# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:49:23 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](NC[C@H]1NC(=O)[C@H](O)[C@@H]1O)c2ccccc2
#
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
 GB6  GB6  (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidin-2-one  ligand  37  19  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GB6
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
 GB6  C15  C  CR16  0  -0.310  -3.9981   0.3296  -1.0388
 GB6  C14  C  CR16  0  -0.242  -5.2814   0.2659  -0.5126
 GB6  C13  C  CR16  0  -0.270  -5.4654   0.1600   0.8597
 GB6  C12  C  CR16  0  -0.242  -4.3571   0.1175   1.6959
 GB6  C11  C  CR16  0  -0.295  -3.0748   0.1732   1.1659
 GB6  C10  C  CR6   0   0.097  -2.8809   0.2831  -0.2093
 GB6  C8   C  CH1   0  -0.146  -1.4969   0.3144  -0.8153
 GB6  C9   C  CH2   0  -0.156  -1.0096  -1.1062  -1.0877
 GB6  O9   O  OH1   0  -0.656  -0.9383  -1.8396   0.1118
 GB6  N7   N  NH1   0  -0.613  -0.5905   1.0483   0.0509
 GB6  C6   C  CH2   0  -0.286   0.7046   1.4071  -0.5051
 GB6  C5   C  CH1   0  -0.105   1.8213   0.9221   0.4151
 GB6  N1   N  NH1   0  -0.617   1.7872  -0.5191   0.5871
 GB6  C2   C  C     0   0.486   2.7206  -1.1731  -0.1119
 GB6  O2   O  O     0  -0.488   2.9282  -2.3749  -0.1499
 GB6  C3   C  CH1   0  -0.084   3.4943  -0.1312  -0.9085
 GB6  O3   O  OH1   0  -0.664   4.8522  -0.4137  -1.0540
 GB6  C4   C  CH1   0  -0.004   3.2368   1.1560  -0.1256
 GB6  O4   O  OH1   0  -0.668   4.1132   1.2647   0.9658
 GB6  H15  H  HCR6  0   0.246  -3.8633   0.4209  -2.1107
 GB6  H14  H  HCR6  0   0.253  -6.1363   0.3070  -1.1753
 GB6  H13  H  HCR6  0   0.253  -6.4645   0.1155   1.2741
 GB6  H12  H  HCR6  0   0.251  -4.4905   0.0380   2.7675
 GB6  H11  H  HCR6  0   0.249  -2.2185   0.1422   1.8259
 GB6  H8   H  HCH1  0   0.230  -1.5838   0.7788  -1.8120
 GB6  H9   H  HCH2  0   0.222  -1.7069  -1.5643  -1.8002
 GB6  H9A  H  HCH2  0   0.204  -0.0347  -1.0653  -1.5923
 GB6  HO9  H  HOH1  0   0.459  -0.6765  -2.7390  -0.1057
 GB6  HN7  H  HNH1  0   0.359  -1.0548   1.8810   0.3840
 GB6  H6   H  HCH2  0   0.229   0.8326   0.9881  -1.5088
 GB6  H6A  H  HCH2  0   0.248   0.7939   2.4913  -0.6193
 GB6  H5   H  HCH1  0   0.267   1.7040   1.4147   1.3840
 GB6  HN1  H  HNH1  0   0.399   0.9740  -0.9800   0.9754
 GB6  H3   H  HCH1  0   0.247   2.9937  -0.0551  -1.8874
 GB6  HO3  H  HOH1  0   0.457   4.9668  -1.3720  -1.0510
 GB6  H4   H  HCH1  0   0.239   3.2791   2.0443  -0.7681
 GB6  HO4  H  HOH1  0   0.450   5.0000   1.0413   0.6605

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
 GB6  C15  C14  aromatic  1.388  0.020  1.388
 GB6  C15  C10  aromatic  1.392  0.020  1.392
 GB6  C14  C13  aromatic  1.389  0.020  1.389
 GB6  C13  C12  aromatic  1.389  0.020  1.389
