# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:45:01 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2R,3R,4S,5R)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-5-methylpyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1N[C@H](CN[C@@H](CO)c2ccccc2)[C@@H](O)[C@H]1O
#
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
 GB3  GB3  (2R,3R,4S,5R)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-5-methylpyrrolidine-3,4-diol  ligand  41  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_GB3
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
 GB3  C15   C  CR16  0  -0.322   2.9768   0.4416   1.2070
 GB3  C14   C  CR16  0  -0.240   4.1664   0.7234   1.8697
 GB3  C13   C  CR16  0  -0.274   5.3691   0.2149   1.4010
 GB3  C12   C  CR16  0  -0.243   5.3733  -0.5815   0.2620
 GB3  C11   C  CR16  0  -0.303   4.1849  -0.8557  -0.3983
 GB3  C10   C  CR6   0   0.143   2.9708  -0.3457   0.0611
 GB3  C8    C  CH1   0  -0.168   1.6992  -0.6520  -0.7060
 GB3  C9    C  CH2   0  -0.162   1.7378   0.0217  -2.0806
 GB3  O9    O  OH1   0  -0.667   1.8018   1.4165  -1.8924
 GB3  N7    N  NH1   0  -0.613   0.5150  -0.3254   0.0643
 GB3  C6    C  CH2   0  -0.242  -0.6993  -0.9626  -0.3974
 GB3  C5    C  CH1   0  -0.132  -1.8825  -0.5072   0.4430
 GB3  N1    N  NH1   0  -0.593  -2.0721   0.9438   0.3347
 GB3  C2    C  CH1   0  -0.113  -3.3125   1.1542  -0.4142
 GB3  C3    C  CH1   0   0.018  -4.2109  -0.0158  -0.0210
 GB3  O3    O  OH1   0  -0.679  -4.7245   0.1893   1.2723
 GB3  C4    C  CH1   0  -0.014  -3.1975  -1.1664  -0.0279
 GB3  O4    O  OH1   0  -0.667  -3.5432  -2.2362   0.8213
 GB3  C21   C  CH3   0  -0.675  -3.8866   2.5382  -0.1910
 GB3  H15   H  HCR6  0   0.241   2.0470   0.8301   1.5999
 GB3  H14   H  HCR6  0   0.250   4.1497   1.3416   2.7585
 GB3  H13   H  HCR6  0   0.251   6.2944   0.4299   1.9200
 GB3  H12   H  HCR6  0   0.251   6.3031  -0.9930  -0.1100
 GB3  H11   H  HCR6  0   0.245   4.2015  -1.4828  -1.2828
 GB3  H8    H  HCH1  0   0.249   1.6811  -1.7318  -0.8936
 GB3  H91   H  HCH2  0   0.199   2.5992  -0.3539  -2.6486
 GB3  H92   H  HCH2  0   0.212   0.8418  -0.2672  -2.6430
 GB3  HO9   H  HOH1  0   0.457   1.5371   1.8430  -2.7115
 GB3  HN7   H  HNH1  0   0.340   0.3584   0.6771   0.0431
 GB3  H61   H  HCH2  0   0.223  -0.5933  -2.0486  -0.3053
 GB3  H62   H  HCH2  0   0.186  -0.9233  -0.7604  -1.4574
 GB3  H5    H  HCH1  0   0.242  -1.6878  -0.7743   1.4857
 GB3  HN1   H  HNH1  0   0.346  -2.1977   1.3269   1.2638
 GB3  H2    H  HCH1  0   0.227  -3.0946   1.0408  -1.4836
 GB3  H3    H  HCH1  0   0.209  -5.0183  -0.1744  -0.7496
 GB3  HO3   H  HOH1  0   0.441  -4.7792  -0.6747   1.6990
 GB3  H4    H  HCH1  0   0.225  -3.0823  -1.5166  -1.0626
 GB3  HO4   H  HOH1  0   0.459  -4.1846  -2.7929   0.3685
 GB3  H211  H  HCH3  0   0.234  -3.1628   3.3005  -0.4814
 GB3  H212  H  HCH3  0   0.232  -4.7860   2.6884  -0.7884
 GB3  H213  H  HCH3  0   0.225  -4.1434   2.6992   0.8567

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
 GB3  C15  C14   aromatic  1.391  0.020  1.391
