# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:34:45 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (4aS,7aS)-1,4-bis[3-(hydroxymethyl)benzyl]hexahydro-1H-pyrrolo[3,4-b]pyrazine-2,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1cccc(CN2[C@H]3CNC[C@@H]3N(Cc4cccc(CO)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
 NI8  NI8  (4aS,7aS)-1,4-bis[3-(hydroxymethyl)benzyl]hexahydro-1H-pyrrolo[3,4-b]pyrazine-2,3-dione  ligand  54  29  .  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_NI8
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
 NI8  C1    C  CR16  0  -0.088   0.7276  -1.0054   0.1887
 NI8  C2    C  CR16  0  -0.077  -0.7415  -0.9926  -0.1571
 NI8  N3    N  NR6   0  -0.477  -1.0511   0.1715  -0.9545
 NI8  C5    C  CH2   0  -0.400  -2.1798   0.1226  -1.8680
 NI8  C6    C  CR6   0   0.126  -3.4934  -0.0971  -1.1574
 NI8  C7    C  CR16  0  -0.351  -3.8595   0.6857  -0.0643
 NI8  C8    C  CR6   0   0.097  -5.0736   0.5003   0.5834
 NI8  C9    C  CH2   0  -0.211  -5.4227   1.3271   1.7898
 NI8  C10   C  CR16  0  -0.300  -5.9487  -0.4781   0.1124
 NI8  C11   C  CR16  0  -0.228  -5.5979  -1.2577  -0.9773
 NI8  C12   C  CR16  0  -0.325  -4.3719  -1.0739  -1.6065
 NI8  C13   C  CR6   0   0.457  -0.4988   1.3460  -0.5955
 NI8  O14   O  O     0  -0.458  -0.7608   2.4175  -1.1034
 NI8  C15   C  CR6   0   0.457   0.5402   1.3492   0.5621
 NI8  O16   O  O     0  -0.459   0.8273   2.4282   1.0400
 NI8  N17   N  NR6   0  -0.475   1.0717   0.1738   0.9510
 NI8  C18   C  CH2   0  -0.411   2.2186   0.1358   1.8451
 NI8  C19   C  CR6   0   0.135   3.5155  -0.0946   1.1082
 NI8  C20   C  CR16  0  -0.351   3.9191   0.7680   0.0910
 NI8  C21   C  CR6   0   0.087   5.1110   0.5706  -0.5941
 NI8  C22   C  CH2   0  -0.202   5.4904   1.4881  -1.7238
 NI8  C23   C  CR16  0  -0.302   5.9240  -0.5050  -0.2382
 NI8  C24   C  CR16  0  -0.228   5.5370  -1.3629   0.7783
 NI8  C25   C  CR16  0  -0.325   4.3343  -1.1640   1.4459
 NI8  C26   C  CH2   0  -0.302  -0.8715  -2.3714  -0.7882
 NI8  N27   N  NH1   0  -0.608  -0.0521  -3.2177   0.0858
 NI8  C28   C  CH2   0  -0.282   0.8549  -2.3631   0.8711
 NI8  O29   O  OH1   0  -0.667   6.8736   1.7474  -1.6819
 NI8  O30   O  OH1   0  -0.667  -6.7358   1.8211   1.6569
 NI8  H1    H  HCR6  0   0.273   1.3107  -1.0273  -0.7419
 NI8  H2    H  HCR6  0   0.269  -1.3313  -0.9843   0.7698
 NI8  H5    H  HCH2  0   0.293  -2.2000   1.0537  -2.4329
 NI8  H5A   H  HCH2  0   0.281  -2.0153  -0.6772  -2.5919
 NI8  H7    H  HCR6  0   0.249  -3.1947   1.4636   0.2960
 NI8  H9    H  HCH2  0   0.220  -5.3261   0.7008   2.6857
 NI8  H9A   H  HCH2  0   0.211  -4.6892   2.1365   1.8946
 NI8  H10   H  HCR6  0   0.252  -6.9027  -0.6366   0.5990
