# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:41:37 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-deoxy-beta-L-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H](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
 RM4  RM4  6-deoxy-beta-L-mannopyranose  L-saccharide  23  11  .  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_RM4
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
 RM4  C1   C  CH1   0   0.267   1.4513  -0.4617  -0.5386
 RM4  C2   C  CH1   0  -0.046   1.0585   0.9604  -0.1479
 RM4  C3   C  CH1   0   0.020  -0.4201   1.1645  -0.4740
 RM4  C4   C  CH1   0   0.028  -1.2680   0.0861   0.1859
 RM4  C5   C  CH1   0   0.010  -0.7204  -1.2984  -0.1974
 RM4  C6   C  CH3   0  -0.695  -1.4483  -2.4255   0.5049
 RM4  O1   O  OH1   0  -0.665   2.7670  -0.6682  -0.1720
 RM4  O2   O  OH1   0  -0.668   1.2564   1.2003   1.2208
 RM4  O3   O  OH1   0  -0.666  -0.8877   2.4229  -0.0660
 RM4  O4   O  OH1   0  -0.671  -2.5932   0.2379  -0.2670
 RM4  O5   O  O2    0  -0.498   0.6502  -1.3974   0.1377
 RM4  H1   H  HCH1  0   0.185   1.3101  -0.5802  -1.6276
 RM4  H2   H  HCH1  0   0.229   1.6501   1.6546  -0.7656
 RM4  H3   H  HCH1  0   0.213  -0.5222   1.0438  -1.5647
 RM4  H4   H  HCH1  0   0.218  -1.2079   0.1951   1.2778
 RM4  H5   H  HCH1  0   0.207  -0.8463  -1.4149  -1.2871
 RM4  H6   H  HCH3  0   0.232  -2.5068  -2.4233   0.2475
 RM4  H6A  H  HCH3  0   0.246  -1.0455  -3.3932   0.2062
 RM4  H6B  H  HCH3  0   0.231  -1.3611  -2.3356   1.5894
 RM4  HO1  H  HOH1  0   0.466   3.0944  -1.4757  -0.5824
 RM4  HO2  H  HOH1  0   0.451   2.1892   1.0712   1.4197
 RM4  HO3  H  HOH1  0   0.451  -0.4565   3.0949  -0.6031
 RM4  HO4  H  HOH1  0   0.455  -3.1849  -0.1740   0.3684

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
 RM4  C2  C1   single  1.526  0.020  1.526
 RM4  C1  O5   single  1.405  0.020  1.405
 RM4  C1  O1   single  1.381  0.020  1.381
 RM4  C1  H1   single  0.970  0.020  1.090
 RM4  C3  C2   single  1.528  0.020  1.528
 RM4  C2  O2   single  1.404  0.020  1.404
 RM4  C2  H2   single  0.970  0.020  1.090
 RM4  O3  C3   single  1.403  0.020  1.403
 RM4  C3  C4   single  1.522  0.020  1.522
 RM4  C3  H3   single  0.970  0.020  1.090
 RM4  O4  C4   single  1.409  0.020  1.409
 RM4  C4  C5   single  1.537  0.020  1.537
 RM4  C4  H4   single  0.970  0.020  1.090
 RM4  C5  C6   single  1.514  0.020  1.514
 RM4  C5  O5   single  1.414  0.020  1.414
 RM4  C5  H5   single  0.970  0.020  1.090
 RM4  C6  H6   single  0.970  0.020  1.090
 RM4  C6  H6A  single  0.970  0.020  1.090
 RM4  C6  H6B  single  0.970  0.020  1.090
 RM4  O1  HO1  single  0.850  0.020  0.980
 RM4  O2  HO2  single  0.850  0.020  0.980
 RM4  O3  HO3  single  0.850  0.020  0.980
 RM4  O4  HO4  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
 RM4  H1   C1  O5   109.28  3.000
 RM4  H1   C1  O1   111.55  3.000
 RM4  O5   C1  O1   108.41  3.000
 RM4  H1   C1  C2   108.63  3.000
 RM4  O1   C1  C2   108.45  3.000
 RM4  O5   C1  C2   110.52  3.000
 RM4  H2   C2  O2   111.30  3.000
 RM4  H2   C2  C3   108.42  3.000
 RM4  O2   C2  C3   108.77  3.000
 RM4  H2   C2  C1   107.78  3.000
 RM4  O2   C2  C1   111.88  3.000
 RM4  C3   C2  C1   108.60  3.000
 RM4  H3   C3  O3   110.80  3.000
 RM4  H3   C3  C4   107.45  3.000
 RM4  O3   C3  C4   108.88  3.000
 RM4  H3   C3  C2   106.63  3.000
 RM4  C4   C3  C2   110.60  3.000
 RM4  O3   C3  C2   112.35  3.000
 RM4  H4   C4  O4   111.11  3.000
 RM4  H4   C4  C5   108.51  3.000
 RM4  O4   C4  C5   110.61  3.000
 RM4  H4   C4  C3   109.27  3.000
 RM4  C5   C4  C3   109.36  3.000
 RM4  O4   C4  C3   107.95  3.000
 RM4  H5   C5  O5   109.71  3.000
 RM4  H5   C5  C6   108.95  3.000
 RM4  O5   C5  C6   107.69  3.000
 RM4  H5   C5  C4   107.50  3.000
 RM4  O5   C5  C4   110.43  3.000
 RM4  C6   C5  C4   112.54  3.000
 RM4  H6B  C6  H6A  108.40  3.000
 RM4  H6B  C6  H6   108.19  3.000
 RM4  H6A  C6  H6   107.22  3.000
 RM4  H6B  C6  C5   111.16  3.000
 RM4  H6A  C6  C5   110.86  3.000
 RM4  H6   C6  C5   110.86  3.000
 RM4  HO1  O1  C1   109.63  3.000
 RM4  HO2  O2  C2   108.38  3.000
 RM4  HO3  O3  C3   108.34  3.000
 RM4  HO4  O4  C4   108.69  3.000
 RM4  C5   O5  C1   113.06  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
 RM4  chir_01  C1  C2  O5  O1  positiv
 RM4  chir_02  C2  O2  C1  C3  negativ
 RM4  chir_03  C3  O3  C2  C4  negativ
 RM4  chir_04  C4  O4  C5  C3  negativ
 RM4  chir_05  C5  O5  C4  C6  positiv

