# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:22:32 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 6-deoxy-L-mannose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C=O
#
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
 RNS  RNS  '6-deoxy-L-mannose        '  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 OK
;

data_comp_RNS
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
 RNS  C1   C  C1    0   0.174   0.3411   0.4154  -2.7709
 RNS  C2   C  CH1   0  -0.099  -0.5216   0.0953  -1.5671
 RNS  C3   C  CH1   0  -0.029   0.3523   0.1438  -0.3017
 RNS  C4   C  CH1   0  -0.005  -0.4520  -0.2101   0.9545
 RNS  C5   C  CH1   0  -0.003   0.3511   0.0088   2.2476
 RNS  C6   C  CH3   0  -0.683  -0.4761  -0.3071   3.4851
 RNS  O1   O  O     0  -0.365   0.7284  -0.3922  -3.5744
 RNS  O2   O  OH1   0  -0.654  -1.6061   0.9871  -1.5141
 RNS  O3   O  OH1   0  -0.660   1.4899  -0.6694  -0.4664
 RNS  O4   O  OH1   0  -0.667  -0.9574  -1.5257   0.8769
 RNS  O5   O  OH1   0  -0.662   0.8733   1.3201   2.2967
 RNS  H11  H  H     0   0.192   0.5917   1.4897  -2.8707
 RNS  H2   H  HCH1  0   0.263  -0.9383  -0.9082  -1.6932
 RNS  H3   H  HCH1  0   0.250   0.7293   1.1660  -0.1912
 RNS  H4   H  HCH1  0   0.233  -1.3261   0.4506   0.9874
 RNS  H5   H  HCH1  0   0.227   1.2253  -0.6513   2.2277
 RNS  H61  H  HCH3  0   0.240   0.1164  -0.1503   4.3869
 RNS  H62  H  HCH3  0   0.222  -1.3580   0.3366   3.5401
 RNS  H63  H  HCH3  0   0.233  -0.8194  -1.3405   3.4914
 RNS  HO2  H  HOH1  0   0.455  -1.2874   1.8715  -1.2994
 RNS  HO3  H  HOH1  0   0.446   1.2127  -1.5692  -0.6720
 RNS  HO4  H  HOH1  0   0.447  -0.2665  -2.1495   1.1251
 RNS  HO5  H  HOH1  0   0.445   0.1417   1.9340   2.4257

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
 RNS  C1  C2   single  1.515  0.020  1.515
 RNS  C1  O1   double  1.203  0.020  1.203
 RNS  C1  H11  single  0.930  0.020  1.080
 RNS  C2  C3   single  1.539  0.020  1.539
 RNS  C2  O2   single  1.405  0.020  1.405
 RNS  C2  H2   single  0.970  0.020  1.090
 RNS  C3  C4   single  1.533  0.020  1.533
 RNS  C3  O3   single  1.408  0.020  1.408
 RNS  C3  H3   single  0.970  0.020  1.090
 RNS  C4  C5   single  1.538  0.020  1.538
 RNS  C4  O4   single  1.411  0.020  1.411
 RNS  C4  H4   single  0.970  0.020  1.090
 RNS  C5  C6   single  1.522  0.020  1.522
 RNS  C5  O5   single  1.412  0.020  1.412
 RNS  C5  H5   single  0.970  0.020  1.090
 RNS  C6  H61  single  0.970  0.020  1.090
 RNS  C6  H62  single  0.970  0.020  1.090
 RNS  C6  H63  single  0.970  0.020  1.090
 RNS  O2  HO2  single  0.850  0.020  0.980
 RNS  O3  HO3  single  0.850  0.020  0.980
 RNS  O4  HO4  single  0.850  0.020  0.980
 RNS  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
 RNS  H11  C1  O1   121.20  3.000
 RNS  H11  C1  C2   113.91  3.000
 RNS  O1   C1  C2   124.89  3.000
 RNS  H2   C2  O2   107.01  3.000
 RNS  H2   C2  C3   109.88  3.000
 RNS  O2   C2  C3   112.79  3.000
 RNS  H2   C2  C1   108.61  3.000
 RNS  O2   C2  C1   109.59  3.000
 RNS  C3   C2  C1   108.87  3.000
 RNS  H3   C3  O3   105.83  3.000
 RNS  H3   C3  C4   108.27  3.000
 RNS  O3   C3  C4   112.73  3.000
 RNS  H3   C3  C2   107.93  3.000
 RNS  O3   C3  C2   110.15  3.000
 RNS  C4   C3  C2   111.64  3.000
 RNS  H4   C4  O4   106.13  3.000
 RNS  H4   C4  C5   107.78  3.000
 RNS  O4   C4  C5   111.46  3.000
 RNS  H4   C4  C3   107.69  3.000
 RNS  O4   C4  C3   110.97  3.000
 RNS  C5   C4  C3   112.47  3.000
 RNS  H5   C5  O5   105.37  3.000
 RNS  H5   C5  C6   108.88  3.000
 RNS  O5   C5  C6   111.44  3.000
 RNS  H5   C5  C4   108.40  3.000
 RNS  O5   C5  C4   110.76  3.000
 RNS  C6   C5  C4   111.74  3.000
 RNS  H63  C6  H62  107.71  3.000
 RNS  H63  C6  H61  107.64  3.000
 RNS  H62  C6  H61  108.18  3.000
 RNS  H63  C6  C5   111.90  3.000
 RNS  H62  C6  C5   110.93  3.000
 RNS  H61  C6  C5   110.32  3.000
 RNS  HO2  O2  C2   109.60  3.000
 RNS  HO3  O3  C3   109.38  3.000
 RNS  HO4  O4  C4   109.43  3.000
 RNS  HO5  O5  C5   108.39  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
 RNS  chir_01  C2  C1  C3  O2  negativ
 RNS  chir_02  C3  O3  C2  C4  negativ
 RNS  chir_03  C4  O4  C3  C5  positiv
 RNS  chir_04  C5  O5  C4  C6  positiv

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
 RNS  plan-1  C1   0.020
 RNS  plan-1  C2   0.020
 RNS  plan-1  O1   0.020
 RNS  plan-1  H11  0.020

