# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:44:43 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (4aS,7aS)-1,4-bis(3-hydroxybenzyl)hexahydro-1H-pyrrolo[3,4-b]pyrazine-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(CN2[C@H]3CNC[C@@H]3N(Cc4cccc(O)c4)C(=O)C2=O)c1
#
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
 NI7  NI7  (4aS,7aS)-1,4-bis(3-hydroxybenzyl)hexahydro-1H-pyrrolo[3,4-b]pyrazine-2,3-dione  ligand  48  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NI7
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
 NI7  C1    C  CR16  0  -0.088   0.6913  -1.1994   0.2566
 NI7  C2    C  CR16  0  -0.076  -0.8005  -1.0941   0.0375
 NI7  N3    N  NR6   0  -0.479  -1.0895  -0.0441  -0.9124
 NI7  C5    C  CH2   0  -0.396  -2.2758  -0.1416  -1.7430
 NI7  C6    C  CR6   0   0.116  -3.5564  -0.1744  -0.9434
 NI7  C7    C  CR16  0  -0.375  -3.7871   0.7566   0.0622
 NI7  C8    C  CR6   0   0.373  -4.9823   0.7406   0.7753
 NI7  O9    O  OH1   0  -0.632  -5.1455   1.6688   1.7384
 NI7  C10   C  CR16  0  -0.393  -5.9558  -0.2115   0.4779
 NI7  C11   C  CR16  0  -0.230  -5.7205  -1.1360  -0.5272
 NI7  C12   C  CR16  0  -0.339  -4.5269  -1.1272  -1.2357
 NI7  C13   C  CR6   0   0.460  -0.4099   1.1114  -0.7945
 NI7  O14   O  O     0  -0.458  -0.6197   2.1100  -1.4534
 NI7  C15   C  CR6   0   0.460   0.7197   1.1904   0.2708
 NI7  O16   O  O     0  -0.455   1.1238   2.2977   0.5626
 NI7  N17   N  NR6   0  -0.471   1.1963   0.0441   0.7941
 NI7  C18   C  CH2   0  -0.441   2.4248   0.0672   1.5820
 NI7  C19   C  CR6   0   0.149   3.6614   0.0484   0.7172
 NI7  C20   C  CR16  0  -0.382   4.2479   1.2424   0.3148
 NI7  C21   C  CR6   0   0.368   5.3715   1.2343  -0.5083
 NI7  O22   O  OH1   0  -0.633   5.8916   2.4260  -0.8642
 NI7  C23   C  CR16  0  -0.391   5.9138   0.0228  -0.9295
 NI7  C24   C  CR16  0  -0.230   5.3299  -1.1661  -0.5191
 NI7  C25   C  CR16  0  -0.333   4.2108  -1.1620   0.3004
 NI7  C26   C  CH2   0  -0.297  -1.1190  -2.5315  -0.3458
 NI7  N27   N  NH1   0  -0.609  -0.2686  -3.3157   0.5554
 NI7  C28   C  CH2   0  -0.294   0.7608  -2.4417   1.1368
 NI7  H1    H  HCR6  0   0.274   1.1758  -1.4202  -0.7039
 NI7  H2    H  HCR6  0   0.269  -1.2857  -0.8762   0.9985
 NI7  H5    H  HCH2  0   0.294  -2.2805   0.7061  -2.4270
 NI7  H5A   H  HCH2  0   0.280  -2.2042  -1.0394  -2.3590
 NI7  H7    H  HCR6  0   0.257  -3.0472   1.5123   0.2988
 NI7  HO9   H  HOH1  0   0.475  -6.0147   1.5825   2.1452
 NI7  H10   H  HCR6  0   0.272  -6.8895  -0.2318   1.0282
 NI7  H11   H  HCR6  0   0.261  -6.4774  -1.8755  -0.7544
 NI7  H12   H  HCR6  0   0.255  -4.3521  -1.8589  -2.0147
 NI7  H18   H  HCH2  0   0.289   2.4108   0.9508   2.2172
 NI7  H18A  H  HCH2  0   0.287   2.4136  -0.7979   2.2437
 NI7  H20   H  HCR6  0   0.261   3.8363   2.1892   0.6406
 NI7  HO22  H  HOH1  0   0.474   6.6598   2.3015  -1.4323
 NI7  H23   H  HCR6  0   0.272   6.7888   0.0070  -1.5691
 NI7  H24   H  HCR6  0   0.261   5.7600  -2.1066  -0.8386
 NI7  H25   H  HCR6  0   0.254   3.7765  -2.1003   0.6221
 NI7  H26   H  HCH2  0   0.260  -2.1696  -2.7873  -0.2163