 NI8  H11   H  HCR6  0   0.256  -6.2772  -2.0193  -1.3381
 NI8  H12   H  HCR6  0   0.257  -4.1018  -1.6923  -2.4545
 NI8  H18   H  HCH2  0   0.293   2.2491   1.0748   2.3956
 NI8  H18A  H  HCH2  0   0.281   2.0653  -0.6537   2.5819
 NI8  H20   H  HCR6  0   0.249   3.3026   1.6213  -0.1715
 NI8  H22   H  HCH2  0   0.222   5.2057   1.0126  -2.6713
 NI8  H22A  H  HCH2  0   0.211   4.8995   2.4105  -1.6518
 NI8  H23   H  HCR6  0   0.252   6.8603  -0.6759  -0.7532
 NI8  H24   H  HCR6  0   0.256   6.1718  -2.1960   1.0518
 NI8  H25   H  HCR6  0   0.256   4.0363  -1.8438   2.2356
 NI8  H26   H  HCH2  0   0.260  -1.8979  -2.7337  -0.8293
 NI8  H26A  H  HCH2  0   0.231  -0.4778  -2.3631  -1.8098
 NI8  HN27  H  HNH1  0   0.366  -0.6469  -3.7444   0.7075
 NI8  H28   H  HCH2  0   0.243   1.8803  -2.7361   0.8455
 NI8  H28A  H  HCH2  0   0.238   0.5486  -2.2964   1.9189
 NI8  HO29  H  HOH1  0   0.459   7.1336   2.1207  -2.5287
 NI8  HO30  H  HOH1  0   0.458  -7.0226   2.1407   2.5171

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
 NI8  C1   C2    single    1.509  0.020  1.509
 NI8  C1   N17   single    1.446  0.020  1.446
 NI8  C1   C28   single    1.525  0.020  1.525
 NI8  C2   N3    single    1.445  0.020  1.445
 NI8  C2   C26   single    1.522  0.020  1.522
 NI8  N3   C5    single    1.453  0.020  1.453
 NI8  N3   C13   single    1.347  0.020  1.347
 NI8  C5   C6    single    1.510  0.020  1.510
 NI8  C6   C7    aromatic  1.393  0.020  1.393
 NI8  C6   C12   aromatic  1.388  0.020  1.388
 NI8  C7   C8    aromatic  1.389  0.020  1.389
 NI8  C8   C9    single    1.504  0.020  1.504
 NI8  C8   C10   aromatic  1.395  0.020  1.395
 NI8  C9   O30   single    1.409  0.020  1.409
 NI8  C10  C11   aromatic  1.385  0.020  1.385
 NI8  C11  C12   aromatic  1.390  0.020  1.390
 NI8  C13  O14   double    1.214  0.020  1.214
 NI8  C13  C15   single    1.555  0.020  1.555
 NI8  C15  O16   double    1.215  0.020  1.215
 NI8  C15  N17   single    1.347  0.020  1.347
 NI8  N17  C18   single    1.455  0.020  1.455
 NI8  C18  C19   single    1.509  0.020  1.509
 NI8  C19  C20   aromatic  1.393  0.020  1.393
 NI8  C19  C25   aromatic  1.389  0.020  1.389
 NI8  C20  C21   aromatic  1.389  0.020  1.389
 NI8  C21  C22   single    1.504  0.020  1.504
 NI8  C21  C23   aromatic  1.394  0.020  1.394
 NI8  C22  O29   single    1.408  0.020  1.408
 NI8  C23  C24   aromatic  1.385  0.020  1.385
 NI8  C24  C25   aromatic  1.390  0.020  1.390
 NI8  C26  N27   single    1.467  0.020  1.467
 NI8  N27  C28   single    1.473  0.020  1.473
 NI8  C1   H1    single    0.970  0.020  1.090
 NI8  C2   H2    single    0.970  0.020  1.090
 NI8  C5   H5    single    0.970  0.020  1.090
