# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:29:13 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2R,2'R)-1,1'-(1,6-dioxohexane-1,6-diyl)dipyrrolidine-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CCCN1C(=O)CCCCC(=O)N2CCC[C@@H]2C(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
 GHE  GHE  '(2R,2'R)-1,1'-(1,6-dioxohexane-1,6-diyl)dipyrrolidine-2-carboxylic acid (non-preferred name)'  ligand  48  24  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GHE
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
 GHE  N1    N  NT    0  -0.488   4.2955  -0.5429  -0.3422
 GHE  C2    C  CH1   0  -0.147   5.6050   0.0722  -0.3817
 GHE  C3    C  CH2   0  -0.484   6.5586  -1.0877  -0.0470
 GHE  C4    C  CH2   0  -0.474   5.7941  -2.3136  -0.5331
 GHE  C5    C  CH2   0  -0.271   4.3523  -1.9891  -0.1678
 GHE  C1    C  C     0   0.538   5.7309   1.1814   0.6405
 GHE  O2    O  O     0  -0.441   5.2003   1.1765   1.7209
 GHE  O1    O  OH1   0  -0.591   6.5681   2.1231   0.2297
 GHE  C6    C  C     0   0.584   3.1950   0.2079  -0.5303
 GHE  O6    O  O     0  -0.506   3.2884   1.4143  -0.7267
 GHE  C7    C  CH2   0  -0.596   1.8688  -0.5154  -0.4911
 GHE  C8    C  CH2   0  -0.411   0.6646   0.4132  -0.5014
 GHE  C9    C  CH2   0  -0.411  -0.6415  -0.3724  -0.5024
 GHE  C10   C  CH2   0  -0.596  -1.8479   0.5530  -0.4827
 GHE  C11   C  C     0   0.585  -3.1711  -0.1757  -0.5276
 GHE  O11   O  O     0  -0.506  -3.2585  -1.3811  -0.7323
 GHE  N2    N  NT    0  -0.488  -4.2755   0.5681  -0.3343
 GHE  C15   C  CH1   0  -0.147  -5.5821  -0.0533  -0.3810
 GHE  C14   C  CH2   0  -0.483  -6.5415   1.0990  -0.0374
 GHE  C13   C  CH2   0  -0.474  -5.7832   2.3324  -0.5144
 GHE  C12   C  CH2   0  -0.271  -4.3398   2.0129  -0.1512
 GHE  C16   C  C     0   0.538  -5.7039  -1.1723   0.6311
 GHE  O16   O  O     0  -0.442  -5.1785  -1.1716   1.7140
 GHE  O17   O  OH1   0  -0.590  -6.5308  -2.1179   0.2087
 GHE  H2    H  HCH1  0   0.284   5.8194   0.4668  -1.3793
 GHE  H31C  H  HCH2  0   0.270   7.5298  -0.9619  -0.5218
 GHE  H32C  H  HCH2  0   0.253   6.7169  -1.1544   1.0316
 GHE  H41C  H  HCH2  0   0.247   5.8919  -2.4187  -1.6153
 GHE  H42C  H  HCH2  0   0.261   6.1407  -3.2369  -0.0718
 GHE  H51C  H  HCH2  0   0.245   4.1296  -2.2681   0.8663
 GHE  H52C  H  HCH2  0   0.261   3.6379  -2.4970  -0.8149
 GHE  H1    H  HOH1  0   0.482   6.6950   2.7845   0.9266
 GHE  H71C  H  HCH2  0   0.270   1.8209  -1.1943  -1.3501
 GHE  H72C  H  HCH2  0   0.264   1.8334  -1.1611   0.3918
 GHE  H81C  H  HCH2  0   0.225   0.6980   1.0721   0.3709
 GHE  H82C  H  HCH2  0   0.226   0.7006   1.0620  -1.3801
 GHE  H91C  H  HCH2  0   0.226  -0.6789  -1.0153  -1.3854
