# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 01:31:38 2021
#   Inital geometry file: a 92 line input string
#   Ligand name: ~{N}-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethyl]-3-methyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(c1)C(=O)NCCN2C(=O)CCC2=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
 SZN  SZN  ~{N}-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethyl]-3-methyl-benzamide  ligand  35  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SZN
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
 SZN  N1   N  NR5   0  -0.528  -36.7688   2.0520   0.9565
 SZN  C4   C  CR16  0  -0.291  -38.6076   8.9422   1.5927
 SZN  C5   C  CR6   0  -0.013  -37.7736   7.9453   1.0970
 SZN  C6   C  CR16  0  -0.350  -36.6263   8.3012   0.3888
 SZN  C7   C  C     0   0.527  -38.1334   6.5222   1.3834
 SZN  C8   C  CH2   0  -0.287  -37.9192   4.1963   0.6123
 SZN  C10  C  CR5   0   0.558  -36.7071   1.1915  -0.1209
 SZN  C13  C  CR5   0   0.559  -37.1520   1.4308   2.1272
 SZN  O2   O  O     0  -0.433  -37.3123   2.0067   3.1757
 SZN  C12  C  CH2   0  -0.589  -37.3364  -0.0374   1.8466
 SZN  C11  C  CH2   0  -0.590  -36.9863  -0.2039   0.3738
 SZN  O1   O  O     0  -0.433  -36.4577   1.5367  -1.2498
 SZN  C9   C  CH2   0  -0.330  -36.5881   3.4834   0.8457
 SZN  N    N  NH1   0  -0.649  -37.7254   5.6173   0.4735
 SZN  O    O  O     0  -0.484  -38.7775   6.2256   2.3798
 SZN  C3   C  CR16  0  -0.228  -38.3032  10.2746   1.3588
 SZN  C2   C  CR16  0  -0.291  -37.1627  10.6170   0.6483
 SZN  C1   C  CR6   0   0.116  -36.3054   9.6342   0.1553
 SZN  C    C  CH3   0  -0.722  -35.0640  10.0131  -0.5980
 SZN  H2   H  HCR6  0   0.249  -35.9465   7.5384   0.0259
 SZN  H3   H  HCH2  0   0.262  -38.5911   4.0204   1.4493
 SZN  H4   H  HCH2  0   0.261  -38.3996   3.8065  -0.2874
 SZN  H5   H  HCH2  0   0.302  -38.3678  -0.3115   2.0708
 SZN  H6   H  HCH2  0   0.301  -37.7887  -0.6456  -0.2164
 SZN  H7   H  HCH2  0   0.276  -36.1197   3.8474   1.7596
 SZN  H8   H  HCH2  0   0.273  -35.8992   3.6756   0.0241
 SZN  H9   H  HNH1  0   0.410  -37.2534   5.9375  -0.3562
 SZN  H10  H  HCR6  0   0.260  -38.9577  11.0504   1.7345
 SZN  H11  H  HCR6  0   0.256  -36.9314  11.6617   0.4773
 SZN  H12  H  HCH3  0   0.250  -34.3844  10.5931   0.0280
 SZN  H13  H  HCH3  0   0.246  -34.5251   9.1350  -0.9509
 SZN  H14  H  HCH3  0   0.249  -35.3044  10.6288  -1.4657
 SZN  H15  H  HCH2  0   0.302  -36.6971  -0.6185   2.5111
 SZN  H16  H  HCH2  0   0.304  -36.0970  -0.8164   0.2194
 SZN  H1   H  HCR6  0   0.258  -39.5001   8.6777   2.1435

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
 SZN  O1   C10  double    1.207  0.020  1.207
 SZN  C    C1   single    1.501  0.020  1.501
 SZN  C10  C11  single    1.507  0.020  1.507
 SZN  C10  N1   single    1.380  0.020  1.380
 SZN  C1   C2   aromatic  1.394  0.020  1.394
 SZN  C1   C6   aromatic  1.391  0.020  1.391
 SZN  C11  C12  single    1.523  0.020  1.523
