# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 19:59:04 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 6-deoxy-alpha-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
 RAM  RAM  6-deoxy-alpha-L-mannopyranose  L-saccharide  23  11  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RAM
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
 RAM  C1   C  CH1   0   0.283  75.8463  60.2595  96.7977
 RAM  C2   C  CH1   0  -0.046  77.0090  59.2651  96.7889
 RAM  C3   C  CH1   0   0.001  76.5461  57.9272  96.2288
 RAM  C4   C  CH1   0  -0.009  75.4541  57.3504  97.1507
 RAM  C5   C  CH1   0  -0.002  74.6757  58.4826  97.8500
 RAM  C6   C  CH3   0  -0.688  73.2557  58.0877  98.1956
 RAM  O1   O  OH1   0  -0.662  76.1129  61.2067  97.7854
 RAM  O2   O  OH1   0  -0.666  78.0554  59.8549  96.0613
 RAM  O3   O  OH1   0  -0.666  76.0940  58.1348  94.9137
 RAM  O4   O  OH1   0  -0.666  76.0881  56.5107  98.0885
 RAM  O5   O  O2    0  -0.498  74.6194  59.6147  97.0001
 RAM  H1   H  HCH1  0   0.215  75.7614  60.7336  95.8131
 RAM  H2   H  HCH1  0   0.226  77.3175  59.0825  97.8297
 RAM  H3   H  HCH1  0   0.230  77.3937  57.2250  96.2455
 RAM  H4   H  HCH1  0   0.217  74.7543  56.7760  96.5245
 RAM  H5   H  HCH1  0   0.219  75.2070  58.7297  98.7801
 RAM  H61  H  HCH3  0   0.242  72.7446  58.8818  98.7402
 RAM  H62  H  HCH3  0   0.231  72.6833  57.8587  97.2951
 RAM  H63  H  HCH3  0   0.230  73.2500  57.1992  98.8286
 RAM  HO1  H  HOH1  0   0.454  75.5264  61.9608  97.6625
 RAM  HO2  H  HOH1  0   0.452  78.8432  59.3128  96.1690
 RAM  HO3  H  HOH1  0   0.450  75.8428  57.2840  94.5406
 RAM  HO4  H  HOH1  0   0.452  75.4180  56.0903  98.6365

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
 RAM  C1  C2   single  1.530  0.020  1.530
 RAM  C1  O1   single  1.394  0.020  1.394
 RAM  C1  O5   single  1.401  0.020  1.401
 RAM  C1  H1   single  0.970  0.020  1.090
 RAM  C2  C3   single  1.523  0.020  1.523
 RAM  C2  O2   single  1.404  0.020  1.404
 RAM  C2  H2   single  0.970  0.020  1.090
 RAM  C3  C4   single  1.541  0.020  1.541
 RAM  C3  O3   single  1.406  0.020  1.406
 RAM  C3  H3   single  0.970  0.020  1.090
 RAM  C4  C5   single  1.542  0.020  1.542
 RAM  C4  O4   single  1.409  0.020  1.409
 RAM  C4  H4   single  0.970  0.020  1.090
 RAM  C5  C6   single  1.514  0.020  1.514
 RAM  C5  O5   single  1.417  0.020  1.417
 RAM  C5  H5   single  0.970  0.020  1.090
 RAM  C6  H61  single  0.970  0.020  1.090
 RAM  C6  H62  single  0.970  0.020  1.090
 RAM  C6  H63  single  0.970  0.020  1.090
 RAM  O1  HO1  single  0.850  0.020  0.980
 RAM  O2  HO2  single  0.850  0.020  0.980
 RAM  O3  HO3  single  0.850  0.020  0.980
 RAM  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
 RAM  H1   C1  O5   105.13  3.000
 RAM  H1   C1  O1   110.93  3.000
 RAM  O5   C1  O1   112.20  3.000
 RAM  H1   C1  C2   109.57  3.000
 RAM  O5   C1  C2   111.55  3.000
 RAM  O1   C1  C2   107.48  3.000
 RAM  H2   C2  O2   110.53  3.000
 RAM  H2   C2  C3   106.70  3.000
 RAM  O2   C2  C3   113.89  3.000
 RAM  H2   C2  C1   108.38  3.000
 RAM  O2   C2  C1   107.23  3.000
 RAM  C3   C2  C1   110.01  3.000
 RAM  H3   C3  O3   110.85  3.000
 RAM  H3   C3  C4   107.32  3.000
 RAM  O3   C3  C4   112.76  3.000
 RAM  H3   C3  C2   108.71  3.000
 RAM  O3   C3  C2   108.19  3.000
 RAM  C4   C3  C2   108.92  3.000
 RAM  H4   C4  O4   110.71  3.000
 RAM  H4   C4  C5   108.68  3.000
 RAM  O4   C4  C5   111.27  3.000
 RAM  H4   C4  C3   107.79  3.000
 RAM  O4   C4  C3   107.59  3.000
 RAM  C5   C4  C3   110.75  3.000
 RAM  H5   C5  O5   110.32  3.000
 RAM  H5   C5  C6   108.60  3.000
 RAM  O5   C5  C6   107.95  3.000
 RAM  H5   C5  C4   107.74  3.000
 RAM  O5   C5  C4   109.56  3.000
 RAM  C6   C5  C4   112.68  3.000
 RAM  H63  C6  H62  107.77  3.000
 RAM  H63  C6  H61  107.51  3.000
 RAM  H62  C6  H61  108.61  3.000
 RAM  H63  C6  C5   110.48  3.000
 RAM  H62  C6  C5   111.00  3.000
 RAM  H61  C6  C5   111.33  3.000
 RAM  HO1  O1  C1   108.97  3.000
 RAM  HO2  O2  C2   108.38  3.000
 RAM  HO3  O3  C3   108.42  3.000
 RAM  HO4  O4  C4   109.03  3.000
 RAM  C5   O5  C1   114.82  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
 RAM  chir_01  C1  C2  O1  O5  positiv
 RAM  chir_02  C2  O2  C1  C3  negativ
 RAM  chir_03  C3  O3  C2  C4  negativ
 RAM  chir_04  C4  O4  C5  C3  negativ
 RAM  chir_05  C5  O5  C4  C6  positiv