 NI8  C5   H5A   single    0.970  0.020  1.090
 NI8  C7   H7    single    0.930  0.020  1.080
 NI8  C9   H9    single    0.970  0.020  1.090
 NI8  C9   H9A   single    0.970  0.020  1.090
 NI8  C10  H10   single    0.930  0.020  1.080
 NI8  C11  H11   single    0.930  0.020  1.080
 NI8  C12  H12   single    0.930  0.020  1.080
 NI8  C18  H18   single    0.970  0.020  1.090
 NI8  C18  H18A  single    0.970  0.020  1.090
 NI8  C20  H20   single    0.930  0.020  1.080
 NI8  C22  H22   single    0.970  0.020  1.090
 NI8  C22  H22A  single    0.970  0.020  1.090
 NI8  C23  H23   single    0.930  0.020  1.080
 NI8  C24  H24   single    0.930  0.020  1.080
 NI8  C25  H25   single    0.930  0.020  1.080
 NI8  C26  H26   single    0.970  0.020  1.090
 NI8  C26  H26A  single    0.970  0.020  1.090
 NI8  N27  HN27  single    0.890  0.020  1.040
 NI8  C28  H28   single    0.970  0.020  1.090
 NI8  C28  H28A  single    0.970  0.020  1.090
 NI8  O29  HO29  single    0.850  0.020  0.980
 NI8  O30  HO30  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
 NI8  H1    C1   C28  108.49  3.000
 NI8  H1    C1   N17  109.67  3.000
 NI8  C28   C1   N17  118.06  3.000
 NI8  H1    C1   C2   108.83  3.000
 NI8  C28   C1   C2   101.03  3.000
 NI8  N17   C1   C2   110.22  3.000
 NI8  H2    C2   C26  108.11  3.000
 NI8  H2    C2   N3   110.16  3.000
 NI8  C26   C2   N3   118.87  3.000
 NI8  H2    C2   C1   109.23  3.000
 NI8  C26   C2   C1    99.81  3.000
 NI8  N3    C2   C1   109.99  3.000
 NI8  C13   N3   C5   121.04  3.000
 NI8  C13   N3   C2   117.89  3.000
 NI8  C5    N3   C2   119.11  3.000
 NI8  H5A   C5   H5   106.57  3.000
 NI8  H5A   C5   C6   109.68  3.000
 NI8  H5    C5   C6   110.64  3.000
 NI8  H5A   C5   N3   108.94  3.000
 NI8  H5    C5   N3   108.16  3.000
 NI8  C6    C5   N3   112.64  3.000
 NI8  C12   C6   C7   118.87  3.000
 NI8  C12   C6   C5   120.05  3.000
 NI8  C7    C6   C5   121.07  3.000
 NI8  H7    C7   C8   118.46  3.000
 NI8  H7    C7   C6   120.16  3.000
 NI8  C8    C7   C6   121.38  3.000
 NI8  C10   C8   C9   120.74  3.000
 NI8  C10   C8   C7   119.00  3.000
 NI8  C9    C8   C7   120.25  3.000
 NI8  H9A   C9   H9   106.51  3.000
 NI8  H9A   C9   O30  111.92  3.000
 NI8  H9    C9   O30  111.05  3.000
 NI8  H9A   C9   C8   109.09  3.000
 NI8  H9    C9   C8   108.71  3.000
 NI8  O30   C9   C8   109.47  3.000
 NI8  H10   C10  C11  119.63  3.000
 NI8  H10   C10  C8   120.25  3.000
 NI8  C11   C10  C8   120.12  3.000
 NI8  H11   C11  C12  119.71  3.000
 NI8  H11   C11  C10  119.96  3.000
 NI8  C12   C11  C10  120.33  3.000
 NI8  H12   C12  C11  119.89  3.000
 NI8  H12   C12  C6   119.80  3.000
 NI8  C11   C12  C6   120.31  3.000
 NI8  C15   C13  O14  116.97  3.000