 NI7  H26A  H  HCH2  0   0.230  -0.8559  -2.7146  -1.3925
 NI7  HN27  H  HNH1  0   0.367  -0.8219  -3.7327   1.2880
 NI7  H28   H  HCH2  0   0.247   1.7429  -2.9175   1.1102
 NI7  H28A  H  HCH2  0   0.236   0.5466  -2.1818   2.1787

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
 NI7  C1   C2    single    1.511  0.020  1.511
 NI7  C1   N17   single    1.446  0.020  1.446
 NI7  C1   C28   single    1.524  0.020  1.524
 NI7  C2   N3    single    1.445  0.020  1.445
 NI7  C2   C26   single    1.521  0.020  1.521
 NI7  N3   C5    single    1.451  0.020  1.451
 NI7  N3   C13   single    1.346  0.020  1.346
 NI7  C5   C6    single    1.510  0.020  1.510
 NI7  C6   C7    aromatic  1.390  0.020  1.390
 NI7  C6   C12   aromatic  1.391  0.020  1.391
 NI7  C7   C8    aromatic  1.392  0.020  1.392
 NI7  C8   O9    single    1.348  0.020  1.348
 NI7  C8   C10   aromatic  1.394  0.020  1.394
 NI7  C10  C11   aromatic  1.386  0.020  1.386
 NI7  C11  C12   aromatic  1.388  0.020  1.388
 NI7  C13  O14   double    1.215  0.020  1.215
 NI7  C13  C15   single    1.555  0.020  1.555
 NI7  C15  O16   double    1.214  0.020  1.214
 NI7  C15  N17   single    1.347  0.020  1.347
 NI7  N17  C18   single    1.460  0.020  1.460
 NI7  C18  C19   single    1.509  0.020  1.509
 NI7  C19  C20   aromatic  1.390  0.020  1.390
 NI7  C19  C25   aromatic  1.393  0.020  1.393
 NI7  C20  C21   aromatic  1.393  0.020  1.393
 NI7  C21  O22   single    1.348  0.020  1.348
 NI7  C21  C23   aromatic  1.393  0.020  1.393
 NI7  C23  C24   aromatic  1.387  0.020  1.387
 NI7  C24  C25   aromatic  1.387  0.020  1.387
 NI7  C26  N27   single    1.466  0.020  1.466
 NI7  N27  C28   single    1.470  0.020  1.470
 NI7  C1   H1    single    0.970  0.020  1.090
 NI7  C2   H2    single    0.970  0.020  1.090
 NI7  C5   H5    single    0.970  0.020  1.090
 NI7  C5   H5A   single    0.970  0.020  1.090
 NI7  C7   H7    single    0.930  0.020  1.080
 NI7  O9   HO9   single    0.850  0.020  0.980
 NI7  C10  H10   single    0.930  0.020  1.080
 NI7  C11  H11   single    0.930  0.020  1.080
 NI7  C12  H12   single    0.930  0.020  1.080
 NI7  C18  H18   single    0.970  0.020  1.090
 NI7  C18  H18A  single    0.970  0.020  1.090
 NI7  C20  H20   single    0.930  0.020  1.080
 NI7  O22  HO22  single    0.850  0.020  0.980
 NI7  C23  H23   single    0.930  0.020  1.080
 NI7  C24  H24   single    0.930  0.020  1.080
 NI7  C25  H25   single    0.930  0.020  1.080
 NI7  C26  H26   single    0.970  0.020  1.090
 NI7  C26  H26A  single    0.970  0.020  1.090
 NI7  N27  HN27  single    0.890  0.020  1.040
 NI7  C28  H28   single    0.970  0.020  1.090
 NI7  C28  H28A  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
 NI7  H1    C1   C28  108.73  3.000
 NI7  H1    C1   N17  110.12  3.000
 NI7  C28   C1   N17  118.06  3.000
 NI7  H1    C1   C2   108.82  3.000
 NI7  C28   C1   C2   100.69  3.000
 NI7  N17   C1   C2   109.80  3.000
 NI7  H2    C2   C26  108.38  3.000
 NI7  H2    C2   N3   110.04  3.000
 NI7  C26   C2   N3   118.62  3.000
 NI7  H2    C2   C1   108.84  3.000
