# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:27:42 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: (2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H](CO)C(O)=O)[C@@H](O)[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
 2M8  2M8  '(2R)-3-hydroxy-2-(alpha-D-mannopyranosyloxy)propanoic acid'  D-saccharide  34  18  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2M8
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
 2M8  C1    C  CH1   0   0.256  19.2130  55.4371  28.9844
 2M8  O1    O  O2    0  -0.500  18.3722  55.2411  30.0858
 2M8  C22   C  CH1   0  -0.092  17.1344  55.8949  30.0435
 2M8  C23   C  CH2   0  -0.205  16.6225  56.0372  31.4768
 2M8  O13   O  OH1   0  -0.662  16.3703  54.7988  32.0895
 2M8  C21   C  C     0   0.515  16.1521  55.1060  29.1920
 2M8  O1A   O  O     0  -0.425  16.3746  54.0308  28.7024
 2M8  O1B   O  OH1   0  -0.592  15.0042  55.7576  29.0688
 2M8  C2    C  CH1   0  -0.020  20.4170  54.5238  29.1918
 2M8  O2    O  OH1   0  -0.672  21.1281  54.5133  27.9789
 2M8  C3    C  CH1   0   0.005  21.2673  55.0477  30.3446
 2M8  O3    O  OH1   0  -0.675  22.4129  54.2344  30.4306
 2M8  C4    C  CH1   0   0.001  21.6238  56.5125  30.1208
 2M8  O4    O  OH1   0  -0.675  22.3272  56.9504  31.2648
 2M8  C5    C  CH1   0  -0.019  20.3416  57.3233  29.9063
 2M8  C6    C  CH2   0  -0.161  20.6292  58.7649  29.5506
 2M8  O6    O  OH1   0  -0.667  19.4113  59.4654  29.4711
 2M8  O5    O  O2    0  -0.495  19.5903  56.7700  28.8356
 2M8  H1    H  HCH1  0   0.246  18.7117  55.1753  28.0451
 2M8  H2    H  HCH1  0   0.238  20.0489  53.5192  29.4428
 2M8  H22   H  HCH1  0   0.276  17.2212  56.9080  29.6288
 2M8  H231  H  HCH2  0   0.247  17.4015  56.5446  32.0507
 2M8  H232  H  HCH2  0   0.234  15.7468  56.6913  31.4806
 2M8  H13   H  HOH1  0   0.458  15.4521  54.5553  31.9437
 2M8  H1B   H  HOH1  0   0.487  14.3782  55.2435  28.5363
 2M8  HO2   H  HOH1  0   0.454  21.9573  54.0461  28.1265
 2M8  H3    H  HCH1  0   0.219  20.6709  54.9819  31.2670
 2M8  HO3   H  HOH1  0   0.453  23.0321  54.6536  31.0383
 2M8  H4    H  HCH1  0   0.226  22.2504  56.5919  29.2229
 2M8  HO4   H  HOH1  0   0.463  22.9769  57.6087  31.0040
 2M8  H5    H  HCH1  0   0.226  19.7595  57.3061  30.8391
 2M8  H61   H  HCH2  0   0.203  21.2837  59.1860  30.3228
 2M8  H62   H  HCH2  0   0.198  21.1847  58.7976  28.6027
 2M8  HO6   H  HOH1  0   0.456  19.6116  60.3896  29.2983

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
 2M8  C1   O1    single  1.399  0.020  1.399
 2M8  C1   C2    single  1.525  0.020  1.525
 2M8  C1   O5    single  1.393  0.020  1.393
 2M8  O1   C22   single  1.401  0.020  1.401
 2M8  C22  C23   single  1.529  0.020  1.529
 2M8  C22  C21   single  1.521  0.020  1.521
 2M8  C23  O13   single  1.405  0.020  1.405
 2M8  C21  O1A   double  1.202  0.020  1.202
 2M8  C21  O1B   single  1.326  0.020  1.326
 2M8  C2   O2    single  1.406  0.020  1.406
 2M8  C2   C3    single  1.525  0.020  1.525
 2M8  C3   O3    single  1.408  0.020  1.408
 2M8  C3   C4    single  1.524  0.020  1.524
 2M8  C4   O4    single  1.413  0.020  1.413
 2M8  C4   C5    single  1.532  0.020  1.532
 2M8  C5   C6    single  1.512  0.020  1.512
 2M8  C5   O5    single  1.420  0.020  1.420
 2M8  C6   O6    single  1.407  0.020  1.407
 2M8  C1   H1    single  0.970  0.020  1.090
 2M8  C2   H2    single  0.970  0.020  1.090
