# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 05:42:49 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]-~{N}-methyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)CCN1C(=O)CCC1=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
 G7Z  G7Z  3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]-~{N}-methyl-propanamide  ligand  25  13  .  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_G7Z
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
 G7Z  C1   C  CH3   0  -0.514   4.8128  -0.2058   0.4083
 G7Z  N1   N  NH1   0  -0.626   3.4025  -0.2522   0.7152
 G7Z  C2   C  C     0   0.561   2.4752   0.2924  -0.0809
 G7Z  O1   O  O     0  -0.505   2.7537   0.8442  -1.1383
 G7Z  C3   C  CH2   0  -0.585   1.0497   0.2080   0.4242
 G7Z  C4   C  CH2   0  -0.306   0.0666   0.0208  -0.7257
 G7Z  N2   N  NT    0  -0.529  -1.3044   0.0040  -0.2591
 G7Z  C5   C  C     0   0.557  -1.9375  -1.1384   0.1818
 G7Z  O2   O  O     0  -0.435  -1.4223  -2.2298   0.2079
 G7Z  C6   C  CH2   0  -0.589  -3.3344  -0.7711   0.6090
 G7Z  C7   C  CH2   0  -0.590  -3.4469   0.7246   0.3449
 G7Z  C8   C  C     0   0.557  -2.0918   1.1326  -0.1720
 G7Z  O3   O  O     0  -0.435  -1.7224   2.2411  -0.4749
 G7Z  H1   H  HCH3  0   0.238   5.0444  -0.7459  -0.5104
 G7Z  H2   H  HCH3  0   0.238   5.1665   0.8200   0.3001
 G7Z  H3   H  HCH3  0   0.251   5.3574  -0.6703   1.2251
 G7Z  H4   H  HNH1  0   0.405   3.1141  -0.7046   1.5660
 G7Z  H5   H  HCH2  0   0.267   0.9384  -0.5979   1.1514
 G7Z  H6   H  HCH2  0   0.274   0.1676   0.8229  -1.4530
 G7Z  H7   H  HCH2  0   0.302  -4.0538  -1.3635   0.0436
 G7Z  H8   H  HCH2  0   0.301  -3.4633  -1.0270   1.6611
 G7Z  H9   H  HCH2  0   0.303  -4.1991   0.9666  -0.4071
 G7Z  H10  H  HCH2  0   0.301  -3.6855   1.3029   1.2375
 G7Z  H11  H  HCH2  0   0.284   0.8267   1.1422   0.9476
 G7Z  H12  H  HCH2  0   0.275   0.2555  -0.9188  -1.2431

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
 G7Z  C3  C2   single  1.515  0.020  1.515
 G7Z  C3  C4   single  1.524  0.020  1.524
 G7Z  C2  O1   double  1.225  0.020  1.225
 G7Z  C2  N1   single  1.338  0.020  1.338
 G7Z  C4  N2   single  1.448  0.020  1.448
 G7Z  N1  C1   single  1.444  0.020  1.444
 G7Z  N2  C8   single  1.379  0.020  1.379
 G7Z  N2  C5   single  1.379  0.020  1.379
 G7Z  O3  C8   double  1.207  0.020  1.207
 G7Z  O2  C5   double  1.207  0.020  1.207
 G7Z  C8  C7   single  1.507  0.020  1.507
 G7Z  C5  C6   single  1.506  0.020  1.506
 G7Z  C7  C6   single  1.523  0.020  1.523
 G7Z  C1  H1   single  0.970  0.020  1.090
 G7Z  C1  H2   single  0.970  0.020  1.090
 G7Z  C1  H3   single  0.970  0.020  1.090
 G7Z  N1  H4   single  0.860  0.020  1.020
 G7Z  C3  H5   single  0.970  0.020  1.090
 G7Z  C4  H6   single  0.970  0.020  1.090
 G7Z  C6  H7   single  0.970  0.020  1.090
 G7Z  C6  H8   single  0.970  0.020  1.090
 G7Z  C7  H9   single  0.970  0.020  1.090
