# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 12:05:22 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: 5-azanylpentan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)CCCN
#
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
 SY8  SY8  "5-azanylpentan-2-one"
  ligand  18  7  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SY8
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
 SY8  N    N  NH2   0  -0.798  196.7830  128.2400  135.5396
 SY8  C    C  CH3   0  -0.775  198.7622  124.0422  135.9688
 SY8  O    O  O     0  -0.398  198.8185  125.8239  137.5439
 SY8  C1   C  C     0   0.386  198.9257  125.4797  136.3868
 SY8  C2   C  CH2   0  -0.564  199.2085  126.4689  135.2830
 SY8  C3   C  CH2   0  -0.445  198.0682  126.5657  134.2620
 SY8  C4   C  CH2   0  -0.298  196.7231  126.9513  134.8645
 SY8  H1   H  HNH2  0   0.348  195.8460  128.5274  135.7913
 SY8  H2   H  HNH2  0   0.340  197.2772  128.1447  136.4182
 SY8  H4   H  HCH3  0   0.261  198.8310  123.3719  136.8232
 SY8  H5   H  HCH3  0   0.268  197.7796  123.9064  135.5096
 SY8  H6   H  HCH3  0   0.256  199.5003  123.7604  135.2178
 SY8  H7   H  HCH2  0   0.268  200.1159  126.1510  134.7614
 SY8  H8   H  HCH2  0   0.251  199.4139  127.4470  135.7213
 SY8  H9   H  HCH2  0   0.234  197.9612  125.6159  133.7328
 SY8  H10  H  HCH2  0   0.240  198.3506  127.3074  133.5117
 SY8  H11  H  HCH2  0   0.232  195.9986  127.0289  134.0511
 SY8  H12  H  HCH2  0   0.195  196.3621  126.1348  135.5079

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
 SY8  C3  C4   single  1.523  0.020  1.523
 SY8  C3  C2   single  1.534  0.020  1.534
 SY8  C4  N    single  1.456  0.020  1.456
 SY8  C2  C1   single  1.509  0.020  1.509
 SY8  C   C1   single  1.506  0.020  1.506
 SY8  C1  O    double  1.212  0.020  1.212
 SY8  N   H1   single  0.890  0.020  1.040
 SY8  N   H2   single  0.890  0.020  1.040
 SY8  C   H4   single  0.970  0.020  1.090
 SY8  C   H5   single  0.970  0.020  1.090
 SY8  C   H6   single  0.970  0.020  1.090
 SY8  C2  H7   single  0.970  0.020  1.090
 SY8  C2  H8   single  0.970  0.020  1.090
 SY8  C3  H9   single  0.970  0.020  1.090
 SY8  C3  H10  single  0.970  0.020  1.090
 SY8  C4  H11  single  0.970  0.020  1.090
 SY8  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
 SY8  H2   N   H1   105.24  3.000
 SY8  H2   N   C4   109.82  3.000
 SY8  H1   N   C4   109.19  3.000
 SY8  H6   C   H5   106.69  3.000
 SY8  H6   C   H4   109.81  3.000
 SY8  H5   C   H4   108.07  3.000
 SY8  H6   C   C1   111.37  3.000
 SY8  H5   C   C1   109.44  3.000
 SY8  H4   C   C1   111.30  3.000
 SY8  C2   C1  O    121.92  3.000
 SY8  O    C1  C    121.77  3.000
 SY8  C2   C1  C    116.30  3.000
 SY8  H8   C2  H7   107.21  3.000
 SY8  H8   C2  C3   110.53  3.000
 SY8  H7   C2  C3   108.52  3.000
 SY8  H8   C2  C1   109.21  3.000
 SY8  H7   C2  C1   108.29  3.000
 SY8  C3   C2  C1   112.89  3.000
 SY8  H10  C3  H9   106.44  3.000
 SY8  H10  C3  C4   109.16  3.000
 SY8  H9   C3  C4   108.97  3.000
 SY8  H10  C3  C2   107.94  3.000
 SY8  H9   C3  C2   109.90  3.000
 SY8  C4   C3  C2   114.15  3.000
 SY8  H12  C4  H11  105.70  3.000
 SY8  H12  C4  C3   109.46  3.000
 SY8  H11  C4  C3   108.01  3.000
 SY8  H12  C4  N    113.53  3.000
 SY8  H11  C4  N    108.04  3.000
 SY8  C3   C4  N    111.78  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
 SY8  Var_01  C2   C3  C4  N     59.10  30.0  1
 SY8  Var_02  C3   C2  C1  C     62.79  30.0  1
 SY8  Var_03  C3   C2  C1  O   -116.28  30.0  1
 SY8  Var_04  C4   C3  C2  C1    57.79  30.0  1
 SY8  Var_05  H9   C3  C4  N   -177.63  30.0  1
 SY8  Var_06  H10  C3  C4  N    -61.77  30.0  1
 SY8  Var_07  H7   C2  C1  C    -57.39  30.0  1
 SY8  Var_08  H8   C2  C1  C   -173.82  30.0  1
 SY8  Var_09  H7   C2  C1  O    123.54  30.0  1
 SY8  Var_10  H8   C2  C1  O      7.11  30.0  1
 SY8  Var_11  H4   C   C1  O    -16.29  30.0  3
 SY8  Var_12  H5   C   C1  O    103.09  30.0  3
 SY8  Var_13  H6   C   C1  O   -139.19  30.0  3
 SY8  Var_14  H9   C3  C2  C1   -64.98  30.0  1
 SY8  Var_15  H10  C3  C2  C1   179.33  30.0  1
 SY8  Var_16  H11  C4  C3  C2   177.82  30.0  3
 SY8  Var_17  H12  C4  C3  C2   -67.56  30.0  3
 SY8  Var_18  H4   C   C1  C2   164.64  30.0  3
 SY8  Var_19  H5   C   C1  C2   -75.98  30.0  3
 SY8  Var_20  H6   C   C1  C2    41.74  30.0  3
 SY8  Var_21  H1   N   C4  C3   170.85  30.0  3
 SY8  Var_22  H2   N   C4  C3   -74.23  30.0  3
 SY8  Var_23  H7   C2  C3  C4   177.84  30.0  3
 SY8  Var_24  H8   C2  C3  C4   -64.86  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
 SY8  plan-1  C   0.020
 SY8  plan-1  O   0.020
 SY8  plan-1  C1  0.020
 SY8  plan-1  C2  0.020

