# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:50:34 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: ~{N}-[(2~{R},3~{S},4~{S},5~{S},6~{S})-2-methyl-4,5,6-tris(oxidanyl)oxan-3-yl]ethanamide
#   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]1NC(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
 MRH  MRH  ~{N}-[(2~{R},3~{S},4~{S},5~{S},6~{S})-2-methyl-4,5,6-tris(oxidanyl)oxan-3-yl]ethanamide  D-saccharide  29  14  .  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_MRH
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
 MRH  C1   C  CH1   0   0.216   2.4446   0.6394  -0.1567
 MRH  O5   O  O2    0  -0.497   1.4940   1.5552   0.3072
 MRH  C5   C  CH1   0   0.054   0.1756   1.3947  -0.1922
 MRH  C6   C  CH3   0  -0.683  -0.6788   2.4592   0.4648
 MRH  C4   C  CH1   0  -0.128  -0.3509  -0.0231   0.0848
 MRH  N4   N  NH1   0  -0.628  -1.6300  -0.1994  -0.5566
 MRH  C7   C  C     0   0.523  -2.7609  -0.5660   0.0730
 MRH  C8   C  CH3   0  -0.782  -3.9624  -0.7346  -0.8240
 MRH  O7   O  O     0  -0.504  -2.8320  -0.7505   1.2803
 MRH  C3   C  CH1   0   0.053   0.6438  -1.0712  -0.4119
 MRH  O3   O  OH1   0  -0.665   0.1566  -2.3400  -0.0614
 MRH  C2   C  CH1   0  -0.029   2.0277  -0.7954   0.1724
 MRH  O2   O  OH1   0  -0.670   1.9583  -0.9803   1.5633
 MRH  O1   O  OH1   0  -0.669   2.6468   0.7155  -1.5332
 MRH  H1   H  HCH1  0   0.234   3.3626   0.8940   0.3893
 MRH  H2   H  HCH1  0   0.211   0.1666   1.5539  -1.2801
 MRH  H3   H  HCH3  0   0.242  -0.3096   3.4563   0.2239
 MRH  H4   H  HCH3  0   0.235  -1.7076   2.3953   0.1142
 MRH  H5   H  HCH3  0   0.229  -0.6822   2.3440   1.5499
 MRH  H6   H  HCH1  0   0.262  -0.5014  -0.1453   1.1590
 MRH  H7   H  HNH1  0   0.396  -1.6595  -0.0982  -1.5593
 MRH  H8   H  HCH3  0   0.266  -4.2820  -1.7770  -0.8055
 MRH  H9   H  HCH3  0   0.264  -4.7884  -0.1358  -0.4415
 MRH  H10  H  HCH3  0   0.247  -3.7792  -0.4517  -1.8589
 MRH  H11  H  HCH1  0   0.221   0.7222  -0.9729  -1.5039
 MRH  H12  H  HOH1  0   0.453   0.6155  -2.9992  -0.5907
 MRH  H13  H  HCH1  0   0.233   2.7574  -1.4802  -0.2837
 MRH  H14  H  HOH1  0   0.454   2.8460  -0.9031   1.9261
 MRH  H15  H  HOH1  0   0.462   3.0571   1.5611  -1.7445

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
 MRH  C6  C5   single  1.515  0.020  1.515
 MRH  O5  C1   single  1.399  0.020  1.399
 MRH  O5  C5   single  1.419  0.020  1.419
 MRH  C1  C2   single  1.530  0.020  1.530
 MRH  C5  C4   single  1.538  0.020  1.538
 MRH  C8  C7   single  1.509  0.020  1.509
 MRH  O7  C7   double  1.223  0.020  1.223
 MRH  C7  N4   single  1.345  0.020  1.345
 MRH  C2  O2   single  1.405  0.020  1.405
 MRH  C2  C3   single  1.527  0.020  1.527
 MRH  C4  N4   single  1.442  0.020  1.442
 MRH  C4  C3   single  1.528  0.020  1.528
 MRH  C3  O3   single  1.404  0.020  1.404
 MRH  C1  O1   single  1.393  0.020  1.393
 MRH  C1  H1   single  0.970  0.020  1.090
 MRH  C5  H2   single  0.970  0.020  1.090
