# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 17:19:42 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{R},5~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-[(2~{R})-oxolan-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@H]([C@H]1S[C@H]([C@H]2CCCO2)C(=N1)C(O)=O)C(O)=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
 R3N  R3N  '(2~{R},5~{S})-2-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-[(2~{R})-oxolan-2-yl]-2,5-dihydro-1,3-thiazole-4-carboxylic acid'  ligand  35  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R3N
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
 R3N  O72   O  OC    -1  -0.592  -17.0644  23.3935  -2.3315
 R3N  C7    C  C      0   0.405  -17.8280  24.0864  -3.0374
 R3N  C6    C  CH1    0  -0.345  -18.7132  25.0858  -2.2579
 R3N  N4    N  N      0  -0.308  -20.4877  25.0164  -0.5181
 R3N  C5    C  CH1    0  -0.235  -19.3079  24.3821  -1.0334
 R3N  C3    C  C      0   0.102  -20.5307  25.1749   0.7344
 R3N  C2    C  CH1    0  -0.493  -19.3665  24.7047   1.5775
 R3N  S1    S  S2     0  -0.039  -18.1093  24.2023   0.3661
 R3N  C31   C  C      0   0.386  -21.7275  25.8580   1.4116
 R3N  O71   O  O      0  -0.595  -17.9273  24.0615  -4.2785
 R3N  C61   C  CH1    0   0.052  -17.8830  26.3508  -1.9525
 R3N  O62   O  OH1    0  -0.673  -18.4617  27.1767  -0.9610
 R3N  C62   C  CH3    0  -0.674  -17.7051  27.2029  -3.1968
 R3N  C14   C  CR15   0   0.118  -19.7687  23.5679   2.5180
 R3N  C15   C  CH2    0  -0.511  -20.4066  22.3549   1.8468
 R3N  C16   C  CH2    0  -0.488  -19.9261  21.2080   2.7285
 R3N  C17   C  CH2    0  -0.154  -18.5273  21.6803   3.0913
 R3N  O18   O  O      0  -0.502  -18.6141  23.0924   3.1973
 R3N  O32   O  O      0  -0.573  -22.7877  25.8985   0.7721
 R3N  O31   O  OC    -1  -0.578  -21.4881  26.3151   2.5452
 R3N  H2    H  HCH1   0   0.217  -19.5677  25.3768  -2.8797
 R3N  H5    H  HCH1   0   0.276  -19.6108  23.3777  -1.3471
 R3N  H111  H  HCH1   0   0.284  -18.9841  25.5306   2.1812
 R3N  H8    H  HCH1   0   0.189  -16.8912  26.0209  -1.6168
 R3N  H9    H  HOH1   0   0.445  -18.3227  26.7355  -0.1158
 R3N  H11   H  HCH3   0   0.225  -17.0631  28.0603  -2.9912
 R3N  H12   H  HCH3   0   0.228  -17.2506  26.6279  -4.0012
 R3N  H10   H  HCH3   0   0.217  -18.6675  27.5736  -3.5558
 R3N  H13   H  HCR5   0   0.225  -20.4597  23.9899   3.2571
 R3N  H14   H  HCH2   0   0.242  -20.0307  22.2258   0.8282
 R3N  H15   H  HCH2   0   0.252  -21.4919  22.4394   1.7974
 R3N  H17   H  HCH2   0   0.234  -20.5484  21.1195   3.6216
 R3N  H16   H  HCH2   0   0.246  -19.9247  20.2435   2.2214
 R3N  H19   H  HCH2   0   0.221  -18.1677  21.2724   4.0387
 R3N  H18   H  HCH2   0   0.197  -17.8110  21.4004   2.3096

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
 R3N  O71  C7    deloc   1.245  0.020  1.245
 R3N  C62  C61   single  1.519  0.020  1.519
 R3N  C7   C6    single  1.546  0.020  1.546
 R3N  C7   O72   deloc   1.250  0.020  1.250
 R3N  C6   C61   single  1.544  0.020  1.544
 R3N  C6   C5    single  1.532  0.020  1.532
 R3N  C61  O62   single  1.414  0.020  1.414
 R3N  C5   N4    single  1.435  0.020  1.435
 R3N  C5   S1    single  1.851  0.020  1.851
 R3N  N4   C3    double  1.263  0.020  1.263
 R3N  S1   C2    single  1.817  0.020  1.817
 R3N  O32  C31   deloc   1.239  0.020  1.239
 R3N  C3   C31   single  1.535  0.020  1.535
 R3N  C3   C2    single  1.512  0.020  1.512
 R3N  C31  O31   deloc   1.245  0.020  1.245
 R3N  C2   C14   single  1.529  0.020  1.529
 R3N  C15  C16   single  1.524  0.020  1.524
 R3N  C15  C14   single  1.526  0.020  1.526
 R3N  C16  C17   single  1.520  0.020  1.520
 R3N  C14  O18   single  1.422  0.020  1.422
 R3N  C17  O18   single  1.419  0.020  1.419
 R3N  C6   H2    single  0.970  0.020  1.090
 R3N  C5   H5    single  0.970  0.020  1.090
 R3N  C2   H111  single  0.970  0.020  1.090
 R3N  C61  H8    single  0.970  0.020  1.090
 R3N  O62  H9    single  0.850  0.020  0.980
 R3N  C62  H11   single  0.970  0.020  1.090
 R3N  C62  H12   single  0.970  0.020  1.090
 R3N  C62  H10   single  0.970  0.020  1.090
 R3N  C14  H13   single  0.970  0.020  1.090
 R3N  C15  H14   single  0.970  0.020  1.090
 R3N  C15  H15   single  0.970  0.020  1.090
 R3N  C16  H17   single  0.970  0.020  1.090
 R3N  C16  H16   single  0.970  0.020  1.090
 R3N  C17  H19   single  0.970  0.020  1.090
 R3N  C17  H18   single  0.970  0.020  1.090