 GB3  C15  C10   aromatic  1.390  0.020  1.390
 GB3  C15  H15   single    0.930  0.020  1.080
 GB3  C14  C13   aromatic  1.387  0.020  1.387
 GB3  C14  H14   single    0.930  0.020  1.080
 GB3  C13  C12   aromatic  1.390  0.020  1.390
 GB3  C13  H13   single    0.930  0.020  1.080
 GB3  C12  C11   aromatic  1.387  0.020  1.387
 GB3  C12  H12   single    0.930  0.020  1.080
 GB3  C11  C10   aromatic  1.395  0.020  1.395
 GB3  C11  H11   single    0.930  0.020  1.080
 GB3  C10  C8    single    1.516  0.020  1.516
 GB3  C8   C9    single    1.531  0.020  1.531
 GB3  C8   N7    single    1.450  0.020  1.450
 GB3  C8   H8    single    0.970  0.020  1.090
 GB3  C9   O9    single    1.409  0.020  1.409
 GB3  C9   H91   single    0.970  0.020  1.090
 GB3  C9   H92   single    0.970  0.020  1.090
 GB3  O9   HO9   single    0.850  0.020  0.980
 GB3  N7   C6    single    1.447  0.020  1.447
 GB3  N7   HN7   single    0.890  0.020  1.040
 GB3  C6   C5    single    1.521  0.020  1.521
 GB3  C6   H61   single    0.970  0.020  1.090
 GB3  C6   H62   single    0.970  0.020  1.090
 GB3  C5   N1    single    1.467  0.020  1.467
 GB3  C5   C4    single    1.545  0.020  1.545
 GB3  C5   H5    single    0.970  0.020  1.090
 GB3  N1   C2    single    1.464  0.020  1.464
 GB3  N1   HN1   single    0.890  0.020  1.040
 GB3  C2   C3    single    1.527  0.020  1.527
 GB3  C2   C21   single    1.515  0.020  1.515
 GB3  C2   H2    single    0.970  0.020  1.090
 GB3  C3   O3    single    1.407  0.020  1.407
 GB3  C3   C4    single    1.533  0.020  1.533
 GB3  C3   H3    single    0.970  0.020  1.090
 GB3  O3   HO3   single    0.850  0.020  0.980
 GB3  C4   O4    single    1.409  0.020  1.409
 GB3  C4   H4    single    0.970  0.020  1.090
 GB3  O4   HO4   single    0.850  0.020  0.980
 GB3  C21  H211  single    0.970  0.020  1.090
 GB3  C21  H212  single    0.970  0.020  1.090
 GB3  C21  H213  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
 GB3  H15   C15  C10   119.94  3.000
 GB3  H15   C15  C14   119.31  3.000
 GB3  C10   C15  C14   120.75  3.000
 GB3  H14   C14  C13   120.00  3.000
 GB3  H14   C14  C15   119.58  3.000
 GB3  C13   C14  C15   120.42  3.000
 GB3  H13   C13  C12   120.27  3.000
 GB3  H13   C13  C14   120.42  3.000
 GB3  C12   C13  C14   119.31  3.000
 GB3  H12   C12  C11   119.81  3.000
 GB3  H12   C12  C13   120.13  3.000
 GB3  C11   C12  C13   120.06  3.000
 GB3  H11   C11  C10   119.56  3.000
 GB3  H11   C11  C12   119.31  3.000
 GB3  C10   C11  C12   121.12  3.000
 GB3  C8    C10  C11   119.31  3.000
 GB3  C8    C10  C15   122.35  3.000
 GB3  C11   C10  C15   118.34  3.000
 GB3  H8    C8   N7    107.42  3.000
 GB3  H8    C8   C9    106.27  3.000
 GB3  N7    C8   C9    113.48  3.000
 GB3  H8    C8   C10   107.43  3.000
 GB3  N7    C8   C10   111.75  3.000
 GB3  C9    C8   C10   110.13  3.000
 GB3  H92   C9   H91   106.59  3.000
 GB3  H92   C9   O9    111.49  3.000
 GB3  H91   C9   O9    111.85  3.000
 GB3  H92   C9   C8    108.90  3.000
 GB3  H91   C9   C8    109.49  3.000
 GB3  O9    C9   C8    108.47  3.000
