# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:01:30 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-beta-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[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
 BM7  BM7  2-(acetylamino)-2-deoxy-beta-D-mannopyranose  D-saccharide  30  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 OK
;

data_comp_BM7
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
 BM7  C1   C  CH1   0   0.279  21.1259  42.2055  3.6104
 BM7  O1   O  OH1   0  -0.681  20.8191  43.2987  2.8479
 BM7  C2   C  CH1   0  -0.158  22.5924  41.7398  3.5549
 BM7  N2   N  NH1   0  -0.638  23.5712  42.6412  4.1497
 BM7  C7   C  C     0   0.558  23.7997  43.9203  3.8375
 BM7  O7   O  O     0  -0.526  23.0678  44.5870  3.1022
 BM7  C8   C  CH3   0  -0.769  25.0326  44.5329  4.4437
 BM7  C3   C  CH1   0  -0.015  22.6504  40.4254  4.3337
 BM7  O3   O  OH1   0  -0.661  23.9730  39.9555  4.3214
 BM7  C4   C  CH1   0  -0.001  22.1321  40.6169  5.7598
 BM7  O4   O  OH1   0  -0.668  22.0984  39.3355  6.3501
 BM7  C5   C  CH1   0  -0.009  20.7426  41.2696  5.7313
 BM7  C6   C  CH2   0  -0.159  20.2697  41.6410  7.1199
 BM7  O6   O  OH1   0  -0.664  18.9481  42.1169  7.0427
 BM7  O5   O  O2    0  -0.493  20.7689  42.4463  4.9518
 BM7  H1   H  HCH1  0   0.199  20.5267  41.3624  3.2277
 BM7  HO1  H  HOH1  0   0.458  21.5925  43.9087  2.8507
 BM7  H2   H  HCH1  0   0.282  22.8500  41.5464  2.5065
 BM7  HN2  H  HNH1  0   0.409  24.2928  42.1794  4.6834
 BM7  H81  H  HCH3  0   0.270  24.7730  45.4769  4.9203
 BM7  H82  H  HCH3  0   0.256  25.5209  43.8929  5.1750
 BM7  H83  H  HCH3  0   0.273  25.7466  44.7537  3.6495
 BM7  H3   H  HCH1  0   0.241  21.9798  39.7175  3.8230
 BM7  HO3  H  HOH1  0   0.454  24.0282  39.2011  4.9194
 BM7  H4   H  HCH1  0   0.230  22.8196  41.2774  6.3062
 BM7  HO4  H  HOH1  0   0.462  22.2835  39.4139  7.2901
 BM7  H5   H  HCH1  0   0.217  20.0375  40.5431  5.2930
 BM7  H61  H  HCH2  0   0.201  20.3409  40.7537  7.7603
 BM7  H62  H  HCH2  0   0.199  20.9534  42.3943  7.5361
 BM7  HO6  H  HOH1  0   0.454  18.6598  42.3438  7.9312