 GB6  C12  C11  aromatic  1.389  0.020  1.389
 GB6  C11  C10  aromatic  1.393  0.020  1.393
 GB6  C10  C8   single    1.511  0.020  1.511
 GB6  C8   C9   single    1.526  0.020  1.526
 GB6  C8   N7   single    1.453  0.020  1.453
 GB6  C9   O9   single    1.408  0.020  1.408
 GB6  N7   C6   single    1.454  0.020  1.454
 GB6  C6   C5   single    1.526  0.020  1.526
 GB6  C5   N1   single    1.452  0.020  1.452
 GB6  C5   C4   single    1.533  0.020  1.533
 GB6  N1   C2   single    1.337  0.020  1.337
 GB6  C2   O2   double    1.220  0.020  1.220
 GB6  C2   C3   single    1.523  0.020  1.523
 GB6  C3   O3   single    1.395  0.020  1.395
 GB6  C3   C4   single    1.528  0.020  1.528
 GB6  C4   O4   single    1.404  0.020  1.404
 GB6  C15  H15  single    0.930  0.020  1.080
 GB6  C14  H14  single    0.930  0.020  1.080
 GB6  C13  H13  single    0.930  0.020  1.080
 GB6  C12  H12  single    0.930  0.020  1.080
 GB6  C11  H11  single    0.930  0.020  1.080
 GB6  C8   H8   single    0.970  0.020  1.090
 GB6  C9   H9   single    0.970  0.020  1.090
 GB6  C9   H9A  single    0.970  0.020  1.090
 GB6  O9   HO9  single    0.850  0.020  0.980
 GB6  N7   HN7  single    0.890  0.020  1.040
 GB6  C6   H6   single    0.970  0.020  1.090
 GB6  C6   H6A  single    0.970  0.020  1.090
 GB6  C5   H5   single    0.970  0.020  1.090
 GB6  N1   HN1  single    0.860  0.020  1.020
 GB6  C3   H3   single    0.970  0.020  1.090
 GB6  O3   HO3  single    0.850  0.020  0.980
 GB6  C4   H4   single    0.970  0.020  1.090
 GB6  O4   HO4  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
 GB6  H15  C15  C10  119.48  3.000
 GB6  H15  C15  C14  119.57  3.000
 GB6  C10  C15  C14  120.95  3.000
 GB6  H14  C14  C13  120.22  3.000
 GB6  H14  C14  C15  119.75  3.000
 GB6  C13  C14  C15  120.03  3.000
 GB6  H13  C13  C12  120.31  3.000
 GB6  H13  C13  C14  120.25  3.000
 GB6  C12  C13  C14  119.44  3.000
 GB6  H12  C12  C11  119.63  3.000
 GB6  H12  C12  C13  119.98  3.000
 GB6  C11  C12  C13  120.38  3.000
 GB6  H11  C11  C10  119.64  3.000
 GB6  H11  C11  C12  119.80  3.000
 GB6  C10  C11  C12  120.56  3.000
 GB6  C8   C10  C11  121.66  3.000
 GB6  C8   C10  C15  119.69  3.000
 GB6  C11  C10  C15  118.63  3.000
 GB6  H8   C8   N7   112.04  3.000
 GB6  H8   C8   C9   104.81  3.000
 GB6  N7   C8   C9   112.17  3.000
 GB6  H8   C8   C10  107.39  3.000
 GB6  N7   C8   C10  110.05  3.000
 GB6  C9   C8   C10  110.16  3.000
 GB6  H9A  C9   H9   106.33  3.000
 GB6  H9A  C9   O9   111.46  3.000
 GB6  H9   C9   O9   111.59  3.000
 GB6  H9A  C9   C8   109.31  3.000
 GB6  H9   C9   C8   107.56  3.000
 GB6  O9   C9   C8   110.42  3.000
 GB6  HO9  O9   C9   107.95  3.000
 GB6  HN7  N7   C6   109.39  3.000
 GB6  HN7  N7   C8   109.05  3.000