 G7Z  C7  H10  single  0.970  0.020  1.090
 G7Z  C3  H11  single  0.970  0.020  1.090
 G7Z  C4  H12  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
 G7Z  H3   C1  H2  108.32  3.000
 G7Z  H3   C1  H1  108.37  3.000
 G7Z  H2   C1  H1  108.26  3.000
 G7Z  H3   C1  N1  108.43  3.000
 G7Z  H2   C1  N1  111.60  3.000
 G7Z  H1   C1  N1  111.75  3.000
 G7Z  H4   N1  C2  119.18  3.000
 G7Z  H4   N1  C1  118.31  3.000
 G7Z  C2   N1  C1  122.51  3.000
 G7Z  C3   C2  O1  121.80  3.000
 G7Z  O1   C2  N1  122.64  3.000
 G7Z  C3   C2  N1  115.54  3.000
 G7Z  H11  C3  H5  106.92  3.000
 G7Z  H11  C3  C4  109.53  3.000
 G7Z  H5   C3  C4  110.26  3.000
 G7Z  H11  C3  C2  107.69  3.000
 G7Z  H5   C3  C2  111.06  3.000
 G7Z  C4   C3  C2  111.24  3.000
 G7Z  H12  C4  H6  107.61  3.000
 G7Z  H12  C4  N2  107.90  3.000
 G7Z  H6   C4  N2  108.18  3.000
 G7Z  H12  C4  C3  110.63  3.000
 G7Z  H6   C4  C3  110.73  3.000
 G7Z  N2   C4  C3  111.65  3.000
 G7Z  C8   N2  C5  113.31  3.000
 G7Z  C5   N2  C4  123.19  3.000
 G7Z  C8   N2  C4  123.47  3.000
 G7Z  C6   C5  O2  127.60  3.000
 G7Z  C6   C5  N2  108.34  3.000
 G7Z  O2   C5  N2  124.06  3.000
 G7Z  H8   C6  H7  107.15  3.000
 G7Z  H8   C6  C7  112.90  3.000
 G7Z  H7   C6  C7  113.27  3.000
 G7Z  H8   C6  C5  109.03  3.000
 G7Z  H7   C6  C5  109.42  3.000
 G7Z  C7   C6  C5  105.00  3.000
 G7Z  H10  C7  H9  107.21  3.000
 G7Z  H10  C7  C8  109.52  3.000
 G7Z  H9   C7  C8  108.88  3.000
 G7Z  H10  C7  C6  113.28  3.000
 G7Z  H9   C7  C6  112.85  3.000
 G7Z  C8   C7  C6  105.01  3.000
 G7Z  O3   C8  C7  127.59  3.000
 G7Z  C7   C8  N2  108.28  3.000
 G7Z  O3   C8  N2  124.12  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
 G7Z  CONST_01  C8  N2  C5  C6     0.00   0.0  0
 G7Z  CONST_02  C6  C5  N2  C4   180.00   0.0  0
 G7Z  CONST_03  C8  N2  C5  O2   180.00   0.0  0
 G7Z  CONST_04  O2  C5  N2  C4     0.00   0.0  0
 G7Z  CONST_05  C3  C2  N1  C1   180.00   0.0  0
 G7Z  CONST_06  O1  C2  N1  C1     0.00   0.0  0
 G7Z  CONST_07  H4  N1  C2  O1   180.00   0.0  0
 G7Z  Var_01    C6  C7  C8  N2     2.50  30.0  1
 G7Z  Var_02    C7  C6  C5  N2     0.78  30.0  1
 G7Z  Var_03    C7  C8  N2  C5    -2.16  30.0  1
 G7Z  Var_04    C8  C7  C6  C5    -1.93  30.0  1
 G7Z  Var_05    C8  N2  C4  C3    91.23  30.0  3
 G7Z  Var_06    N2  C4  C3  C2  -177.21  30.0  3
 G7Z  Var_07    C4  C3  C2  N1  -145.09  30.0  1
 G7Z  Var_08    H1  C1  N1  C2   -63.33  30.0  3

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
 G7Z  plan-1  C1  0.020
 G7Z  plan-1  N1  0.020
 G7Z  plan-1  C2  0.020
 G7Z  plan-1  O1  0.020
 G7Z  plan-1  C3  0.020
 G7Z  plan-1  H4  0.020
 G7Z  plan-2  N2  0.020
 G7Z  plan-2  C7  0.020
 G7Z  plan-2  C8  0.020
 G7Z  plan-2  O3  0.020
 G7Z  plan-3  C4  0.020
 G7Z  plan-3  N2  0.020
 G7Z  plan-3  C5  0.020
 G7Z  plan-3  O2  0.020
 G7Z  plan-3  C6  0.020
 G7Z  plan-3  C8  0.020

