# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:27:17 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-1-methylpyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H](CN[C@@H](CO)c2ccccc2)[C@@H](O)[C@@H](O)C1=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
 GB7  GB7  (3R,4R,5R)-3,4-dihydroxy-5-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-1-methylpyrrolidin-2-one  ligand  40  20  .  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_GB7
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
 GB7  C11  C  CR16  0  -0.315  -4.1784   1.0577  -0.6561
 GB7  C12  C  CR16  0  -0.242  -5.3883   0.9206   0.0122
 GB7  C13  C  CR16  0  -0.271  -5.4693   0.1221   1.1450
 GB7  C14  C  CR16  0  -0.243  -4.3323  -0.5322   1.6024
 GB7  C15  C  CR16  0  -0.295  -3.1253  -0.3976   0.9294
 GB7  C10  C  CR6   0   0.093  -3.0356   0.3997  -0.2101
 GB7  C8   C  CH1   0  -0.131  -1.7424   0.5280  -0.9805
 GB7  C9   C  CH2   0  -0.155  -1.6102  -0.6206  -1.9787
 GB7  O9   O  OH1   0  -0.652  -1.5119  -1.8454  -1.2978
 GB7  N7   N  NH1   0  -0.595  -0.6228   0.5787  -0.0594
 GB7  C6   C  CH2   0  -0.239   0.6428   0.9675  -0.6393
 GB7  C5   C  CR15  0  -0.143   1.7477   0.8565   0.4058
 GB7  N1   N  NR5   0  -0.436   2.0607  -0.5227   0.7595
 GB7  C1   C  CH3   0  -0.523   1.1994  -1.3332   1.5858
 GB7  C2   C  CR5   0   0.500   3.2078  -0.9536   0.2249
 GB7  O2   O  O     0  -0.497   3.7543  -2.0333   0.3936
 GB7  C3   C  CR15  0  -0.076   3.7383   0.1469  -0.6796
 GB7  O3   O  OH1   0  -0.665   5.1315   0.2161  -0.7202
 GB7  C4   C  CR15  0  -0.001   3.0976   1.3965  -0.0820
 GB7  O4   O  OH1   0  -0.667   3.8232   1.8436   1.0325
 GB7  H11  H  HCR6  0   0.246  -4.1212   1.6926  -1.5331
 GB7  H12  H  HCR6  0   0.252  -6.2645   1.4448  -0.3479
 GB7  H13  H  HCR6  0   0.252  -6.4092   0.0146   1.6710
 GB7  H14  H  HCR6  0   0.251  -4.3862  -1.1541   2.4872
 GB7  H15  H  HCR6  0   0.260  -2.2451  -0.9082   1.2961
 GB7  H8   H  HCH1  0   0.221  -1.8085   1.4401  -1.5992
 GB7  H9   H  HCH2  0   0.210  -2.4897  -0.5814  -2.6338
 GB7  H9A  H  HCH2  0   0.203  -0.7392  -0.4482  -2.6255
 GB7  HO9  H  HOH1  0   0.453  -1.5835  -2.5506  -1.9469
 GB7  HN7  H  HNH1  0   0.348  -0.8451   1.2283   0.6856
 GB7  H6   H  HCH2  0   0.231   0.8810   0.3121  -1.4800
 GB7  H6A  H  HCH2  0   0.212   0.6322   1.9945  -1.0375
 GB7  H5   H  HCR5  0   0.269   1.4345   1.3981   1.3057
 GB7  H1   H  HCH3  0   0.262   0.3178  -1.6544   1.0341
 GB7  H1A  H  HCH3  0   0.244   1.7509  -2.2021   1.9367
 GB7  H1B  H  HCH3  0   0.238   0.8709  -0.7571   2.4506
 GB7  H3   H  HCR5  0   0.252   3.3222  -0.0287  -1.6835
 GB7  HO3  H  HOH1  0   0.456   5.4863  -0.6472  -0.4734
 GB7  H4   H  HCR5  0   0.242   2.9657   2.1922  -0.8246
 GB7  HO4  H  HOH1  0   0.449   4.7609   1.8054   0.8103

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
 GB7  C11  C12  aromatic  1.389  0.020  1.389
 GB7  C11  C10  aromatic  1.392  0.020  1.392
 GB7  C12  C13  aromatic  1.388  0.020  1.388