 GB6  C6   N7   C8   116.89  3.000
 GB6  H6A  C6   H6   105.90  3.000
 GB6  H6A  C6   C5   108.56  3.000
 GB6  H6   C6   C5   110.21  3.000
 GB6  H6A  C6   N7   110.93  3.000
 GB6  H6   C6   N7   111.10  3.000
 GB6  C5   C6   N7   110.04  3.000
 GB6  H5   C5   C4   110.05  3.000
 GB6  H5   C5   N1   109.86  3.000
 GB6  C4   C5   N1   102.41  3.000
 GB6  H5   C5   C6   108.22  3.000
 GB6  C4   C5   C6   114.48  3.000
 GB6  N1   C5   C6   111.70  3.000
 GB6  HN1  N1   C2   122.60  3.000
 GB6  HN1  N1   C5   121.09  3.000
 GB6  C2   N1   C5   114.03  3.000
 GB6  C3   C2   O2   124.83  3.000
 GB6  C3   C2   N1   107.07  3.000
 GB6  O2   C2   N1   128.09  3.000
 GB6  H3   C3   C4   108.68  3.000
 GB6  H3   C3   O3   111.32  3.000
 GB6  C4   C3   O3   112.84  3.000
 GB6  H3   C3   C2   106.33  3.000
 GB6  C4   C3   C2   102.87  3.000
 GB6  O3   C3   C2   114.25  3.000
 GB6  HO3  O3   C3   108.44  3.000
 GB6  H4   C4   O4   111.62  3.000
 GB6  H4   C4   C3   112.05  3.000
 GB6  O4   C4   C3   110.99  3.000
 GB6  H4   C4   C5   111.45  3.000
 GB6  O4   C4   C5   108.30  3.000
 GB6  C3   C4   C5   101.99  3.000
 GB6  HO4  O4   C4   108.06  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
 GB6  CONST_01  C12  C13  C14  C15     0.00   0.0  0
 GB6  CONST_02  C12  C11  C10  C15     0.00   0.0  0
 GB6  CONST_03  C11  C10  C15  C14     0.00   0.0  0
 GB6  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 GB6  CONST_05  C10  C15  C14  C13     0.00   0.0  0
 GB6  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 GB6  CONST_07  C3   C2   N1   C5      0.00   0.0  0
 GB6  CONST_08  C8   C10  C15  C14   180.00   0.0  0
 GB6  CONST_09  C8   C10  C11  C12   180.00   0.0  0
 GB6  CONST_10  O2   C2   N1   C5    180.00   0.0  0
 GB6  CONST_11  H13  C13  C14  C15   180.00   0.0  0
 GB6  CONST_12  H11  C11  C10  C15   180.00   0.0  0
 GB6  CONST_13  H12  C12  C13  C14   180.00   0.0  0
 GB6  CONST_14  H15  C15  C14  C13   180.00   0.0  0
 GB6  CONST_15  H14  C14  C13  C12   180.00   0.0  0
 GB6  Var_01    C5   C6   N7   C8   -126.68  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
 GB6  chir_01  C8  C10  C9  N7  positiv
 GB6  chir_02  C5  N1   C6  C4  positiv
 GB6  chir_03  C3  O3   C2  C4  negativ
 GB6  chir_04  C4  O4   C3  C5  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
 GB6  plan-1  C15  0.020
 GB6  plan-1  C14  0.020
 GB6  plan-1  C13  0.020
 GB6  plan-1  C12  0.020
 GB6  plan-1  C11  0.020
 GB6  plan-1  C10  0.020
 GB6  plan-1  C8   0.020
 GB6  plan-1  H15  0.020
 GB6  plan-1  H14  0.020
 GB6  plan-1  H13  0.020
 GB6  plan-1  H12  0.020
 GB6  plan-1  H11  0.020
 GB6  plan-2  C5   0.020
 GB6  plan-2  N1   0.020
 GB6  plan-2  C2   0.020
 GB6  plan-2  O2   0.020
 GB6  plan-2  C3   0.020
 GB6  plan-2  HN1  0.020