 MRH  C6  H3   single  0.970  0.020  1.090
 MRH  C6  H4   single  0.970  0.020  1.090
 MRH  C6  H5   single  0.970  0.020  1.090
 MRH  C4  H6   single  0.970  0.020  1.090
 MRH  N4  H7   single  0.860  0.020  1.020
 MRH  C8  H8   single  0.970  0.020  1.090
 MRH  C8  H9   single  0.970  0.020  1.090
 MRH  C8  H10  single  0.970  0.020  1.090
 MRH  C3  H11  single  0.970  0.020  1.090
 MRH  O3  H12  single  0.850  0.020  0.980
 MRH  C2  H13  single  0.970  0.020  1.090
 MRH  O2  H14  single  0.850  0.020  0.980
 MRH  O1  H15  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
 MRH  H1   C1  O1  110.93  3.000
 MRH  H1   C1  C2  109.77  3.000
 MRH  O1   C1  C2  107.65  3.000
 MRH  H1   C1  O5  104.56  3.000
 MRH  O1   C1  O5  112.99  3.000
 MRH  C2   C1  O5  110.94  3.000
 MRH  C5   O5  C1  116.14  3.000
 MRH  H2   C5  C4  107.99  3.000
 MRH  H2   C5  C6  108.83  3.000
 MRH  C4   C5  C6  112.14  3.000
 MRH  H2   C5  O5  109.84  3.000
 MRH  C4   C5  O5  111.04  3.000
 MRH  C6   C5  O5  106.97  3.000
 MRH  H5   C6  H4  108.12  3.000
 MRH  H5   C6  H3  108.50  3.000
 MRH  H4   C6  H3  107.61  3.000
 MRH  H5   C6  C5  111.03  3.000
 MRH  H4   C6  C5  110.61  3.000
 MRH  H3   C6  C5  110.85  3.000
 MRH  H6   C4  C3  109.45  3.000
 MRH  H6   C4  N4  107.56  3.000
 MRH  C3   C4  N4  110.43  3.000
 MRH  H6   C4  C5  109.13  3.000
 MRH  C3   C4  C5  110.55  3.000
 MRH  N4   C4  C5  109.66  3.000
 MRH  H7   N4  C7  117.91  3.000
 MRH  H7   N4  C4  117.14  3.000
 MRH  C7   N4  C4  124.82  3.000
 MRH  O7   C7  C8  121.57  3.000
 MRH  O7   C7  N4  123.49  3.000
 MRH  C8   C7  N4  114.94  3.000
 MRH  H10  C8  H9  108.58  3.000
 MRH  H10  C8  H8  108.30  3.000
 MRH  H9   C8  H8  107.29  3.000
 MRH  H10  C8  C7  113.71  3.000
 MRH  H9   C8  C7  109.48  3.000
 MRH  H8   C8  C7  109.28  3.000
 MRH  H11  C3  C2  107.41  3.000
 MRH  H11  C3  O3  110.71  3.000
 MRH  C2   C3  O3  112.47  3.000
 MRH  H11  C3  C4  107.94  3.000
 MRH  O3   C3  C4  108.24  3.000
 MRH  C2   C3  C4  109.98  3.000
 MRH  H12  O3  C3  108.45  3.000
 MRH  H13  C2  O2  111.19  3.000
 MRH  H13  C2  C3  109.28  3.000
 MRH  O2   C2  C3  108.07  3.000
 MRH  H13  C2  C1  108.30  3.000
 MRH  C3   C2  C1  109.50  3.000
 MRH  O2   C2  C1  110.48  3.000
 MRH  H14  O2  C2  108.50  3.000
 MRH  H15  O1  C1  109.06  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
 MRH  CONST_01  C8  C7  N4  C4  180.00   0.0  0
 MRH  CONST_02  O7  C7  N4  C4    0.00   0.0  0
 MRH  CONST_03  H7  N4  C7  C8    0.00   0.0  0
 MRH  Var_01    H8  C8  C7  N4  116.03  30.0  3

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
 MRH  chir_01  C1  O5  C2  O1  negativ
 MRH  chir_02  C5  O5  C6  C4  positiv
 MRH  chir_03  C4  N4  C3  C5  negativ
 MRH  chir_04  C3  O3  C2  C4  positiv
 MRH  chir_05  C2  O2  C3  C1  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
 MRH  plan-1  C4  0.020
 MRH  plan-1  N4  0.020
 MRH  plan-1  C7  0.020
 MRH  plan-1  C8  0.020
 MRH  plan-1  O7  0.020
 MRH  plan-1  H7  0.020