 GB7  C13  C14  aromatic  1.389  0.020  1.389
 GB7  C14  C15  aromatic  1.388  0.020  1.388
 GB7  C15  C10  aromatic  1.394  0.020  1.394
 GB7  C10  C8   single    1.511  0.020  1.511
 GB7  C8   C9   single    1.528  0.020  1.528
 GB7  C8   N7   single    1.451  0.020  1.451
 GB7  C9   O9   single    1.405  0.020  1.405
 GB7  N7   C6   single    1.445  0.020  1.445
 GB7  C6   C5   single    1.525  0.020  1.525
 GB7  C5   N1   single    1.458  0.020  1.458
 GB7  C5   C4   single    1.534  0.020  1.534
 GB7  N1   C1   single    1.443  0.020  1.443
 GB7  N1   C2   single    1.337  0.020  1.337
 GB7  C2   O2   double    1.222  0.020  1.222
 GB7  C2   C3   single    1.520  0.020  1.520
 GB7  C3   O3   single    1.395  0.020  1.395
 GB7  C3   C4   single    1.526  0.020  1.526
 GB7  C4   O4   single    1.403  0.020  1.403
 GB7  C11  H11  single    0.930  0.020  1.080
 GB7  C12  H12  single    0.930  0.020  1.080
 GB7  C13  H13  single    0.930  0.020  1.080
 GB7  C14  H14  single    0.930  0.020  1.080
 GB7  C15  H15  single    0.930  0.020  1.080
 GB7  C8   H8   single    0.970  0.020  1.090
 GB7  C9   H9   single    0.970  0.020  1.090
 GB7  C9   H9A  single    0.970  0.020  1.090
 GB7  O9   HO9  single    0.850  0.020  0.980
 GB7  N7   HN7  single    0.890  0.020  1.040
 GB7  C6   H6   single    0.970  0.020  1.090
 GB7  C6   H6A  single    0.970  0.020  1.090
 GB7  C5   H5   single    0.970  0.020  1.090
 GB7  C1   H1   single    0.970  0.020  1.090
 GB7  C1   H1A  single    0.970  0.020  1.090
 GB7  C1   H1B  single    0.970  0.020  1.090
 GB7  C3   H3   single    0.970  0.020  1.090
 GB7  O3   HO3  single    0.850  0.020  0.980
 GB7  C4   H4   single    0.970  0.020  1.090
 GB7  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
 GB7  H11  C11  C10  119.52  3.000
 GB7  H11  C11  C12  119.53  3.000
 GB7  C10  C11  C12  120.95  3.000
 GB7  H12  C12  C13  120.18  3.000
 GB7  H12  C12  C11  119.81  3.000
 GB7  C13  C12  C11  120.01  3.000
 GB7  H13  C13  C14  120.25  3.000
 GB7  H13  C13  C12  120.28  3.000
 GB7  C14  C13  C12  119.46  3.000
 GB7  H14  C14  C15  119.67  3.000
 GB7  H14  C14  C13  119.92  3.000
 GB7  C15  C14  C13  120.41  3.000
 GB7  H15  C15  C10  119.66  3.000
 GB7  H15  C15  C14  119.82  3.000
 GB7  C10  C15  C14  120.52  3.000
 GB7  C8   C10  C15  121.38  3.000
 GB7  C8   C10  C11  119.95  3.000
 GB7  C15  C10  C11  118.65  3.000
 GB7  H8   C8   N7   111.91  3.000
 GB7  H8   C8   C9   105.08  3.000
 GB7  N7   C8   C9   111.99  3.000
 GB7  H8   C8   C10  107.74  3.000
 GB7  N7   C8   C10  109.87  3.000
 GB7  C9   C8   C10  110.09  3.000
 GB7  H9A  C9   H9   106.16  3.000
 GB7  H9A  C9   O9   111.52  3.000
 GB7  H9   C9   O9   112.12  3.000
 GB7  H9A  C9   C8   109.59  3.000
 GB7  H9   C9   C8   107.09  3.000
 GB7  O9   C9   C8   110.18  3.000
 GB7  HO9  O9   C9   107.89  3.000
 GB7  HN7  N7   C6   108.34  3.000
 GB7  HN7  N7   C8   108.66  3.000
 GB7  C6   N7   C8   115.50  3.000
 GB7  H6A  C6   H6   106.45  3.000
 GB7  H6A  C6   C5   108.82  3.000