 NI8  C15   C13  N3   118.31  3.000
 NI8  O14   C13  N3   124.71  3.000
 NI8  N17   C15  O16  124.62  3.000
 NI8  N17   C15  C13  118.46  3.000
 NI8  O16   C15  C13  116.91  3.000
 NI8  C18   N17  C15  120.75  3.000
 NI8  C18   N17  C1   119.36  3.000
 NI8  C15   N17  C1   117.74  3.000
 NI8  H18A  C18  H18  106.65  3.000
 NI8  H18A  C18  C19  109.88  3.000
 NI8  H18   C18  C19  110.76  3.000
 NI8  H18A  C18  N17  108.86  3.000
 NI8  H18   C18  N17  108.07  3.000
 NI8  C19   C18  N17  112.42  3.000
 NI8  C25   C19  C20  118.91  3.000
 NI8  C25   C19  C18  120.36  3.000
 NI8  C20   C19  C18  120.72  3.000
 NI8  H20   C20  C21  118.69  3.000
 NI8  H20   C20  C19  119.93  3.000
 NI8  C21   C20  C19  121.38  3.000
 NI8  C23   C21  C22  121.01  3.000
 NI8  C23   C21  C20  118.95  3.000
 NI8  C22   C21  C20  120.02  3.000
 NI8  H22A  C22  H22  106.31  3.000
 NI8  H22A  C22  O29  111.85  3.000
 NI8  H22   C22  O29  111.12  3.000
 NI8  H22A  C22  C21  109.12  3.000
 NI8  H22   C22  C21  108.58  3.000
 NI8  O29   C22  C21  109.74  3.000
 NI8  H23   C23  C24  119.54  3.000
 NI8  H23   C23  C21  120.32  3.000
 NI8  C24   C23  C21  120.14  3.000
 NI8  H24   C24  C25  119.75  3.000
 NI8  H24   C24  C23  119.88  3.000
 NI8  C25   C24  C23  120.37  3.000
 NI8  H25   C25  C24  119.88  3.000
 NI8  H25   C25  C19  119.88  3.000
 NI8  C24   C25  C19  120.24  3.000
 NI8  H26A  C26  H26  107.82  3.000
 NI8  H26A  C26  N27  111.07  3.000
 NI8  H26   C26  N27  110.92  3.000
 NI8  H26A  C26  C2   110.44  3.000
 NI8  H26   C26  C2   113.42  3.000
 NI8  N27   C26  C2   103.18  3.000
 NI8  HN27  N27  C28  109.72  3.000
 NI8  HN27  N27  C26  109.82  3.000
 NI8  C28   N27  C26  109.08  3.000
 NI8  H28A  C28  H28  107.84  3.000
 NI8  H28A  C28  N27  111.94  3.000
 NI8  H28   C28  N27  111.57  3.000
 NI8  H28A  C28  C1   110.55  3.000
 NI8  H28   C28  C1   111.86  3.000
 NI8  N27   C28  C1   103.10  3.000
 NI8  HO29  O29  C22  108.12  3.000
 NI8  HO30  O30  C9   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
 NI8  CONST_01  C10  C8   C7   C6     0.00   0.0  0
 NI8  CONST_02  C10  C11  C12  C6     0.00   0.0  0
 NI8  CONST_03  C11  C12  C6   C7     0.00   0.0  0
 NI8  CONST_04  C11  C10  C8   C7     0.00   0.0  0
 NI8  CONST_05  C12  C6   C7   C8     0.00   0.0  0
 NI8  CONST_06  C12  C11  C10  C8     0.00   0.0  0
 NI8  CONST_07  C23  C21  C20  C19    0.00   0.0  0
 NI8  CONST_08  C23  C24  C25  C19    0.00   0.0  0
 NI8  CONST_09  C24  C25  C19  C20    0.00   0.0  0
 NI8  CONST_10  C24  C23  C21  C20    0.00   0.0  0
 NI8  CONST_11  C25  C19  C20  C21    0.00   0.0  0
 NI8  CONST_12  C25  C24  C23  C21    0.00   0.0  0
 NI8  CONST_13  C13  C15  N17  C1     0.00   0.0  0
