# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:21:57 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 1-deoxy-L-mannitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](O)[C@@H](O)[C@@H](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
 RNT  RNT  '1-deoxy-L-mannitol       '  L-saccharide  25  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 OK
;

data_comp_RNT
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
 RNT  C1   C  CH2   0  -0.157   0.6512   0.0506  -2.7177
 RNT  C2   C  CH1   0  -0.026  -0.3043   0.0043  -1.5347
 RNT  C3   C  CH1   0  -0.017   0.4665  -0.0779  -0.2052
 RNT  C4   C  CH1   0   0.001  -0.4692  -0.0731   1.0101
 RNT  C5   C  CH1   0   0.001   0.2953   0.0190   2.3416
 RNT  C6   C  CH3   0  -0.683  -0.6496   0.0446   3.5348
 RNT  O1   O  OH1   0  -0.671  -0.1011   0.0481  -3.9086
 RNT  O2   O  OH1   0  -0.660  -1.1939   1.0978  -1.5436
 RNT  O3   O  OH1   0  -0.668   1.3303  -1.1972  -0.1827
 RNT  O4   O  OH1   0  -0.670  -1.3309  -1.1938   0.9937
 RNT  O5   O  OH1   0  -0.664   1.1635   1.1340   2.3477
 RNT  H11  H  HCH2  0   0.188   1.2752   0.9544  -2.6343
 RNT  H12  H  HCH2  0   0.205   1.3289  -0.8073  -2.6681
 RNT  H2   H  HCH1  0   0.226  -0.9350  -0.8877  -1.6303
 RNT  H3   H  HCH1  0   0.231   1.1174   0.8001  -0.1342
 RNT  H4   H  HCH1  0   0.227  -1.1195   0.8050   0.9360
 RNT  H5   H  HCH1  0   0.222   0.9492  -0.8560   2.4275
 RNT  H61  H  HCH3  0   0.238  -0.0857   0.1236   4.4647
 RNT  H62  H  HCH3  0   0.221  -1.3309   0.8974   3.4756
 RNT  H63  H  HCH3  0   0.231  -1.2527  -0.8602   3.5915
 RNT  HO1  H  HOH1  0   0.454   0.5133   0.0198  -4.6469
 RNT  HO2  H  HOH1  0   0.444  -0.6801   1.9131  -1.5264
 RNT  HO3  H  HOH1  0   0.442   0.8240  -1.9865  -0.4038
 RNT  HO4  H  HOH1  0   0.442  -0.8420  -1.9716   1.2834
 RNT  HO5  H  HOH1  0   0.444   0.6285   1.9351   2.3683

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
 RNT  C1  C2   single  1.521  0.020  1.521
 RNT  C1  O1   single  1.409  0.020  1.409
 RNT  C1  H11  single  0.970  0.020  1.090
 RNT  C1  H12  single  0.970  0.020  1.090
 RNT  C2  C3   single  1.539  0.020  1.539
 RNT  C2  O2   single  1.410  0.020  1.410
 RNT  C2  H2   single  0.970  0.020  1.090
 RNT  C3  C4   single  1.534  0.020  1.534
 RNT  C3  O3   single  1.414  0.020  1.414
 RNT  C3  H3   single  0.970  0.020  1.090
 RNT  C4  C5   single  1.538  0.020  1.538
 RNT  C4  O4   single  1.414  0.020  1.414
 RNT  C4  H4   single  0.970  0.020  1.090
 RNT  C5  C6   single  1.522  0.020  1.522
 RNT  C5  O5   single  1.413  0.020  1.413
 RNT  C5  H5   single  0.970  0.020  1.090
 RNT  C6  H61  single  0.970  0.020  1.090
 RNT  C6  H62  single  0.970  0.020  1.090
 RNT  C6  H63  single  0.970  0.020  1.090
 RNT  O1  HO1  single  0.850  0.020  0.980
 RNT  O2  HO2  single  0.850  0.020  0.980
 RNT  O3  HO3  single  0.850  0.020  0.980
 RNT  O4  HO4  single  0.850  0.020  0.980
 RNT  O5  HO5  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
 RNT  H12  C1  H11  106.79  3.000
 RNT  H12  C1  O1   111.57  3.000
 RNT  H11  C1  O1   111.60  3.000
 RNT  H12  C1  C2   109.25  3.000
 RNT  H11  C1  C2   108.78  3.000
 RNT  O1   C1  C2   108.78  3.000
 RNT  H2   C2  O2   105.51  3.000
 RNT  H2   C2  C3   108.66  3.000
 RNT  O2   C2  C3   111.28  3.000
 RNT  H2   C2  C1   108.55  3.000
 RNT  O2   C2  C1   111.57  3.000
 RNT  C3   C2  C1   111.03  3.000
 RNT  H3   C3  O3   105.70  3.000
 RNT  H3   C3  C4   107.98  3.000
 RNT  O3   C3  C4   111.26  3.000
 RNT  H3   C3  C2   108.11  3.000
 RNT  O3   C3  C2   111.22  3.000
 RNT  C4   C3  C2   112.26  3.000
 RNT  H4   C4  O4   105.84  3.000
 RNT  H4   C4  C5   107.80  3.000
 RNT  O4   C4  C5   111.12  3.000
 RNT  H4   C4  C3   108.13  3.000
 RNT  O4   C4  C3   111.11  3.000
 RNT  C5   C4  C3   112.51  3.000
 RNT  H5   C5  O5   105.25  3.000
 RNT  H5   C5  C6   108.81  3.000
 RNT  O5   C5  C6   111.39  3.000
 RNT  H5   C5  C4   108.46  3.000
 RNT  O5   C5  C4   110.87  3.000
 RNT  C6   C5  C4   111.78  3.000
 RNT  H63  C6  H62  107.81  3.000
 RNT  H63  C6  H61  107.59  3.000
 RNT  H62  C6  H61  108.18  3.000
 RNT  H63  C6  C5   111.76  3.000
 RNT  H62  C6  C5   110.95  3.000
 RNT  H61  C6  C5   110.40  3.000
 RNT  HO1  O1  C1   107.95  3.000
 RNT  HO2  O2  C2   108.64  3.000
 RNT  HO3  O3  C3   108.89  3.000
 RNT  HO4  O4  C4   109.10  3.000
 RNT  HO5  O5  C5   108.36  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
 RNT  chir_01  C2  C1  C3  O2  negativ
 RNT  chir_02  C3  O3  C2  C4  negativ
 RNT  chir_03  C4  O4  C3  C5  positiv
 RNT  chir_04  C5  O5  C4  C6  positiv

