# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 02:07:28 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (3~{S})-3-[(2~{S})-2-azanyl-3-azanylidene-propyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@H]1CCNC1=O)C=N
#
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
 79I  79I  "3-[(2S)-2-azanyl-3-azanylidene-propyl]pyrrolidin-2-one"  ligand  24  11  .  2022-09-16  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_79I
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
 79I  C16  C  C1    0  -0.013  -17.1853  19.7885  -29.7851
 79I  C12  C  CH2   0  -0.258  -18.3748  21.9540  -24.4029
 79I  C14  C  CR5   0   0.570  -16.2285  21.3721  -25.1609
 79I  C11  C  CH2   0  -0.462  -18.5341  21.3528  -25.8004
 79I  C10  C  CR15  0  -0.437  -17.2183  20.6098  -26.0327
 79I  C8   C  CH1   0  -0.142  -17.7636  19.8088  -28.3998
 79I  C9   C  CH2   0  -0.418  -16.7626  20.5168  -27.4816
 79I  N7   N  NH2   0  -0.809  -17.9688  18.4318  -27.9741
 79I  N13  N  NR15  0  -0.630  -16.9409  22.1231  -24.3043
 79I  N17  N  N     0  -0.541  -17.6428  20.5115  -30.7138
 79I  H1   H  H     0   0.217  -16.3338  19.1101  -29.9053
 79I  H2   H  HCH2  0   0.250  -18.8923  22.9061  -24.2941
 79I  H3   H  HCH2  0   0.235  -18.7479  21.2778  -23.6281
 79I  H4   H  HCH2  0   0.256  -19.4125  20.7137  -25.8748
 79I  H5   H  HCH2  0   0.246  -18.6403  22.1519  -26.5383
 79I  H7   H  HCR5  0   0.279  -17.2808  19.6039  -25.5976
 79I  H17  H  HCH1  0   0.221  -18.6864  20.4047  -28.4370
 79I  H18  H  HCH2  0   0.241  -16.6026  21.5272  -27.8693
 79I  H19  H  HCH2  0   0.238  -15.8013  19.9980  -27.5279
 79I  H33  H  HNH2  0   0.357  -18.3523  18.4104  -27.0376
 79I  H34  H  HNR5  0   0.394  -16.5044  22.6316  -23.5506
 79I  H35  H  H     0   0.342  -17.1053  20.3779  -31.5662
 79I  H9   H  HNH2  0   0.351  -18.6718  17.9982  -28.5600
 79I  O15  O  O     0  -0.485  -15.0125  21.3037  -25.2225

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
 79I  C16  C8   single  1.501  0.020  1.501
 79I  C16  N17  double  1.263  0.020  1.263
 79I  C12  C11  single  1.530  0.020  1.530
 79I  C12  N13  single  1.447  0.020  1.447
 79I  C14  C10  single  1.523  0.020  1.523
 79I  C14  N13  single  1.344  0.020  1.344
 79I  C14  O15  double  1.219  0.020  1.219
 79I  C10  C9   single  1.522  0.020  1.522
 79I  C8   C9   single  1.532  0.020  1.532
 79I  C8   N7   single  1.456  0.020  1.456
 79I  C16  H1   single  0.930  0.020  1.080
 79I  C12  H2   single  0.970  0.020  1.090
 79I  C12  H3   single  0.970  0.020  1.090
 79I  C11  H4   single  0.970  0.020  1.090
 79I  C11  H5   single  0.970  0.020  1.090
 79I  C10  H7   single  0.970  0.020  1.090
 79I  C8   H17  single  0.970  0.020  1.090
 79I  C9   H18  single  0.970  0.020  1.090
 79I  C9   H19  single  0.970  0.020  1.090
 79I  N7   H33  single  0.890  0.020  1.040
 79I  N13  H34  single  0.860  0.020  1.020
 79I  N17  H35  single  0.890  0.020  1.040
 79I  N7   H9   single  0.890  0.020  1.040
 79I  C11  C10  single  1.529  0.020  1.529