 SZN  C2   C3   aromatic  1.387  0.020  1.387
 SZN  C6   C5   aromatic  1.395  0.020  1.395
 SZN  N    C8   single    1.441  0.020  1.441
 SZN  N    C7   single    1.347  0.020  1.347
 SZN  C9   N1   single    1.447  0.020  1.447
 SZN  C9   C8   single    1.528  0.020  1.528
 SZN  N1   C13  single    1.380  0.020  1.380
 SZN  C3   C4   aromatic  1.387  0.020  1.387
 SZN  C5   C4   aromatic  1.391  0.020  1.391
 SZN  C5   C7   single    1.496  0.020  1.496
 SZN  C7   O    double    1.223  0.020  1.223
 SZN  C12  C13  single    1.506  0.020  1.506
 SZN  C13  O2   double    1.207  0.020  1.207
 SZN  C4   H1   single    0.930  0.020  1.080
 SZN  C6   H2   single    0.930  0.020  1.080
 SZN  C8   H3   single    0.970  0.020  1.090
 SZN  C8   H4   single    0.970  0.020  1.090
 SZN  C12  H5   single    0.970  0.020  1.090
 SZN  C11  H6   single    0.970  0.020  1.090
 SZN  C9   H7   single    0.970  0.020  1.090
 SZN  C9   H8   single    0.970  0.020  1.090
 SZN  N    H9   single    0.860  0.020  1.020
 SZN  C3   H10  single    0.930  0.020  1.080
 SZN  C2   H11  single    0.930  0.020  1.080
 SZN  C    H12  single    0.970  0.020  1.090
 SZN  C    H13  single    0.970  0.020  1.090
 SZN  C    H14  single    0.970  0.020  1.090
 SZN  C12  H15  single    0.970  0.020  1.090
 SZN  C11  H16  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
 SZN  C9   N1   C13  123.03  3.000
 SZN  C13  N1   C10  113.21  3.000
 SZN  C9   N1   C10  123.46  3.000
 SZN  H1   C4   C3   120.13  3.000
 SZN  H1   C4   C5   120.06  3.000
 SZN  C3   C4   C5   119.80  3.000
 SZN  C7   C5   C6   122.55  3.000
 SZN  C7   C5   C4   118.00  3.000
 SZN  C6   C5   C4   119.43  3.000
 SZN  H2   C6   C1   118.26  3.000
 SZN  H2   C6   C5   120.42  3.000
 SZN  C1   C6   C5   121.31  3.000
 SZN  O    C7   N    123.18  3.000
 SZN  O    C7   C5   120.89  3.000
 SZN  N    C7   C5   115.92  3.000
 SZN  H4   C8   H3   107.74  3.000
 SZN  H4   C8   N    109.38  3.000
 SZN  H3   C8   N    108.47  3.000
 SZN  H4   C8   C9   110.03  3.000
 SZN  H3   C8   C9   110.19  3.000
 SZN  N    C8   C9   110.96  3.000
 SZN  O1   C10  C11  127.63  3.000
 SZN  C11  C10  N1   108.23  3.000
 SZN  O1   C10  N1   124.14  3.000
 SZN  C12  C13  O2   127.64  3.000
 SZN  O2   C13  N1   124.00  3.000
 SZN  C12  C13  N1   108.35  3.000
 SZN  H15  C12  H5   107.18  3.000
 SZN  H15  C12  C11  113.36  3.000
 SZN  H5   C12  C11  112.87  3.000
 SZN  H15  C12  C13  109.54  3.000
 SZN  H5   C12  C13  108.82  3.000
 SZN  C11  C12  C13  104.99  3.000
 SZN  H16  C11  H6   107.22  3.000
 SZN  H16  C11  C12  112.69  3.000
 SZN  H6   C11  C12  113.50  3.000
 SZN  H16  C11  C10  108.82  3.000
 SZN  H6   C11  C10  109.52  3.000
 SZN  C12  C11  C10  105.00  3.000
 SZN  H8   C9   H7   107.56  3.000
 SZN  H8   C9   C8   110.70  3.000
 SZN  H7   C9   C8   110.29  3.000
 SZN  H8   C9   N1   108.14  3.000
 SZN  H7   C9   N1   108.66  3.000
 SZN  C8   C9   N1   111.38  3.000
 SZN  H9   N    C8   117.13  3.000
 SZN  H9   N    C7   119.03  3.000
