 TMX  O6  HO6  single  0.850  0.020  0.980
 TMX  C7  H17  single  0.970  0.020  1.090
 TMX  C7  H27  single  0.970  0.020  1.090
 TMX  C7  H37  single  0.970  0.020  1.090
 TMX  C8  H18  single  0.970  0.020  1.090
 TMX  C8  H28  single  0.970  0.020  1.090
 TMX  C8  H38  single  0.970  0.020  1.090
 TMX  C9  H19  single  0.970  0.020  1.090
 TMX  C9  H29  single  0.970  0.020  1.090
 TMX  C9  H39  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
 TMX  H1   C1  O5   103.63  3.000
 TMX  H1   C1  C2   111.91  3.000
 TMX  O5   C1  C2   112.00  3.000
 TMX  H1   C1  O1   110.30  3.000
 TMX  O5   C1  O1   113.82  3.000
 TMX  C2   C1  O1   105.35  3.000
 TMX  HO1  O1  C1   109.19  3.000
 TMX  H2   C2  C3   108.10  3.000
 TMX  H2   C2  N2   104.09  3.000
 TMX  C3   C2  N2   113.15  3.000
 TMX  H2   C2  C1   108.17  3.000
 TMX  C3   C2  C1   111.12  3.000
 TMX  N2   C2  C1   111.79  3.000
 TMX  C9   N2  C8   106.55  3.000
 TMX  C9   N2  C7   109.11  3.000
 TMX  C8   N2  C7   108.11  3.000
 TMX  C7   N2  C2   113.11  3.000
 TMX  C9   N2  C2   109.28  3.000
 TMX  C8   N2  C2   110.46  3.000
 TMX  H3   C3  C4   106.03  3.000
 TMX  H3   C3  O3   111.13  3.000
 TMX  C4   C3  O3   110.71  3.000
 TMX  H3   C3  C2   109.82  3.000
 TMX  C4   C3  C2   110.83  3.000
 TMX  O3   C3  C2   108.33  3.000
 TMX  HO3  O3  C3   107.60  3.000
 TMX  H4   C4  C5   110.96  3.000
 TMX  H4   C4  O4   110.40  3.000
 TMX  C5   C4  O4   110.09  3.000
 TMX  H4   C4  C3   109.07  3.000
 TMX  C5   C4  C3   109.53  3.000
 TMX  O4   C4  C3   106.68  3.000
 TMX  HO4  O4  C4   109.24  3.000
 TMX  H5   C5  C6   108.42  3.000
 TMX  H5   C5  O5   105.36  3.000
 TMX  C6   C5  O5   111.22  3.000
 TMX  H5   C5  C4   106.99  3.000
 TMX  C6   C5  C4   112.21  3.000
 TMX  O5   C5  C4   112.24  3.000
 TMX  C5   O5  C1   117.62  3.000
 TMX  H62  C6  H61  106.86  3.000
 TMX  H62  C6  O6   111.99  3.000
 TMX  H61  C6  O6   111.50  3.000
 TMX  H62  C6  C5   109.69  3.000
 TMX  H61  C6  C5   107.98  3.000
 TMX  O6   C6  C5   108.74  3.000
 TMX  HO6  O6  C6   108.13  3.000
 TMX  H37  C7  H27  109.02  3.000
 TMX  H37  C7  H17  110.06  3.000
 TMX  H27  C7  H17  108.93  3.000
 TMX  H37  C7  N2   110.02  3.000
 TMX  H27  C7  N2   107.98  3.000
 TMX  H17  C7  N2   110.77  3.000
 TMX  H38  C8  H28  109.88  3.000
 TMX  H38  C8  H18  110.41  3.000
 TMX  H28  C8  H18  109.09  3.000
 TMX  H38  C8  N2   109.30  3.000
 TMX  H28  C8  N2   107.79  3.000
 TMX  H18  C8  N2   110.34  3.000
 TMX  H39  C9  H29  109.68  3.000
 TMX  H39  C9  H19  108.89  3.000
 TMX  H29  C9  H19  109.81  3.000
 TMX  H39  C9  N2   108.50  3.000
 TMX  H29  C9  N2   108.95  3.000
 TMX  H19  C9  N2   110.98  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
 TMX  Var_01  H18  C8  N2  C2   68.05  30.0  3
 TMX  Var_02  H19  C9  N2  C2  -61.93  30.0  3
 TMX  Var_03  H17  C7  N2  C2   64.80  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
 TMX  chir_01  C1  C2  O1  O5  positiv
 TMX  chir_02  C2  N2  C3  C1  positiv
 TMX  chir_03  C3  O3  C2  C4  positiv
 TMX  chir_04  C4  O4  C3  C5  negativ
 TMX  chir_05  C5  O5  C4  C6  negativ

