# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:47:22 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-beta-D-mannopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@H](O)O[C@@H]([C@@H](O)[C@@H]1O)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
 49S  49S  '2-(acetylamino)-2-deoxy-beta-D-mannopyranuronic acid'  D-saccharide  28  16  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_49S
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
 49S  C8   C  CH3    0  -0.781  -3.4366   0.1234  -2.1588
 49S  C7   C  C      0   0.525  -2.9961  -0.3176  -0.7846
 49S  O7   O  O      0  -0.508  -3.7632  -0.8852  -0.0189
 49S  N2   N  NH1    0  -0.616  -1.7195  -0.0278  -0.4788
 49S  C2   C  CH1    0  -0.180  -1.0948  -0.3313   0.7841
 49S  C3   C  CH1    0   0.054  -0.0721  -1.4632   0.6742
 49S  O3   O  OH1    0  -0.663  -0.7129  -2.5882   0.1318
 49S  C1   C  CH1    0   0.281  -0.3816   0.9009   1.3380
 49S  O1   O  OH1    0  -0.652  -1.2760   1.9450   1.4180
 49S  O5   O  O2     0  -0.495   0.6686   1.2729   0.4758
 49S  C5   C  CH1    0  -0.155   1.6840   0.2997   0.4151
 49S  C6   C  C      0   0.437   2.8640   0.8205  -0.4272
 49S  OAK  O  O      0  -0.560   2.9162   2.0211  -0.6994
 49S  O6   O  OC    -1  -0.616   3.6973  -0.0662  -0.7553
 49S  C4   C  CH1    0   0.008   1.1329  -1.0213  -0.1475
 49S  O4   O  OH1    0  -0.706   2.1064  -2.0311  -0.1045
 49S  H1   H  HCH3   0   0.247  -2.6418   0.5739  -2.7502
 49S  H2   H  HCH3   0   0.264  -3.8322  -0.7320  -2.7058
 49S  H3   H  HCH3   0   0.266  -4.2452   0.8479  -2.0616
 49S  H4   H  HNH1   0   0.396  -1.1713   0.4659  -1.1647
 49S  H5   H  HCH1   0   0.279  -1.8762  -0.6302   1.4849
 49S  H6   H  HCH1   0   0.206   0.2881  -1.6723   1.6949
 49S  H7   H  HOH1   0   0.451  -0.0723  -3.3057   0.0918
 49S  H8   H  HCH1   0   0.199   0.0365   0.6453   2.3275
 49S  H9   H  HOH1   0   0.463  -0.8921   2.6456   1.9562
 49S  H10  H  HCH1   0   0.225   2.0708   0.0915   1.4296
 49S  H12  H  HCH1   0   0.192   0.7997  -0.8434  -1.1851
 49S  H13  H  HOH1   0   0.440   2.9247  -1.5641  -0.3930

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
 49S  C8   C7   single  1.509  0.020  1.509
 49S  O1   C1   single  1.377  0.020  1.377
 49S  C7   N2   single  1.344  0.020  1.344
 49S  C7   O7   double  1.224  0.020  1.224
 49S  O5   C1   single  1.409  0.020  1.409
 49S  O5   C5   single  1.408  0.020  1.408
 49S  N2   C2   single  1.441  0.020  1.441
 49S  OAK  C6   deloc   1.232  0.020  1.232
 49S  C1   C2   single  1.528  0.020  1.528
 49S  C2   C3   single  1.529  0.020  1.529
 49S  C6   C5   single  1.540  0.020  1.540
 49S  C6   O6   deloc   1.260  0.020  1.260
 49S  C5   C4   single  1.538  0.020  1.538
 49S  C4   C3   single  1.524  0.020  1.524
 49S  C4   O4   single  1.403  0.020  1.403
 49S  C3   O3   single  1.404  0.020  1.404
 49S  C8   H1   single  0.970  0.020  1.090
 49S  C8   H2   single  0.970  0.020  1.090