 NI8  CONST_14  C15  C13  N3   C2     0.00   0.0  0
 NI8  CONST_15  C8   C7   C6   C5   180.00   0.0  0
 NI8  CONST_16  C11  C12  C6   C5   180.00   0.0  0
 NI8  CONST_17  C9   C8   C7   C6   180.00   0.0  0
 NI8  CONST_18  C11  C10  C8   C9   180.00   0.0  0
 NI8  CONST_19  C21  C20  C19  C18  180.00   0.0  0
 NI8  CONST_20  C24  C25  C19  C18  180.00   0.0  0
 NI8  CONST_21  C22  C21  C20  C19  180.00   0.0  0
 NI8  CONST_22  C24  C23  C21  C22  180.00   0.0  0
 NI8  CONST_23  O16  C15  N17  C1   180.00   0.0  0
 NI8  CONST_24  O14  C13  N3   C2   180.00   0.0  0
 NI8  CONST_25  C15  C13  N3   C5   180.00   0.0  0
 NI8  CONST_26  C18  N17  C15  C13  180.00   0.0  0
 NI8  CONST_27  H11  C11  C12  C6   180.00   0.0  0
 NI8  CONST_28  H12  C12  C6   C7   180.00   0.0  0
 NI8  CONST_29  H10  C10  C8   C7   180.00   0.0  0
 NI8  CONST_30  H7   C7   C8   C10  180.00   0.0  0
 NI8  CONST_31  H24  C24  C25  C19  180.00   0.0  0
 NI8  CONST_32  H25  C25  C19  C20  180.00   0.0  0
 NI8  CONST_33  H23  C23  C21  C20  180.00   0.0  0
 NI8  CONST_34  H20  C20  C21  C23  180.00   0.0  0
 NI8  CONST_35  O14  C13  N3   C5     0.00   0.0  0
 NI8  CONST_36  C18  N17  C15  O16    0.00   0.0  0
 NI8  Var_01    C26  N27  C28  C1   -11.79  30.0  1
 NI8  Var_02    C28  N27  C26  C2   -18.27  30.0  1
 NI8  Var_03    N17  C15  C13  N3    14.88  30.0  1
 NI8  Var_04    C19  C18  N17  C1    63.10  30.0  3
 NI8  Var_05    C6   C5   N3   C2    62.05  30.0  3
 NI8  Var_06    C7   C6   C5   N3    50.14  30.0  2
 NI8  Var_07    C20  C19  C18  N17   57.13  30.0  2
 NI8  Var_08    O30  C9   C8   C7   133.06  30.0  2
 NI8  Var_09    O29  C22  C21  C20  140.99  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
 NI8  chir_01  C1  C2  N17  C28  negativ
 NI8  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
 NI8  plan-1  C5   0.020
 NI8  plan-1  C6   0.020
 NI8  plan-1  C7   0.020
 NI8  plan-1  C8   0.020
 NI8  plan-1  C9   0.020
 NI8  plan-1  C10  0.020
 NI8  plan-1  C11  0.020
 NI8  plan-1  C12  0.020
 NI8  plan-1  H7   0.020
 NI8  plan-1  H10  0.020
 NI8  plan-1  H11  0.020
 NI8  plan-1  H12  0.020
 NI8  plan-2  C18  0.020
 NI8  plan-2  C19  0.020
 NI8  plan-2  C20  0.020
 NI8  plan-2  C21  0.020
 NI8  plan-2  C22  0.020
 NI8  plan-2  C23  0.020
 NI8  plan-2  C24  0.020
 NI8  plan-2  C25  0.020
 NI8  plan-2  H20  0.020
 NI8  plan-2  H23  0.020
 NI8  plan-2  H24  0.020
 NI8  plan-2  H25  0.020
 NI8  plan-3  C2   0.020
 NI8  plan-3  N3   0.020
 NI8  plan-3  C5   0.020
 NI8  plan-3  C13  0.020
 NI8  plan-3  O14  0.020
 NI8  plan-3  C15  0.020
 NI8  plan-4  C1   0.020
 NI8  plan-4  C13  0.020
 NI8  plan-4  C15  0.020
 NI8  plan-4  O16  0.020
 NI8  plan-4  N17  0.020
 NI8  plan-4  C18  0.020