 GB3  HO9   O9   C9    108.24  3.000
 GB3  HN7   N7   C6    107.39  3.000
 GB3  HN7   N7   C8    109.72  3.000
 GB3  C6    N7   C8    114.62  3.000
 GB3  H62   C6   H61   106.42  3.000
 GB3  H62   C6   C5    108.56  3.000
 GB3  H61   C6   C5    109.00  3.000
 GB3  H62   C6   N7    113.37  3.000
 GB3  H61   C6   N7    109.19  3.000
 GB3  C5    C6   N7    110.16  3.000
 GB3  H5    C5   C4    109.75  3.000
 GB3  H5    C5   N1    109.56  3.000
 GB3  C4    C5   N1    106.83  3.000
 GB3  H5    C5   C6    108.37  3.000
 GB3  C4    C5   C6    111.47  3.000
 GB3  N1    C5   C6    110.84  3.000
 GB3  HN1   N1   C2    108.05  3.000
 GB3  HN1   N1   C5    108.81  3.000
 GB3  C2    N1   C5    106.82  3.000
 GB3  H2    C2   C21   108.26  3.000
 GB3  H2    C2   C3    106.78  3.000
 GB3  C21   C2   C3    116.06  3.000
 GB3  H2    C2   N1    108.39  3.000
 GB3  C21   C2   N1    112.15  3.000
 GB3  C3    C2   N1    104.87  3.000
 GB3  H3    C3   C4    111.98  3.000
 GB3  H3    C3   O3    111.24  3.000
 GB3  C4    C3   O3    110.79  3.000
 GB3  H3    C3   C2    111.85  3.000
 GB3  C4    C3   C2    100.66  3.000
 GB3  O3    C3   C2    109.88  3.000
 GB3  HO3   O3   C3    107.26  3.000
 GB3  H4    C4   O4    110.57  3.000
 GB3  H4    C4   C3    108.23  3.000
 GB3  O4    C4   C3    113.89  3.000
 GB3  H4    C4   C5    109.51  3.000
 GB3  O4    C4   C5    110.43  3.000
 GB3  C3    C4   C5    103.95  3.000
 GB3  HO4   O4   C4    108.61  3.000
 GB3  H213  C21  H212  108.17  3.000
 GB3  H213  C21  H211  108.00  3.000
 GB3  H212  C21  H211  107.78  3.000
 GB3  H213  C21  C2    111.45  3.000
 GB3  H212  C21  C2    110.96  3.000
 GB3  H211  C21  C2    110.36  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
 GB3  CONST_01  C12  C13  C14  C15     0.00   0.0  0
 GB3  CONST_02  C12  C11  C10  C15     0.00   0.0  0
 GB3  CONST_03  C11  C10  C15  C14     0.00   0.0  0
 GB3  CONST_04  C11  C12  C13  C14     0.00   0.0  0
 GB3  CONST_05  C10  C15  C14  C13     0.00   0.0  0
 GB3  CONST_06  C10  C11  C12  C13     0.00   0.0  0
 GB3  CONST_07  C8   C10  C15  C14   180.00   0.0  0
 GB3  CONST_08  C8   C10  C11  C12   180.00   0.0  0
 GB3  CONST_09  H13  C13  C14  C15   180.00   0.0  0
 GB3  CONST_10  H11  C11  C10  C15   180.00   0.0  0
 GB3  CONST_11  H12  C12  C13  C14   180.00   0.0  0
 GB3  CONST_12  H15  C15  C14  C13   180.00   0.0  0
 GB3  CONST_13  H14  C14  C13  C12   180.00   0.0  0
 GB3  Var_01    C5   C6   N7   C8   -177.69  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
 GB3  chir_01  C8  C10  C9   N7  positiv
 GB3  chir_02  C5  N1   C6   C4  positiv
 GB3  chir_03  C2  N1   C21  C3  positiv
 GB3  chir_04  C3  O3   C2   C4  negativ
 GB3  chir_05  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
 GB3  plan-1  C15  0.020
 GB3  plan-1  C14  0.020
 GB3  plan-1  C13  0.020
 GB3  plan-1  C12  0.020
 GB3  plan-1  C11  0.020
 GB3  plan-1  C10  0.020
 GB3  plan-1  C8   0.020
 GB3  plan-1  H15  0.020
 GB3  plan-1  H14  0.020
 GB3  plan-1  H13  0.020
 GB3  plan-1  H12  0.020
 GB3  plan-1  H11  0.020

