# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:42:41 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 2-deoxy-2-{[(1S)-1-hydroxyethyl]amino}-D-mannitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)N[C@H](CO)[C@@H](O)[C@H](O)[C@H](O)CO
#
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
 MMN  MMN  2-deoxy-2-{[(1S)-1-hydroxyethyl]amino}-D-mannitol  saccharide  34  15  .  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_MMN
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
 MMN  C8   C  CH3   0  -0.710   2.2487  -2.6666   0.8289
 MMN  C7   C  CH1   0   0.176   2.1903  -1.5877  -0.2399
 MMN  O7   O  OH1   0  -0.666   3.3665  -1.5517  -1.0225
 MMN  N1   N  NH1   0  -0.631   1.9632  -0.3080   0.3722
 MMN  C2   C  CH1   0  -0.152   1.3974   0.7491  -0.4443
 MMN  C1   C  CH2   0  -0.130   2.2159   2.0243  -0.2998
 MMN  O1   O  OH1   0  -0.677   2.1239   2.4866   1.0287
 MMN  C3   C  CH1   0   0.026  -0.0950   0.9827  -0.1375
 MMN  O3   O  OH1   0  -0.670  -0.6134   2.0857  -0.8538
 MMN  C4   C  CH1   0  -0.022  -0.9502  -0.2681  -0.3762
 MMN  O4   O  OH1   0  -0.666  -0.9065  -0.6808  -1.7265
 MMN  C5   C  CH1   0  -0.018  -2.4023  -0.0819   0.1003
 MMN  O5   O  OH1   0  -0.660  -2.4480   0.3559   1.4394
 MMN  C6   C  CH2   0  -0.157  -3.2108  -1.3546  -0.1028
 MMN  O6   O  OH1   0  -0.671  -4.5439  -1.1109   0.2818
 MMN  H81  H  HCH3  0   0.229   3.0081  -2.4350   1.5793
 MMN  H82  H  HCH3  0   0.228   1.2887  -2.7622   1.3387
 MMN  H83  H  HCH3  0   0.241   2.4880  -3.6325   0.3861
 MMN  H7   H  HCH1  0   0.203   1.4074  -1.8480  -0.9638
 MMN  HO7  H  HOH1  0   0.430   4.0683  -1.2067  -0.4584
 MMN  HN1  H  HNH1  0   0.357   1.5514  -0.3697   1.2919
 MMN  H2   H  HCH1  0   0.240   1.4959   0.4495  -1.4945
 MMN  H11  H  HCH2  0   0.199   3.2512   1.7791  -0.5693
 MMN  H12  H  HCH2  0   0.186   1.8724   2.7809  -1.0155
 MMN  HO1  H  HOH1  0   0.455   2.6567   3.2824   1.1069
 MMN  H3   H  HCH1  0   0.230  -0.1834   1.2472   0.9197
 MMN  HO3  H  HOH1  0   0.442  -0.3454   2.0194  -1.7762
 MMN  H4   H  HCH1  0   0.223  -0.5186  -1.0947   0.2008
 MMN  HO4  H  HOH1  0   0.443  -1.4047  -0.0539  -2.2626
 MMN  H5   H  HCH1  0   0.228  -2.8630   0.7204  -0.4877
 MMN  HO5  H  HOH1  0   0.444  -2.1101  -0.3464   2.0066
 MMN  H61  H  HCH2  0   0.206  -3.1444  -1.6607  -1.1516
 MMN  H62  H  HCH2  0   0.187  -2.7588  -2.1644   0.4916
 MMN  HO6  H  HOH1  0   0.455  -5.0657  -1.8820   0.0442

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
 MMN  C8  C7   single  1.520  0.020  1.520
 MMN  C8  H81  single  0.970  0.020  1.090
 MMN  C8  H82  single  0.970  0.020  1.090
 MMN  C8  H83  single  0.970  0.020  1.090
 MMN  C7  O7   single  1.413  0.020  1.413
 MMN  C7  N1   single  1.437  0.020  1.437
 MMN  C7  H7   single  0.970  0.020  1.090
 MMN  O7  HO7  single  0.850  0.020  0.980
 MMN  N1  C2   single  1.451  0.020  1.451
 MMN  N1  HN1  single  0.890  0.020  1.040
 MMN  C2  C1   single  1.522  0.020  1.522
 MMN  C2  C3   single  1.541  0.020  1.541
 MMN  C2  H2   single  0.970  0.020  1.090