 49S  C8   H3   single  0.970  0.020  1.090
 49S  N2   H4   single  0.860  0.020  1.020
 49S  C2   H5   single  0.970  0.020  1.090
 49S  C3   H6   single  0.970  0.020  1.090
 49S  O3   H7   single  0.850  0.020  0.980
 49S  C1   H8   single  0.970  0.020  1.090
 49S  O1   H9   single  0.850  0.020  0.980
 49S  C5   H10  single  0.970  0.020  1.090
 49S  C4   H12  single  0.970  0.020  1.090
 49S  O4   H13  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
 49S  H3   C8  H2   107.29  3.000
 49S  H3   C8  H1   108.36  3.000
 49S  H2   C8  H1   108.50  3.000
 49S  H3   C8  C7   109.25  3.000
 49S  H2   C8  C7   109.50  3.000
 49S  H1   C8  C7   113.74  3.000
 49S  N2   C7  O7   123.58  3.000
 49S  O7   C7  C8   121.50  3.000
 49S  N2   C7  C8   114.92  3.000
 49S  H4   N2  C2   117.64  3.000
 49S  H4   N2  C7   117.88  3.000
 49S  C2   N2  C7   124.44  3.000
 49S  H5   C2  C1   108.80  3.000
 49S  H5   C2  C3   108.80  3.000
 49S  C1   C2  C3   108.10  3.000
 49S  H5   C2  N2   108.06  3.000
 49S  C3   C2  N2   112.50  3.000
 49S  C1   C2  N2   110.50  3.000
 49S  H6   C3  C4   107.21  3.000
 49S  H6   C3  O3   110.79  3.000
 49S  C4   C3  O3   112.64  3.000
 49S  H6   C3  C2   107.00  3.000
 49S  O3   C3  C2   108.40  3.000
 49S  C4   C3  C2   110.66  3.000
 49S  H7   O3  C3   108.03  3.000
 49S  H8   C1  O5   109.11  3.000
 49S  H8   C1  O1   111.68  3.000
 49S  O5   C1  O1   108.63  3.000
 49S  H8   C1  C2   108.36  3.000
 49S  O5   C1  C2   109.83  3.000
 49S  O1   C1  C2   109.23  3.000
 49S  H9   O1  C1   108.97  3.000
 49S  C5   O5  C1   112.43  3.000
 49S  H10  C5  C4   107.42  3.000
 49S  H10  C5  C6   107.30  3.000
 49S  C4   C5  C6   111.40  3.000
 49S  H10  C5  O5   110.06  3.000
 49S  C4   C5  O5   110.55  3.000
 49S  C6   C5  O5   110.02  3.000
 49S  O6   C6  OAK  126.87  3.000
 49S  O6   C6  C5   114.26  3.000
 49S  OAK  C6  C5   118.86  3.000
 49S  H12  C4  O4   110.74  3.000
 49S  H12  C4  C5   108.27  3.000
 49S  O4   C4  C5   111.00  3.000
 49S  H12  C4  C3   108.35  3.000
 49S  O4   C4  C3   108.86  3.000
 49S  C5   C4  C3   109.58  3.000
 49S  H13  O4  C4   103.06  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
 49S  CONST_01  C2  N2  C7  C8   180.00   0.0  0
 49S  CONST_02  C2  N2  C7  O7     0.00   0.0  0
 49S  CONST_03  H4  N2  C7  C8     0.00   0.0  0
 49S  Var_01    H1  C8  C7  O7  -177.34  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
 49S  chir_01  C2  N2  C1  C3  positiv
 49S  chir_02  C3  O3  C2  C4  positiv
 49S  chir_03  C1  O1  O5  C2  positiv
 49S  chir_04  C5  O5  C4  C6  negativ
 49S  chir_05  C4  O4  C5  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
 49S  plan-1  C8   0.020
 49S  plan-1  C7   0.020
 49S  plan-1  O7   0.020
 49S  plan-1  N2   0.020
 49S  plan-1  C2   0.020
 49S  plan-1  H4   0.020
 49S  plan-2  C5   0.020
 49S  plan-2  C6   0.020
 49S  plan-2  OAK  0.020
 49S  plan-2  O6   0.020