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
 BM7  O7  C7   double  1.233  0.020  1.233
 BM7  C8  C7   single  1.504  0.020  1.504
 BM7  O1  C1   single  1.368  0.020  1.368
 BM7  C7  N2   single  1.336  0.020  1.336
 BM7  C2  C1   single  1.540  0.020  1.540
 BM7  C2  N2   single  1.458  0.020  1.458
 BM7  C2  C3   single  1.529  0.020  1.529
 BM7  C1  O5   single  1.409  0.020  1.409
 BM7  C3  O3   single  1.404  0.020  1.404
 BM7  C3  C4   single  1.529  0.020  1.529
 BM7  O5  C5   single  1.412  0.020  1.412
 BM7  C5  C4   single  1.535  0.020  1.535
 BM7  C5  C6   single  1.513  0.020  1.513
 BM7  C4  O4   single  1.411  0.020  1.411
 BM7  C6  O6   single  1.407  0.020  1.407
 BM7  C1  H1   single  0.970  0.020  1.090
 BM7  O1  HO1  single  0.850  0.020  0.980
 BM7  C2  H2   single  0.970  0.020  1.090
 BM7  N2  HN2  single  0.860  0.020  1.020
 BM7  C8  H81  single  0.970  0.020  1.090
 BM7  C8  H82  single  0.970  0.020  1.090
 BM7  C8  H83  single  0.970  0.020  1.090
 BM7  C3  H3   single  0.970  0.020  1.090
 BM7  O3  HO3  single  0.850  0.020  0.980
 BM7  C4  H4   single  0.970  0.020  1.090
 BM7  O4  HO4  single  0.850  0.020  0.980
 BM7  C5  H5   single  0.970  0.020  1.090
 BM7  C6  H61  single  0.970  0.020  1.090
 BM7  C6  H62  single  0.970  0.020  1.090
 BM7  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
 BM7  H1   C1  O5   108.87  3.000
 BM7  H1   C1  C2   105.89  3.000
 BM7  O5   C1  C2   109.11  3.000
 BM7  H1   C1  O1   107.20  3.000
 BM7  O5   C1  O1   109.72  3.000
 BM7  C2   C1  O1   115.80  3.000
 BM7  HO1  O1  C1   108.49  3.000
 BM7  H2   C2  C3   109.05  3.000
 BM7  H2   C2  N2   109.96  3.000
 BM7  C3   C2  N2   107.35  3.000
 BM7  H2   C2  C1   108.15  3.000
 BM7  C3   C2  C1   106.13  3.000
 BM7  N2   C2  C1   115.97  3.000
 BM7  HN2  N2  C7   116.06  3.000
 BM7  HN2  N2  C2   114.38  3.000
 BM7  C7   N2  C2   127.69  3.000
 BM7  C8   C7  O7   120.43  3.000
 BM7  C8   C7  N2   115.83  3.000
 BM7  O7   C7  N2   123.74  3.000
 BM7  H83  C8  H82  108.35  3.000
 BM7  H83  C8  H81  107.41  3.000
 BM7  H82  C8  H81  108.84  3.000
 BM7  H83  C8  C7   109.00  3.000
 BM7  H82  C8  C7   113.54  3.000
 BM7  H81  C8  C7   109.52  3.000
 BM7  H3   C3  C4   107.86  3.000
 BM7  H3   C3  O3   110.77  3.000
 BM7  C4   C3  O3   111.68  3.000
 BM7  H3   C3  C2   107.06  3.000
 BM7  C4   C3  C2   110.76  3.000
 BM7  O3   C3  C2   108.61  3.000
 BM7  HO3  O3  C3   108.09  3.000
 BM7  H4   C4  C5   108.65  3.000
 BM7  H4   C4  O4   110.65  3.000
 BM7  C5   C4  O4   111.85  3.000
 BM7  H4   C4  C3   109.08  3.000
 BM7  O4   C4  C3   106.53  3.000
 BM7  C5   C4  C3   110.04  3.000
 BM7  HO4  O4  C4   109.29  3.000
 BM7  H5   C5  O5   109.97  3.000
 BM7  H5   C5  C6   109.05  3.000
 BM7  O5   C5  C6   107.94  3.000
 BM7  H5   C5  C4   107.80  3.000
 BM7  C6   C5  C4   111.72  3.000
 BM7  O5   C5  C4   110.35  3.000
 BM7  H62  C6  H61  107.04  3.000
 BM7  H62  C6  O6   111.93  3.000
 BM7  H61  C6  O6   111.52  3.000
 BM7  H62  C6  C5   108.74  3.000
 BM7  H61  C6  C5   108.48  3.000
 BM7  O6   C6  C5   109.04  3.000
 BM7  HO6  O6  C6   108.11  3.000
 BM7  C5   O5  C1   112.83  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
 BM7  CONST_01  O7   C7  N2  C2     0.00   0.0  0
 BM7  CONST_02  C8   C7  N2  C2   180.00   0.0  0
 BM7  CONST_03  HN2  N2  C7  O7   180.00   0.0  0
 BM7  Var_01    H81  C8  C7  N2  -129.64  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
 BM7  chir_01  C1  O1  C2  O5  negativ
 BM7  chir_02  C2  N2  C3  C1  negativ
 BM7  chir_03  C3  O3  C2  C4  positiv
 BM7  chir_04  C4  O4  C5  C3  positiv
 BM7  chir_05  C5  O5  C4  C6  negativ

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
 BM7  plan-1  C2   0.020
 BM7  plan-1  N2   0.020
 BM7  plan-1  C7   0.020
 BM7  plan-1  O7   0.020
 BM7  plan-1  C8   0.020
 BM7  plan-1  HN2  0.020