 MMN  C1  O1   single  1.410  0.020  1.410
 MMN  C1  H11  single  0.970  0.020  1.090
 MMN  C1  H12  single  0.970  0.020  1.090
 MMN  O1  HO1  single  0.850  0.020  0.980
 MMN  C3  O3   single  1.414  0.020  1.414
 MMN  C3  C4   single  1.534  0.020  1.534
 MMN  C3  H3   single  0.970  0.020  1.090
 MMN  O3  HO3  single  0.850  0.020  0.980
 MMN  C4  O4   single  1.413  0.020  1.413
 MMN  C4  C5   single  1.540  0.020  1.540
 MMN  C4  H4   single  0.970  0.020  1.090
 MMN  O4  HO4  single  0.850  0.020  0.980
 MMN  C5  O5   single  1.410  0.020  1.410
 MMN  C5  C6   single  1.521  0.020  1.521
 MMN  C5  H5   single  0.970  0.020  1.090
 MMN  O5  HO5  single  0.850  0.020  0.980
 MMN  C6  O6   single  1.409  0.020  1.409
 MMN  C6  H61  single  0.970  0.020  1.090
 MMN  C6  H62  single  0.970  0.020  1.090
 MMN  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
 MMN  H83  C8  H82  107.79  3.000
 MMN  H83  C8  H81  108.34  3.000
 MMN  H82  C8  H81  108.01  3.000
 MMN  H83  C8  C7   110.61  3.000
 MMN  H82  C8  C7   110.91  3.000
 MMN  H81  C8  C7   111.06  3.000
 MMN  H7   C7  N1   112.30  3.000
 MMN  H7   C7  O7   103.56  3.000
 MMN  N1   C7  O7   110.17  3.000
 MMN  H7   C7  C8   108.84  3.000
 MMN  N1   C7  C8   109.80  3.000
 MMN  O7   C7  C8   112.06  3.000
 MMN  HO7  O7  C7   106.91  3.000
 MMN  HN1  N1  C2   113.47  3.000
 MMN  HN1  N1  C7   113.46  3.000
 MMN  C2   N1  C7   118.10  3.000
 MMN  H2   C2  C3   108.60  3.000
 MMN  H2   C2  C1   105.76  3.000
 MMN  C3   C2  C1   112.01  3.000
 MMN  H2   C2  N1   107.76  3.000
 MMN  C3   C2  N1   112.09  3.000
 MMN  C1   C2  N1   110.32  3.000
 MMN  H12  C1  H11  106.82  3.000
 MMN  H12  C1  O1   111.61  3.000
 MMN  H11  C1  O1   111.49  3.000
 MMN  H12  C1  C2   110.34  3.000
 MMN  H11  C1  C2   107.26  3.000
 MMN  O1   C1  C2   109.22  3.000
 MMN  HO1  O1  C1   108.19  3.000
 MMN  H3   C3  C4   107.61  3.000
 MMN  H3   C3  O3   105.76  3.000
 MMN  C4   C3  O3   110.67  3.000
 MMN  H3   C3  C2   107.91  3.000
 MMN  C4   C3  C2   112.66  3.000
 MMN  O3   C3  C2   111.87  3.000
 MMN  HO3  O3  C3   109.25  3.000
 MMN  H4   C4  C5   107.43  3.000
 MMN  H4   C4  O4   105.69  3.000
 MMN  C5   C4  O4   111.12  3.000
 MMN  H4   C4  C3   108.27  3.000
 MMN  C5   C4  C3   112.28  3.000
 MMN  O4   C4  C3   111.70  3.000
 MMN  HO4  O4  C4   109.01  3.000
 MMN  H5   C5  C6   108.50  3.000
 MMN  H5   C5  O5   105.59  3.000
 MMN  C6   C5  O5   111.68  3.000
 MMN  H5   C5  C4   108.60  3.000
 MMN  C6   C5  C4   111.02  3.000
 MMN  O5   C5  C4   111.23  3.000
 MMN  HO5  O5  C5   108.74  3.000
 MMN  H62  C6  H61  106.65  3.000
 MMN  H62  C6  O6   111.61  3.000
 MMN  H61  C6  O6   111.55  3.000
 MMN  H62  C6  C5   108.96  3.000
 MMN  H61  C6  C5   109.24  3.000
 MMN  O6   C6  C5   108.76  3.000
 MMN  HO6  O6  C6   107.91  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
 MMN  chir_01  C7  C8  O7  N1  positiv
 MMN  chir_02  C2  N1  C1  C3  positiv
 MMN  chir_03  C3  O3  C2  C4  positiv
 MMN  chir_04  C4  O4  C3  C5  negativ
 MMN  chir_05  C5  O5  C4  C6  negativ