 GHE  H92C  H  HCH2  0   0.225  -0.6719  -1.0374   0.3652
 GHE  H101  H  HCH2  0   0.264  -1.8147   1.1907   0.4062
 GHE  H102  H  HCH2  0   0.270  -1.8026   1.2399  -1.3354
 GHE  H15   H  HCH1  0   0.284  -5.7930  -0.4401  -1.3823
 GHE  H141  H  HCH2  0   0.270  -7.5120   0.9719  -0.5131
 GHE  H142  H  HCH2  0   0.253  -6.6998   1.1566   1.0417
 GHE  H131  H  HCH2  0   0.247  -5.8814   2.4445  -1.5958
 GHE  H132  H  HCH2  0   0.261  -6.1349   3.2507  -0.0468
 GHE  H121  H  HCH2  0   0.245  -4.1181   2.2867   0.8846
 GHE  H122  H  HCH2  0   0.261  -3.6283   2.5284  -0.7954
 GHE  H17   H  HOH1  0   0.482  -6.6536  -2.7868   0.8993

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
 GHE  C1   O1    single  1.325  0.020  1.325
 GHE  C1   O2    double  1.204  0.020  1.204
 GHE  C1   C2    single  1.514  0.020  1.514
 GHE  C2   C3    single  1.538  0.020  1.538
 GHE  C2   N1    single  1.447  0.020  1.447
 GHE  C3   C4    single  1.524  0.020  1.524
 GHE  C4   C5    single  1.522  0.020  1.522
 GHE  C5   N1    single  1.458  0.020  1.458
 GHE  N1   C6    single  1.345  0.020  1.345
 GHE  C6   O6    double  1.226  0.020  1.226
 GHE  C6   C7    single  1.511  0.020  1.511
 GHE  C7   C8    single  1.521  0.020  1.521
 GHE  C8   C9    single  1.524  0.020  1.524
 GHE  C9   C10   single  1.521  0.020  1.521
 GHE  C10  C11   single  1.511  0.020  1.511
 GHE  C11  O11   double  1.226  0.020  1.226
 GHE  C11  N2    single  1.345  0.020  1.345
 GHE  N2   C12   single  1.458  0.020  1.458
 GHE  N2   C15   single  1.448  0.020  1.448
 GHE  C12  C13   single  1.522  0.020  1.522
 GHE  C13  C14   single  1.524  0.020  1.524
 GHE  C14  C15   single  1.538  0.020  1.538
 GHE  C15  C16   single  1.514  0.020  1.514
 GHE  C16  O16   double  1.204  0.020  1.204
 GHE  C16  O17   single  1.325  0.020  1.325
 GHE  O1   H1    single  0.850  0.020  0.980
 GHE  C2   H2    single  0.970  0.020  1.090
 GHE  C3   H31C  single  0.970  0.020  1.090
 GHE  C3   H32C  single  0.970  0.020  1.090
 GHE  C4   H41C  single  0.970  0.020  1.090
 GHE  C4   H42C  single  0.970  0.020  1.090
 GHE  C5   H51C  single  0.970  0.020  1.090
 GHE  C5   H52C  single  0.970  0.020  1.090
 GHE  C7   H71C  single  0.970  0.020  1.090
 GHE  C7   H72C  single  0.970  0.020  1.090
 GHE  C8   H81C  single  0.970  0.020  1.090
 GHE  C8   H82C  single  0.970  0.020  1.090
 GHE  C9   H91C  single  0.970  0.020  1.090
 GHE  C9   H92C  single  0.970  0.020  1.090
 GHE  C10  H101  single  0.970  0.020  1.090
 GHE  C10  H102  single  0.970  0.020  1.090
 GHE  C12  H121  single  0.970  0.020  1.090
 GHE  C12  H122  single  0.970  0.020  1.090
 GHE  C15  H15   single  0.970  0.020  1.090
 GHE  C13  H131  single  0.970  0.020  1.090
