# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:36:37 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 4,6-O-[(1S)-1-carboxyethylidene]-beta-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(OC[C@H]2O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]2O1)C(O)=O
#
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
 46M  46M  4,6-O-[(1S)-1-carboxyethylidene]-beta-D-mannopyranose  D-saccharide  30  17  .  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_46M
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
 46M  O3   O  OH1    0  -0.661  -0.8144  -54.8833  48.8374
 46M  C3   C  CH1    0   0.013  -1.3183  -55.4890  47.6767
 46M  C4   C  CH1    0   0.011  -0.3517  -56.5548  47.2032
 46M  O4   O  O2     0  -0.503   0.8944  -55.9916  46.8758
 46M  C7   C  CT     0   0.379   1.8216  -56.9485  46.4176
 46M  C9   C  C      0   0.356   2.2406  -57.9585  47.5439
 46M  O7   O  OC    -1  -0.589   2.2533  -57.5058  48.7015
 46M  O8   O  O      0  -0.586   2.5968  -59.0850  47.1594
 46M  C8   C  CH3    0  -0.701   3.0556  -56.1823  45.9767
 46M  O6   O  O2     0  -0.492   1.3192  -57.5971  45.2727
 46M  C6   C  CH2    0  -0.218   0.0790  -58.2395  45.4620
 46M  C5   C  CH1    0   0.005  -0.9269  -57.2140  45.9531
 46M  O5   O  O2     0  -0.483  -2.1625  -57.8281  46.2204
 46M  C1   C  CH1    0   0.260  -3.1218  -56.8908  46.6184
 46M  O1   O  OH1    0  -0.656  -4.2709  -57.6400  46.8511
 46M  C2   C  CH1    0  -0.057  -2.6873  -56.1438  47.8897
 46M  O2   O  OH1    0  -0.664  -2.6126  -57.0119  48.9895
 46M  HO3  H  HOH1   0   0.450  -1.4029  -54.1641  49.0891
 46M  H3   H  HCH1   0   0.212  -1.4379  -54.7509  46.8674
 46M  H4   H  HCH1   0   0.224  -0.2393  -57.3164  47.9869
 46M  H81  H  HCH3   0   0.233   3.8095  -56.8661  45.5876
 46M  H82  H  HCH3   0   0.234   2.8106  -55.4589  45.1968
 46M  H83  H  HCH3   0   0.234   3.4897  -55.6473  46.8204
 46M  H61  H  HCH2   0   0.243  -0.2194  -58.6575  44.4984
 46M  H62  H  HCH2   0   0.210   0.1494  -59.0657  46.1805
 46M  H5   H  HCH1   0   0.215  -1.0499  -56.4392  45.1782
 46M  H1   H  HCH1   0   0.195  -3.2795  -56.1491  45.8155
 46M  HO1  H  HOH1   0   0.466  -5.0434  -57.0790  46.7258
 46M  H2   H  HCH1   0   0.223  -3.4308  -55.3470  48.0618
 46M  HO2  H  HOH1   0   0.445  -3.4238  -57.5332  49.0057

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
 46M  O3  C3   single  1.403  0.020  1.403
 46M  O3  HO3  single  0.850  0.020  0.980
 46M  C3  C4   single  1.515  0.020  1.515
 46M  C3  C2   single  1.532  0.020  1.532
 46M  C3  H3   single  0.970  0.020  1.090
 46M  C4  O4   single  1.406  0.020  1.406
 46M  C4  C5   single  1.526  0.020  1.526
 46M  C4  H4   single  0.970  0.020  1.090
 46M  O4  C7   single  1.409  0.020  1.409
 46M  C7  C9   single  1.570  0.020  1.570
 46M  C7  C8   single  1.518  0.020  1.518
 46M  C7  O6   single  1.409  0.020  1.409
 46M  C9  O7   deloc   1.243  0.020  1.243
 46M  C9  O8   deloc   1.242  0.020  1.242
 46M  C8  H81  single  0.970  0.020  1.090
 46M  C8  H82  single  0.970  0.020  1.090
 46M  C8  H83  single  0.970  0.020  1.090