 NI7  C26   C2   C1   100.21  3.000
 NI7  N3    C2   C1   110.07  3.000
 NI7  C13   N3   C5   121.37  3.000
 NI7  C13   N3   C2   117.73  3.000
 NI7  C5    N3   C2   119.39  3.000
 NI7  H5A   C5   H5   106.62  3.000
 NI7  H5A   C5   C6   109.67  3.000
 NI7  H5    C5   C6   110.22  3.000
 NI7  H5A   C5   N3   108.95  3.000
 NI7  H5    C5   N3   108.10  3.000
 NI7  C6    C5   N3   113.05  3.000
 NI7  C12   C6   C7   119.68  3.000
 NI7  C12   C6   C5   119.69  3.000
 NI7  C7    C6   C5   120.62  3.000
 NI7  H7    C7   C8   118.84  3.000
 NI7  H7    C7   C6   120.79  3.000
 NI7  C8    C7   C6   120.37  3.000
 NI7  C10   C8   O9   122.58  3.000
 NI7  C10   C8   C7   119.89  3.000
 NI7  O9    C8   C7   117.53  3.000
 NI7  HO9   O9   C8   110.44  3.000
 NI7  H10   C10  C11  120.13  3.000
 NI7  H10   C10  C8   120.40  3.000
 NI7  C11   C10  C8   119.47  3.000
 NI7  H11   C11  C12  119.90  3.000
 NI7  H11   C11  C10  119.30  3.000
 NI7  C12   C11  C10  120.80  3.000
 NI7  H12   C12  C11  120.11  3.000
 NI7  H12   C12  C6   120.09  3.000
 NI7  C11   C12  C6   119.80  3.000
 NI7  C15   C13  O14  117.09  3.000
 NI7  C15   C13  N3   118.07  3.000
 NI7  O14   C13  N3   124.83  3.000
 NI7  N17   C15  O16  124.39  3.000
 NI7  N17   C15  C13  118.68  3.000
 NI7  O16   C15  C13  116.92  3.000
 NI7  C18   N17  C15  119.60  3.000
 NI7  C18   N17  C1   120.55  3.000
 NI7  C15   N17  C1   117.64  3.000
 NI7  H18A  C18  H18  106.87  3.000
 NI7  H18A  C18  C19  110.29  3.000
 NI7  H18   C18  C19  110.80  3.000
 NI7  H18A  C18  N17  107.86  3.000
 NI7  H18   C18  N17  108.48  3.000
 NI7  C19   C18  N17  112.34  3.000
 NI7  C25   C19  C20  119.57  3.000
 NI7  C25   C19  C18  120.36  3.000
 NI7  C20   C19  C18  120.07  3.000
 NI7  H20   C20  C21  119.31  3.000
 NI7  H20   C20  C19  120.25  3.000
 NI7  C21   C20  C19  120.43  3.000
 NI7  C23   C21  O22  122.61  3.000
 NI7  C23   C21  C20  119.86  3.000
 NI7  O22   C21  C20  117.52  3.000
 NI7  HO22  O22  C21  110.43  3.000
 NI7  H23   C23  C24  120.14  3.000
 NI7  H23   C23  C21  120.36  3.000
 NI7  C24   C23  C21  119.50  3.000
 NI7  H24   C24  C25  119.85  3.000
 NI7  H24   C24  C23  119.36  3.000
 NI7  C25   C24  C23  120.80  3.000
 NI7  H25   C25  C24  119.77  3.000
 NI7  H25   C25  C19  120.39  3.000
 NI7  C24   C25  C19  119.84  3.000
 NI7  H26A  C26  H26  107.83  3.000
 NI7  H26A  C26  N27  111.03  3.000
 NI7  H26   C26  N27  111.15  3.000
 NI7  H26A  C26  C2   110.40  3.000
 NI7  H26   C26  C2   113.19  3.000
 NI7  N27   C26  C2   103.24  3.000
 NI7  HN27  N27  C28  110.05  3.000
 NI7  HN27  N27  C26  110.45  3.000
 NI7  C28   N27  C26  109.34  3.000
 NI7  H28A  C28  H28  107.61  3.000
 NI7  H28A  C28  N27  112.36  3.000
 NI7  H28   C28  N27  111.17  3.000
 NI7  H28A  C28  C1   110.31  3.000
 NI7  H28   C28  C1   112.48  3.000
 NI7  N27   C28  C1   102.96  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
 NI7  CONST_01  C10  C8   C7   C6     0.00   0.0  0
 NI7  CONST_02  C10  C11  C12  C6     0.00   0.0  0
 NI7  CONST_03  C11  C12  C6   C7     0.00   0.0  0
 NI7  CONST_04  C11  C10  C8   C7     0.00   0.0  0