 GHE  C13  H132  single  0.970  0.020  1.090
 GHE  C14  H141  single  0.970  0.020  1.090
 GHE  C14  H142  single  0.970  0.020  1.090
 GHE  O17  H17   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
 GHE  C6    N1   C5    127.03  3.000
 GHE  C6    N1   C2    119.94  3.000
 GHE  C5    N1   C2    112.93  3.000
 GHE  H2    C2   C1    109.58  3.000
 GHE  H2    C2   C3    110.42  3.000
 GHE  C1    C2   C3    110.74  3.000
 GHE  H2    C2   N1    110.83  3.000
 GHE  C3    C2   N1    103.56  3.000
 GHE  C1    C2   N1    111.60  3.000
 GHE  H32C  C3   H31C  107.97  3.000
 GHE  H32C  C3   C4    109.78  3.000
 GHE  H31C  C3   C4    113.67  3.000
 GHE  H32C  C3   C2    110.53  3.000
 GHE  H31C  C3   C2    111.79  3.000
 GHE  C4    C3   C2    103.07  3.000
 GHE  H42C  C4   H41C  108.05  3.000
 GHE  H42C  C4   C5    112.37  3.000
 GHE  H41C  C4   C5    110.08  3.000
 GHE  H42C  C4   C3    112.78  3.000
 GHE  H41C  C4   C3    110.40  3.000
 GHE  C5    C4   C3    103.12  3.000
 GHE  H52C  C5   H51C  108.00  3.000
 GHE  H52C  C5   C4    112.28  3.000
 GHE  H51C  C5   C4    111.42  3.000
 GHE  H52C  C5   N1    111.46  3.000
 GHE  H51C  C5   N1    110.98  3.000
 GHE  C4    C5   N1    102.69  3.000
 GHE  O1    C1   O2    124.03  3.000
 GHE  O2    C1   C2    124.51  3.000
 GHE  O1    C1   C2    111.34  3.000
 GHE  H1    O1   C1    110.16  3.000
 GHE  C7    C6   O6    122.83  3.000
 GHE  C7    C6   N1    116.56  3.000
 GHE  O6    C6   N1    120.61  3.000
 GHE  H72C  C7   H71C  105.39  3.000
 GHE  H72C  C7   C8    109.89  3.000
 GHE  H71C  C7   C8    109.78  3.000
 GHE  H72C  C7   C6    109.37  3.000
 GHE  H71C  C7   C6    108.33  3.000
 GHE  C8    C7   C6    113.74  3.000
 GHE  H82C  C8   H81C  106.42  3.000
 GHE  H82C  C8   C9    109.49  3.000
 GHE  H81C  C8   C9    109.71  3.000
 GHE  H82C  C8   C7    109.99  3.000
 GHE  H81C  C8   C7    109.77  3.000
 GHE  C9    C8   C7    111.34  3.000
 GHE  H92C  C9   H91C  106.40  3.000
 GHE  H92C  C9   C10   109.74  3.000
 GHE  H91C  C9   C10   109.96  3.000
 GHE  H92C  C9   C8    109.68  3.000
 GHE  H91C  C9   C8    109.45  3.000
 GHE  C10   C9   C8    111.48  3.000
 GHE  H102  C10  H101  105.40  3.000
 GHE  H102  C10  C11   108.39  3.000
 GHE  H101  C10  C11   109.37  3.000
 GHE  H102  C10  C9    109.79  3.000
 GHE  H101  C10  C9    109.94  3.000
 GHE  C11   C10  C9    113.63  3.000
 GHE  N2    C11  O11   120.61  3.000
 GHE  N2    C11  C10   116.60  3.000
 GHE  O11   C11  C10   122.79  3.000
 GHE  C12   N2   C15   112.93  3.000
 GHE  C15   N2   C11   119.93  3.000
 GHE  C12   N2   C11   127.02  3.000
 GHE  H15   C15  C16   109.58  3.000
 GHE  H15   C15  C14   110.43  3.000
 GHE  C16   C15  C14   110.75  3.000
 GHE  H15   C15  N2    110.81  3.000