 2M8  C22  H22   single  0.970  0.020  1.090
 2M8  C23  H231  single  0.970  0.020  1.090
 2M8  C23  H232  single  0.970  0.020  1.090
 2M8  O13  H13   single  0.850  0.020  0.980
 2M8  O1B  H1B   single  0.850  0.020  0.980
 2M8  O2   HO2   single  0.850  0.020  0.980
 2M8  C3   H3    single  0.970  0.020  1.090
 2M8  O3   HO3   single  0.850  0.020  0.980
 2M8  C4   H4    single  0.970  0.020  1.090
 2M8  O4   HO4   single  0.850  0.020  0.980
 2M8  C5   H5    single  0.970  0.020  1.090
 2M8  C6   H61   single  0.970  0.020  1.090
 2M8  C6   H62   single  0.970  0.020  1.090
 2M8  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
 2M8  H1    C1   O5    105.12  3.000
 2M8  H1    C1   C2    109.54  3.000
 2M8  O5    C1   C2    111.94  3.000
 2M8  H1    C1   O1    111.48  3.000
 2M8  O5    C1   O1    112.38  3.000
 2M8  C2    C1   O1    106.46  3.000
 2M8  C22   O1   C1    116.22  3.000
 2M8  H22   C22  C21   108.56  3.000
 2M8  H22   C22  C23   107.14  3.000
 2M8  C21   C22  C23   110.92  3.000
 2M8  H22   C22  O1    111.85  3.000
 2M8  C21   C22  O1    110.23  3.000
 2M8  C23   C22  O1    108.12  3.000
 2M8  H232  C23  H231  106.95  3.000
 2M8  H232  C23  O13   112.47  3.000
 2M8  H231  C23  O13   107.96  3.000
 2M8  H232  C23  C22   109.10  3.000
 2M8  H231  C23  C22   107.28  3.000
 2M8  O13   C23  C22   112.77  3.000
 2M8  H13   O13  C23   109.19  3.000
 2M8  O1B   C21  O1A   124.20  3.000
 2M8  O1B   C21  C22   110.88  3.000
 2M8  O1A   C21  C22   124.92  3.000
 2M8  H1B   O1B  C21   110.46  3.000
 2M8  H2    C2   C3    109.16  3.000
 2M8  H2    C2   O2    111.08  3.000
 2M8  C3    C2   O2    111.88  3.000
 2M8  H2    C2   C1    108.30  3.000
 2M8  C3    C2   C1    109.70  3.000
 2M8  O2    C2   C1    106.64  3.000
 2M8  HO2   O2   C2    107.87  3.000
 2M8  H3    C3   C4    107.90  3.000
 2M8  H3    C3   O3    110.82  3.000
 2M8  C4    C3   O3    111.96  3.000
 2M8  H3    C3   C2    108.11  3.000
 2M8  C4    C3   C2    110.46  3.000
 2M8  O3    C3   C2    107.54  3.000
 2M8  HO3   O3   C3    108.07  3.000
 2M8  H4    C4   C5    108.96  3.000
 2M8  H4    C4   O4    110.84  3.000
 2M8  C5    C4   O4    111.47  3.000
 2M8  H4    C4   C3    108.86  3.000
 2M8  C5    C4   C3    109.48  3.000
 2M8  O4    C4   C3    107.19  3.000
 2M8  HO4   O4   C4    109.22  3.000
 2M8  H5    C5   O5    110.70  3.000
 2M8  H5    C5   C6    108.36  3.000
 2M8  O5    C5   C6    107.14  3.000
 2M8  H5    C5   C4    108.42  3.000
 2M8  O5    C5   C4    110.00  3.000
 2M8  C6    C5   C4    112.22  3.000
 2M8  H62   C6   H61   107.11  3.000
 2M8  H62   C6   O6    111.95  3.000
 2M8  H61   C6   O6    111.43  3.000
 2M8  H62   C6   C5    109.10  3.000
 2M8  H61   C6   C5    108.30  3.000
 2M8  O6    C6   C5    108.86  3.000
 2M8  HO6   O6   C6    107.96  3.000
 2M8  C5    O5   C1    115.82  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
 2M8  CONST_01  H1B  O1B  C21  C22  180.00  0.0  0

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
 2M8  chir_01  C1   O1  C2   O5   positiv
 2M8  chir_02  C22  O1  C23  C21  positiv
 2M8  chir_03  C2   O2  C1   C3   positiv
 2M8  chir_04  C3   O3  C2   C4   positiv
 2M8  chir_05  C4   O4  C5   C3   positiv
 2M8  chir_06  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
 2M8  plan-1  C22  0.020
 2M8  plan-1  C21  0.020
 2M8  plan-1  O1A  0.020
 2M8  plan-1  O1B  0.020
 2M8  plan-1  H1B  0.020