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
 79I  H1   C16  N17  123.75  3.000
 79I  H1   C16  C8   114.15  3.000
 79I  N17  C16  C8   122.09  3.000
 79I  H3   C12  H2   107.91  3.000
 79I  H3   C12  N13  111.21  3.000
 79I  H2   C12  N13  111.22  3.000
 79I  H3   C12  C11  111.63  3.000
 79I  H2   C12  C11  112.67  3.000
 79I  N13  C12  C11  102.20  3.000
 79I  O15  C14  N13  126.31  3.000
 79I  O15  C14  C10  126.22  3.000
 79I  N13  C14  C10  107.46  3.000
 79I  H5   C11  H4   107.74  3.000
 79I  H5   C11  C10  109.66  3.000
 79I  H4   C11  C10  113.50  3.000
 79I  C10  C11  C12  103.90  3.000
 79I  H5   C11  C12  109.85  3.000
 79I  H4   C11  C12  112.16  3.000
 79I  H7   C10  C9   109.78  3.000
 79I  H7   C10  C11  109.64  3.000
 79I  C9   C10  C11  115.60  3.000
 79I  C11  C10  C14  103.25  3.000
 79I  H7   C10  C14  105.59  3.000
 79I  C9   C10  C14  112.39  3.000
 79I  H17  C8   N7   113.85  3.000
 79I  H17  C8   C9   108.57  3.000
 79I  N7   C8   C9   110.74  3.000
 79I  H17  C8   C16  107.43  3.000
 79I  N7   C8   C16  108.14  3.000
 79I  C9   C8   C16  107.92  3.000
 79I  H19  C9   H18  107.14  3.000
 79I  H19  C9   C8   109.26  3.000
 79I  H18  C9   C8   108.06  3.000
 79I  H19  C9   C10  109.43  3.000
 79I  H18  C9   C10  108.95  3.000
 79I  C8   C9   C10  113.78  3.000
 79I  H9   N7   H33  105.26  3.000
 79I  H9   N7   C8   109.49  3.000
 79I  H33  N7   C8   110.12  3.000
 79I  H34  N13  C14  121.93  3.000
 79I  H34  N13  C12  122.59  3.000
 79I  C14  N13  C12  114.62  3.000
 79I  H35  N17  C16  110.48  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
 79I  CONST_01  C10  C14  N13  C12     0.00   0.0  0
 79I  CONST_02  O15  C14  N13  C12   180.00   0.0  0
 79I  CONST_03  H34  N13  C14  C10   180.00   0.0  0
 79I  CONST_04  H34  N13  C14  O15     0.00   0.0  0
 79I  CONST_05  H35  N17  C16  C8    180.00   0.0  0
 79I  CONST_06  H35  N17  C16  H1      0.00   0.0  0
 79I  Var_01    C11  C12  N13  C14   -19.99  30.0  1
 79I  Var_02    N13  C12  C11  C10    28.17  30.0  1
 79I  Var_03    H2   C12  N13  C14  -140.45  30.0  1
 79I  Var_04    H3   C12  N13  C14    99.24  30.0  1
 79I  Var_05    H34  N13  C12  C11   170.47  30.0  1
 79I  Var_06    H2   C12  C11  C10   147.61  30.0  1
 79I  Var_07    H3   C12  C11  C10   -90.77  30.0  1
 79I  Var_08    H4   C11  C12  N13   151.15  30.0  1
 79I  Var_09    H5   C11  C12  N13   -89.07  30.0  1

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
 79I  chir_01  C10  C14  C9   C11  positiv
 79I  chir_02  C8   N7   C16  C9   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
 79I  plan-1  C12  0.020
 79I  plan-1  C14  0.020
 79I  plan-1  C10  0.020
 79I  plan-1  N13  0.020
 79I  plan-1  H34  0.020
 79I  plan-1  O15  0.020
 79I  plan-2  C16  0.020
 79I  plan-2  C8   0.020
 79I  plan-2  N17  0.020
 79I  plan-2  H1   0.020
 79I  plan-2  H35  0.020