 NI7  CONST_05  C12  C6   C7   C8     0.00   0.0  0
 NI7  CONST_06  C12  C11  C10  C8     0.00   0.0  0
 NI7  CONST_07  C23  C21  C20  C19    0.00   0.0  0
 NI7  CONST_08  C23  C24  C25  C19    0.00   0.0  0
 NI7  CONST_09  C24  C25  C19  C20    0.00   0.0  0
 NI7  CONST_10  C24  C23  C21  C20    0.00   0.0  0
 NI7  CONST_11  C25  C19  C20  C21    0.00   0.0  0
 NI7  CONST_12  C25  C24  C23  C21    0.00   0.0  0
 NI7  CONST_13  C13  C15  N17  C1     0.00   0.0  0
 NI7  CONST_14  C15  C13  N3   C2     0.00   0.0  0
 NI7  CONST_15  C8   C7   C6   C5   180.00   0.0  0
 NI7  CONST_16  C11  C12  C6   C5   180.00   0.0  0
 NI7  CONST_17  O9   C8   C7   C6   180.00   0.0  0
 NI7  CONST_18  C11  C10  C8   O9   180.00   0.0  0
 NI7  CONST_19  C21  C20  C19  C18  180.00   0.0  0
 NI7  CONST_20  C24  C25  C19  C18  180.00   0.0  0
 NI7  CONST_21  O22  C21  C20  C19  180.00   0.0  0
 NI7  CONST_22  C24  C23  C21  O22  180.00   0.0  0
 NI7  CONST_23  O16  C15  N17  C1   180.00   0.0  0
 NI7  CONST_24  O14  C13  N3   C2   180.00   0.0  0
 NI7  CONST_25  C15  C13  N3   C5   180.00   0.0  0
 NI7  CONST_26  C18  N17  C15  C13  180.00   0.0  0
 NI7  CONST_27  H11  C11  C12  C6   180.00   0.0  0
 NI7  CONST_28  H12  C12  C6   C7   180.00   0.0  0
 NI7  CONST_29  H10  C10  C8   C7   180.00   0.0  0
 NI7  CONST_30  H7   C7   C8   C10  180.00   0.0  0
 NI7  CONST_31  H24  C24  C25  C19  180.00   0.0  0
 NI7  CONST_32  H25  C25  C19  C20  180.00   0.0  0
 NI7  CONST_33  H23  C23  C21  C20  180.00   0.0  0
 NI7  CONST_34  H20  C20  C21  C23  180.00   0.0  0
 NI7  CONST_35  O14  C13  N3   C5     0.00   0.0  0
 NI7  CONST_36  C18  N17  C15  O16    0.00   0.0  0
 NI7  Var_01    C26  N27  C28  C1   -14.17  30.0  1
 NI7  Var_02    C28  N27  C26  C2   -15.82  30.0  1
 NI7  Var_03    N17  C15  C13  N3    16.09  30.0  1
 NI7  Var_04    C19  C18  N17  C1    80.55  30.0  3
 NI7  Var_05    C6   C5   N3   C2    61.18  30.0  3
 NI7  Var_06    C7   C6   C5   N3    48.67  30.0  2
 NI7  Var_07    C20  C19  C18  N17   91.58  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
 NI7  chir_01  C1  C2  N17  C28  negativ
 NI7  chir_02  C2  N3  C1   C26  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
 NI7  plan-1  C5   0.020
 NI7  plan-1  C6   0.020
 NI7  plan-1  C7   0.020
 NI7  plan-1  C8   0.020
 NI7  plan-1  O9   0.020
 NI7  plan-1  C10  0.020
 NI7  plan-1  C11  0.020
 NI7  plan-1  C12  0.020
 NI7  plan-1  H7   0.020
 NI7  plan-1  H10  0.020
 NI7  plan-1  H11  0.020
 NI7  plan-1  H12  0.020
 NI7  plan-2  C18  0.020
 NI7  plan-2  C19  0.020
 NI7  plan-2  C20  0.020
 NI7  plan-2  C21  0.020
 NI7  plan-2  O22  0.020
 NI7  plan-2  C23  0.020
 NI7  plan-2  C24  0.020
 NI7  plan-2  C25  0.020
 NI7  plan-2  H20  0.020
 NI7  plan-2  H23  0.020
 NI7  plan-2  H24  0.020
 NI7  plan-2  H25  0.020
 NI7  plan-3  C2   0.020
 NI7  plan-3  N3   0.020
 NI7  plan-3  C5   0.020
 NI7  plan-3  C13  0.020
 NI7  plan-3  O14  0.020
 NI7  plan-3  C15  0.020
 NI7  plan-4  C1   0.020
 NI7  plan-4  C13  0.020
 NI7  plan-4  C15  0.020
 NI7  plan-4  O16  0.020
 NI7  plan-4  N17  0.020
 NI7  plan-4  C18  0.020