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
 R3N  O71   C7   C6   118.02  3.000
 R3N  C6    C7   O72  115.06  3.000
 R3N  O71   C7   O72  126.91  3.000
 R3N  H2    C6   C61  108.30  3.000
 R3N  H2    C6   C5   105.82  3.000
 R3N  C61   C6   C5   115.27  3.000
 R3N  H2    C6   C7   109.39  3.000
 R3N  C5    C6   C7   109.16  3.000
 R3N  C61   C6   C7   108.76  3.000
 R3N  C3    N4   C5   116.07  3.000
 R3N  H5    C5   S1   107.85  3.000
 R3N  H5    C5   N4   106.31  3.000
 R3N  S1    C5   N4   107.68  3.000
 R3N  H5    C5   C6   107.44  3.000
 R3N  S1    C5   C6   113.42  3.000
 R3N  N4    C5   C6   113.76  3.000
 R3N  C31   C3   C2   119.50  3.000
 R3N  C2    C3   N4   119.18  3.000
 R3N  C31   C3   N4   121.31  3.000
 R3N  H111  C2   C14  108.31  3.000
 R3N  H111  C2   S1   109.60  3.000
 R3N  C14   C2   S1   112.74  3.000
 R3N  H111  C2   C3   110.04  3.000
 R3N  C14   C2   C3   111.81  3.000
 R3N  S1    C2   C3   104.30  3.000
 R3N  C2    S1   C5    91.67  3.000
 R3N  O31   C31  O32  128.49  3.000
 R3N  O31   C31  C3   114.51  3.000
 R3N  O32   C31  C3   117.00  3.000
 R3N  H8    C61  C62  108.26  3.000
 R3N  H8    C61  O62  109.31  3.000
 R3N  C62   C61  O62  107.14  3.000
 R3N  H8    C61  C6   107.46  3.000
 R3N  O62   C61  C6   113.41  3.000
 R3N  C62   C61  C6   111.14  3.000
 R3N  H9    O62  C61  106.78  3.000
 R3N  H10   C62  H12  107.73  3.000
 R3N  H10   C62  H11  108.29  3.000
 R3N  H12   C62  H11  108.00  3.000
 R3N  H10   C62  C61  110.89  3.000
 R3N  H12   C62  C61  110.99  3.000
 R3N  H11   C62  C61  110.83  3.000
 R3N  H13   C14  O18  108.57  3.000
 R3N  H13   C14  C15  109.82  3.000
 R3N  O18   C14  C15  106.49  3.000
 R3N  H13   C14  C2   107.11  3.000
 R3N  O18   C14  C2   109.21  3.000
 R3N  C15   C14  C2   115.49  3.000
 R3N  H15   C15  H14  108.01  3.000
 R3N  H15   C15  C16  113.48  3.000
 R3N  H14   C15  C16  109.98  3.000
 R3N  H15   C15  C14  112.00  3.000
 R3N  H14   C15  C14  111.09  3.000
 R3N  C16   C15  C14  102.23  3.000
 R3N  H16   C16  H17  108.04  3.000
 R3N  H16   C16  C17  112.63  3.000
 R3N  H17   C16  C17  110.75  3.000
 R3N  H16   C16  C15  113.40  3.000
 R3N  H17   C16  C15  110.76  3.000
 R3N  C17   C16  C15  101.20  3.000
 R3N  H18   C17  H19  107.93  3.000
 R3N  H18   C17  O18  110.32  3.000
 R3N  H19   C17  O18  109.08  3.000
 R3N  H18   C17  C16  110.59  3.000
 R3N  H19   C17  C16  113.19  3.000
 R3N  O18   C17  C16  105.71  3.000
 R3N  C17   O18  C14  110.30  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
 R3N  Var_01  C2   C3   N4   C5     0.29  30.0  1
 R3N  Var_02  C17  C16  C15  C14  -35.79  30.0  1
 R3N  Var_03  O18  C17  C16  C15   34.58  30.0  1
 R3N  Var_04  O32  C31  C3   N4    20.19  30.0  2

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
 R3N  chir_01  C6   C7   C61  C5  positiv
 R3N  chir_02  C5   S1   N4   C6  negativ
 R3N  chir_03  C2   S1   C14  C3  positiv
 R3N  chir_04  C61  O62  C62  C6  positiv
 R3N  chir_05  C14  O18  C15  C2  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
 R3N  plan-1  O72  0.020
 R3N  plan-1  C7   0.020
 R3N  plan-1  C6   0.020
 R3N  plan-1  O71  0.020
 R3N  plan-2  C3   0.020
 R3N  plan-2  C31  0.020
 R3N  plan-2  O32  0.020
 R3N  plan-2  O31  0.020

