# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:58:01 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: D-ribulose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)C(=O)CO
#
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
 RBL  RBL  'D-ribulose               '  D-saccharide  20  10  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RBL
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
 RBL  C2    C  CH2   0  -0.265   2.1485   0.6861   0.5964
 RBL  C3    C  C     0   0.366   1.2840  -0.2581  -0.1819
 RBL  C5    C  CH1   0  -0.124  -0.0724  -0.6039   0.4304
 RBL  O13   O  OH1   0  -0.637  -0.2706  -1.9919   0.4265
 RBL  C6    C  CH1   0  -0.015  -1.1722   0.1474  -0.3409
 RBL  O14   O  OH1   0  -0.640  -0.8178   1.5012  -0.5094
 RBL  C7    C  CH2   0  -0.149  -2.5197  -0.0252   0.3352
 RBL  O8    O  OH1   0  -0.648  -3.5127   0.5481  -0.4799
 RBL  O4    O  O     0  -0.389   1.6256  -0.7627  -1.2237
 RBL  O1    O  OH1   0  -0.643   3.3110   0.9753  -0.1148
 RBL  H2    H  HCH2  0   0.228   1.5481   1.5758   0.8327
 RBL  H2A   H  HCH2  0   0.271   2.3433   0.1993   1.5658
 RBL  H5    H  HCH1  0   0.292  -0.0923  -0.2927   1.4813
 RBL  HO13  H  HOH1  0   0.429  -0.1795  -2.3113  -0.4792
 RBL  H6    H  HCH1  0   0.227  -1.2238  -0.2769  -1.3506
 RBL  HO14  H  HOH1  0   0.427  -1.0012   1.9794   0.3067
 RBL  H7    H  HCH2  0   0.213  -2.6961  -1.0929   0.5044
 RBL  H7A   H  HCH2  0   0.178  -2.4802   0.4524   1.3269
 RBL  HO8   H  HOH1  0   0.437  -4.3631   0.4121  -0.0532
 RBL  HO1   H  HOH1  0   0.441   3.8387   1.5822   0.4120

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
 RBL  C2   C3    single  1.498  0.020  1.498
 RBL  C2   O1    single  1.393  0.020  1.393
 RBL  C3   C5    single  1.528  0.020  1.528
 RBL  C3   O4    double  1.207  0.020  1.207
 RBL  C5   O13   single  1.402  0.020  1.402
 RBL  C5   C6    single  1.539  0.020  1.539
 RBL  C6   O14   single  1.410  0.020  1.410
 RBL  C6   C7    single  1.517  0.020  1.517
 RBL  C7   O8    single  1.407  0.020  1.407
 RBL  C2   H2    single  0.970  0.020  1.090
 RBL  C2   H2A   single  0.970  0.020  1.090
 RBL  C5   H5    single  0.970  0.020  1.090
 RBL  O13  HO13  single  0.850  0.020  0.980
 RBL  C6   H6    single  0.970  0.020  1.090
 RBL  O14  HO14  single  0.850  0.020  0.980
 RBL  C7   H7    single  0.970  0.020  1.090
 RBL  C7   H7A   single  0.970  0.020  1.090
 RBL  O8   HO8   single  0.850  0.020  0.980
 RBL  O1   HO1   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
 RBL  H2A   C2   H2   105.37  3.000
 RBL  H2A   C2   O1   113.16  3.000
 RBL  H2    C2   O1   113.43  3.000
 RBL  H2A   C2   C3   106.29  3.000
 RBL  H2    C2   C3   107.86  3.000
 RBL  O1    C2   C3   110.31  3.000
 RBL  O4    C3   C5   120.17  3.000
 RBL  O4    C3   C2   123.27  3.000
 RBL  C5    C3   C2   116.53  3.000
 RBL  H5    C5   C6   109.20  3.000
 RBL  H5    C5   O13  106.33  3.000
 RBL  C6    C5   O13  112.38  3.000
 RBL  H5    C5   C3   109.64  3.000
 RBL  C6    C5   C3   108.85  3.000
 RBL  O13   C5   C3   110.39  3.000
 RBL  HO13  O13  C5   108.49  3.000
 RBL  H6    C6   C7   108.94  3.000
 RBL  H6    C6   O14  105.87  3.000
 RBL  C7    C6   O14  112.69  3.000
 RBL  H6    C6   C5   107.83  3.000
 RBL  C7    C6   C5   110.84  3.000
 RBL  O14   C6   C5   110.43  3.000
 RBL  HO14  O14  C6   109.12  3.000
 RBL  H7A   C7   H7   106.82  3.000
 RBL  H7A   C7   O8   111.73  3.000
 RBL  H7    C7   O8   111.90  3.000
 RBL  H7A   C7   C6   108.67  3.000
 RBL  H7    C7   C6   108.83  3.000
 RBL  O8    C7   C6   108.80  3.000
 RBL  HO8   O8   C7   108.04  3.000
 RBL  HO1   O1   C2   108.02  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
 RBL  Var_01  O1  C2  C3  C5  -176.33  30.0  1

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
 RBL  chir_01  C5  C3   O13  C6  positiv
 RBL  chir_02  C6  O14  C5   C7  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
 RBL  plan-1  C2  0.020
 RBL  plan-1  C3  0.020
 RBL  plan-1  C5  0.020
 RBL  plan-1  O4  0.020