 SZN  C8   N    C7   123.84  3.000
 SZN  H10  C3   C2   119.89  3.000
 SZN  H10  C3   C4   119.83  3.000
 SZN  C2   C3   C4   120.28  3.000
 SZN  H11  C2   C1   119.50  3.000
 SZN  H11  C2   C3   119.64  3.000
 SZN  C1   C2   C3   120.86  3.000
 SZN  C    C1   C2   120.54  3.000
 SZN  C2   C1   C6   118.32  3.000
 SZN  C    C1   C6   121.14  3.000
 SZN  H14  C    H13  107.84  3.000
 SZN  H14  C    H12  107.08  3.000
 SZN  H13  C    H12  107.83  3.000
 SZN  H14  C    C1   111.07  3.000
 SZN  H13  C    C1   111.62  3.000
 SZN  H12  C    C1   111.20  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
 SZN  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 SZN  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 SZN  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 SZN  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 SZN  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 SZN  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 SZN  CONST_07  C11  C10  N1   C13     0.00   0.0  0
 SZN  CONST_08  C    C1   C6   C5    180.00   0.0  0
 SZN  CONST_09  C1   C6   C5   C7    180.00   0.0  0
 SZN  CONST_10  C3   C4   C5   C7    180.00   0.0  0
 SZN  CONST_11  C    C1   C2   C3    180.00   0.0  0
 SZN  CONST_12  O1   C10  N1   C13   180.00   0.0  0
 SZN  CONST_13  C9   N1   C10  C11   180.00   0.0  0
 SZN  CONST_14  H11  C2   C3   C4    180.00   0.0  0
 SZN  CONST_15  H2   C6   C5   C4    180.00   0.0  0
 SZN  CONST_16  H10  C3   C4   C5    180.00   0.0  0
 SZN  CONST_17  H1   C4   C5   C6    180.00   0.0  0
 SZN  CONST_18  C9   N1   C10  O1      0.00   0.0  0
 SZN  CONST_19  C8   N    C7   C5    180.00   0.0  0
 SZN  CONST_20  H9   N    C7   C5      0.00   0.0  0
 SZN  CONST_21  O    C7   N    C8      0.00   0.0  0
 SZN  Var_01    C12  C11  C10  N1      4.74  30.0  1
 SZN  Var_02    C11  C12  C13  N1      1.12  30.0  1
 SZN  Var_03    C13  C12  C11  C10    -3.46  30.0  1
 SZN  Var_04    C12  C13  N1   C10     2.02  30.0  1
 SZN  Var_05    N    C7   C5   C4    151.64  30.0  2
 SZN  Var_06    C10  N1   C9   C8     90.71  30.0  3
 SZN  Var_07    H12  C    C1   C6   -117.62  30.0  2
 SZN  Var_08    N    C8   C9   N1   -178.71  30.0  3
 SZN  Var_09    C9   C8   N    C7   -110.77  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
 SZN  plan-1  C4   0.020
 SZN  plan-1  C5   0.020
 SZN  plan-1  C6   0.020
 SZN  plan-1  C7   0.020
 SZN  plan-1  C3   0.020
 SZN  plan-1  C2   0.020
 SZN  plan-1  C1   0.020
 SZN  plan-1  C    0.020
 SZN  plan-1  H2   0.020
 SZN  plan-1  H10  0.020
 SZN  plan-1  H11  0.020
 SZN  plan-1  H1   0.020
 SZN  plan-2  C5   0.020
 SZN  plan-2  C7   0.020
 SZN  plan-2  C8   0.020
 SZN  plan-2  N    0.020
 SZN  plan-2  O    0.020
 SZN  plan-2  H9   0.020
 SZN  plan-3  N1   0.020
 SZN  plan-3  C13  0.020
 SZN  plan-3  O2   0.020
 SZN  plan-3  C12  0.020
 SZN  plan-4  N1   0.020
 SZN  plan-4  C10  0.020
 SZN  plan-4  C13  0.020
 SZN  plan-4  C11  0.020
 SZN  plan-4  O1   0.020
 SZN  plan-4  C9   0.020