 GHE  C16   C15  N2    111.61  3.000
 GHE  C14   C15  N2    103.55  3.000
 GHE  H142  C14  H141  107.98  3.000
 GHE  H142  C14  C13   109.79  3.000
 GHE  H141  C14  C13   113.66  3.000
 GHE  H142  C14  C15   110.52  3.000
 GHE  H141  C14  C15   111.79  3.000
 GHE  C13   C14  C15   103.06  3.000
 GHE  H132  C13  H131  108.04  3.000
 GHE  H132  C13  C12   112.38  3.000
 GHE  H131  C13  C12   110.07  3.000
 GHE  H132  C13  C14   112.79  3.000
 GHE  H131  C13  C14   110.38  3.000
 GHE  C12   C13  C14   103.13  3.000
 GHE  H122  C12  H121  108.00  3.000
 GHE  H122  C12  C13   112.26  3.000
 GHE  H121  C12  C13   111.44  3.000
 GHE  H122  C12  N2    111.46  3.000
 GHE  H121  C12  N2    110.98  3.000
 GHE  C13   C12  N2    102.70  3.000
 GHE  O17   C16  O16   124.02  3.000
 GHE  O17   C16  C15   111.38  3.000
 GHE  O16   C16  C15   124.47  3.000
 GHE  H17   O17  C16   110.14  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
 GHE  CONST_01  O6   C6   N1   C2     0.00   0.0  0
 GHE  CONST_02  C7   C6   N1   C2   180.00   0.0  0
 GHE  CONST_03  O6   C6   N1   C5   180.00   0.0  0
 GHE  CONST_04  C7   C6   N1   C5     0.00   0.0  0
 GHE  CONST_05  C12  N2   C11  C10    0.00   0.0  0
 GHE  CONST_06  C15  N2   C11  C10  180.00   0.0  0
 GHE  CONST_07  C12  N2   C11  O11  180.00   0.0  0
 GHE  CONST_08  C15  N2   C11  O11    0.00   0.0  0
 GHE  CONST_09  H1   O1   C1   C2   180.00   0.0  0
 GHE  CONST_10  H17  O17  C16  C15  180.00   0.0  0
 GHE  Var_01    C3   C4   C5   N1    33.74  30.0  1
 GHE  Var_02    C5   C4   C3   C2   -38.06  30.0  1
 GHE  Var_03    C14  C13  C12  N2    33.67  30.0  1
 GHE  Var_04    C13  C12  N2   C15  -17.01  30.0  1
 GHE  Var_05    C12  C13  C14  C15  -38.09  30.0  1
 GHE  Var_06    C8   C7   C6   N1   171.33  30.0  3
 GHE  Var_07    N2   C11  C10  C9   171.44  30.0  3
 GHE  Var_08    C9   C8   C7   C6   178.32  30.0  3
 GHE  Var_09    C10  C9   C8   C7   178.78  30.0  3
 GHE  Var_10    C11  C10  C9   C8   178.15  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
 GHE  chir_01  C2   C1  C3   N1   negativ
 GHE  chir_02  C15  N2  C14  C16  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
 GHE  plan-1  N1   0.020
 GHE  plan-1  C2   0.020
 GHE  plan-1  C5   0.020
 GHE  plan-1  C6   0.020
 GHE  plan-1  O6   0.020
 GHE  plan-1  C7   0.020
 GHE  plan-2  C10  0.020
 GHE  plan-2  C11  0.020
 GHE  plan-2  O11  0.020
 GHE  plan-2  N2   0.020
 GHE  plan-2  C15  0.020
 GHE  plan-2  C12  0.020
 GHE  plan-3  C2   0.020
 GHE  plan-3  C1   0.020
 GHE  plan-3  O2   0.020
 GHE  plan-3  O1   0.020
 GHE  plan-3  H1   0.020
 GHE  plan-4  C15  0.020
 GHE  plan-4  C16  0.020
 GHE  plan-4  O16  0.020
 GHE  plan-4  O17  0.020
 GHE  plan-4  H17  0.020