 46M  O6  C6   single  1.409  0.020  1.409
 46M  C6  C5   single  1.518  0.020  1.518
 46M  C6  H61  single  0.970  0.020  1.090
 46M  C6  H62  single  0.970  0.020  1.090
 46M  C5  O5   single  1.405  0.020  1.405
 46M  C5  H5   single  0.970  0.020  1.090
 46M  O5  C1   single  1.399  0.020  1.399
 46M  C1  O1   single  1.391  0.020  1.391
 46M  C1  C2   single  1.537  0.020  1.537
 46M  C1  H1   single  0.970  0.020  1.090
 46M  O1  HO1  single  0.850  0.020  0.980
 46M  C2  O2   single  1.403  0.020  1.403
 46M  C2  H2   single  0.970  0.020  1.090
 46M  O2  HO2  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
 46M  HO3  O3  C3   108.62  3.000
 46M  H3   C3  C2   106.94  3.000
 46M  H3   C3  C4   108.11  3.000
 46M  C2   C3  C4   108.23  3.000
 46M  H3   C3  O3   110.95  3.000
 46M  C2   C3  O3   112.98  3.000
 46M  C4   C3  O3   109.46  3.000
 46M  H4   C4  C5   108.87  3.000
 46M  H4   C4  O4   110.68  3.000
 46M  C5   C4  O4   108.44  3.000
 46M  H4   C4  C3   109.27  3.000
 46M  C5   C4  C3   108.63  3.000
 46M  O4   C4  C3   110.89  3.000
 46M  C7   O4  C4   112.76  3.000
 46M  O6   C7  C8   106.63  3.000
 46M  O6   C7  C9   112.47  3.000
 46M  C8   C7  C9   108.43  3.000
 46M  O6   C7  O4   110.01  3.000
 46M  C8   C7  O4   106.65  3.000
 46M  C9   C7  O4   112.29  3.000
 46M  O8   C9  O7   127.98  3.000
 46M  O8   C9  C7   115.97  3.000
 46M  O7   C9  C7   115.89  3.000
 46M  H83  C8  H82  108.51  3.000
 46M  H83  C8  H81  108.00  3.000
 46M  H82  C8  H81  108.43  3.000
 46M  H83  C8  C7   110.30  3.000
 46M  H82  C8  C7   111.08  3.000
 46M  H81  C8  C7   110.45  3.000
 46M  C6   O6  C7   114.49  3.000
 46M  H62  C6  H61  107.89  3.000
 46M  H62  C6  C5   109.84  3.000
 46M  H61  C6  C5   111.29  3.000
 46M  H62  C6  O6   112.01  3.000
 46M  H61  C6  O6   107.24  3.000
 46M  C5   C6  O6   108.58  3.000
 46M  H5   C5  O5   110.04  3.000
 46M  H5   C5  C6   108.74  3.000
 46M  O5   C5  C6   110.42  3.000
 46M  H5   C5  C4   108.31  3.000
 46M  O5   C5  C4   111.37  3.000
 46M  C6   C5  C4   107.88  3.000
 46M  C1   O5  C5   111.36  3.000
 46M  H1   C1  C2   108.38  3.000
 46M  H1   C1  O1   111.43  3.000
 46M  C2   C1  O1   110.90  3.000
 46M  H1   C1  O5   109.95  3.000
 46M  C2   C1  O5   111.53  3.000
 46M  O1   C1  O5   104.66  3.000
 46M  HO1  O1  C1   109.09  3.000
 46M  H2   C2  O2   111.13  3.000
 46M  H2   C2  C1   106.83  3.000
 46M  O2   C2  C1   111.26  3.000
 46M  H2   C2  C3   108.37  3.000
 46M  O2   C2  C3   109.01  3.000
 46M  C1   C2  C3   110.19  3.000
 46M  HO2  O2  C2   107.63  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
 46M  Var_01  C5  C6  O6  C7  57.01  30.0  1

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
 46M  chir_01  C3  O3  C4  C2  negativ
 46M  chir_02  C4  O4  C5  C3  positiv
 46M  chir_03  C7  O4  O6  C9  positiv
 46M  chir_04  C5  O5  C4  C6  negativ
 46M  chir_05  C1  O1  O5  C2  positiv
 46M  chir_06  C2  O2  C1  C3  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 46M  plan-1  C7  0.020
 46M  plan-1  C9  0.020
 46M  plan-1  O7  0.020
 46M  plan-1  O8  0.020