 GB7  H6   C6   C5   109.02  3.000
 GB7  H6A  C6   N7   112.79  3.000
 GB7  H6   C6   N7   109.78  3.000
 GB7  C5   C6   N7   109.87  3.000
 GB7  H5   C5   C4   109.80  3.000
 GB7  H5   C5   N1   109.25  3.000
 GB7  C4   C5   N1   102.78  3.000
 GB7  H5   C5   C6   108.65  3.000
 GB7  C4   C5   C6   113.22  3.000
 GB7  N1   C5   C6   113.00  3.000
 GB7  C2   N1   C1   124.06  3.000
 GB7  C2   N1   C5   113.09  3.000
 GB7  C1   N1   C5   122.84  3.000
 GB7  H1B  C1   H1A  108.61  3.000
 GB7  H1B  C1   H1   108.30  3.000
 GB7  H1A  C1   H1   109.80  3.000
 GB7  H1B  C1   N1   109.72  3.000
 GB7  H1A  C1   N1   109.33  3.000
 GB7  H1   C1   N1   111.04  3.000
 GB7  C3   C2   O2   124.46  3.000
 GB7  C3   C2   N1   107.70  3.000
 GB7  O2   C2   N1   127.84  3.000
 GB7  H3   C3   C4   109.21  3.000
 GB7  H3   C3   O3   111.03  3.000
 GB7  C4   C3   O3   112.95  3.000
 GB7  H3   C3   C2   107.17  3.000
 GB7  C4   C3   C2   102.31  3.000
 GB7  O3   C3   C2   113.68  3.000
 GB7  HO3  O3   C3   108.36  3.000
 GB7  H4   C4   O4   111.66  3.000
 GB7  H4   C4   C3   112.30  3.000
 GB7  O4   C4   C3   110.78  3.000
 GB7  H4   C4   C5   111.41  3.000
 GB7  O4   C4   C5   108.35  3.000
 GB7  C3   C4   C5   101.87  3.000
 GB7  HO4  O4   C4   107.90  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
 GB7  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 GB7  CONST_02  C14  C15  C10  C11     0.00   0.0  0
 GB7  CONST_03  C15  C10  C11  C12     0.00   0.0  0
 GB7  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 GB7  CONST_05  C10  C11  C12  C13     0.00   0.0  0
 GB7  CONST_06  C10  C15  C14  C13     0.00   0.0  0
 GB7  CONST_07  C3   C2   N1   C5      0.00   0.0  0
 GB7  CONST_08  C8   C10  C11  C12   180.00   0.0  0
 GB7  CONST_09  C8   C10  C15  C14   180.00   0.0  0
 GB7  CONST_10  O2   C2   N1   C5    180.00   0.0  0
 GB7  CONST_11  C3   C2   N1   C1    180.00   0.0  0
 GB7  CONST_12  H13  C13  C12  C11   180.00   0.0  0
 GB7  CONST_13  H15  C15  C10  C11   180.00   0.0  0
 GB7  CONST_14  H14  C14  C13  C12   180.00   0.0  0
 GB7  CONST_15  H11  C11  C12  C13   180.00   0.0  0
 GB7  CONST_16  H12  C12  C13  C14   180.00   0.0  0
 GB7  CONST_17  O2   C2   N1   C1      0.00   0.0  0
 GB7  Var_01    H1   C1   N1   C5     74.28  30.0  3
 GB7  Var_02    C5   C6   N7   C8   -174.89  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
 GB7  chir_01  C8  C10  C9  N7  positiv
 GB7  chir_02  C5  N1   C6  C4  positiv
 GB7  chir_03  C3  O3   C4  C2  positiv
 GB7  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
 GB7  plan-1  C11  0.020
 GB7  plan-1  C12  0.020
 GB7  plan-1  C13  0.020
 GB7  plan-1  C14  0.020
 GB7  plan-1  C15  0.020
 GB7  plan-1  C10  0.020
 GB7  plan-1  C8   0.020
 GB7  plan-1  H11  0.020
 GB7  plan-1  H12  0.020
 GB7  plan-1  H13  0.020
 GB7  plan-1  H14  0.020
 GB7  plan-1  H15  0.020
 GB7  plan-2  C5   0.020
 GB7  plan-2  N1   0.020
 GB7  plan-2  C1   0.020
 GB7  plan-2  C2   0.020
 GB7  plan-2  O2   0.020
 GB7  plan-2  C3   0.020

