# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:15:47 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: cyclopropyl-[4-[(2~{S})-oxolan-2-yl]carbonylpiperazin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(C1CC1)N2CCN(CC2)C(=O)[C@@H]3CCCO3
#
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
 S9G  S9G  cyclopropyl-[4-[(2~{S})-oxolan-2-yl]carbonylpiperazin-1-yl]methanone  ligand  38  18  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_S9G
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
 S9G  C10  C  C     0   0.532  -11.6587  86.9020  103.6179
 S9G  C13  C  CH2   0  -0.487  -14.1439  86.6012  103.9303
 S9G  C15  C  CH2   0  -0.150  -13.5846  84.4270  103.1301
 S9G  C17  C  CH2   0  -0.312  -10.1660  88.4602  104.7613
 S9G  C03  C  CH1   0  -0.432  -11.7453  92.7032  105.9104
 S9G  C04  C  CH2   0  -0.461  -11.5100  93.9372  106.7407
 S9G  C05  C  CH2   0  -0.464  -11.0665  93.9183  105.3246
 S9G  C07  C  CH2   0  -0.314  -12.5597  89.9836  105.1096
 S9G  C08  C  CH2   0  -0.322  -12.1949  89.3366  103.7779
 S9G  C12  C  CH1   0  -0.112  -12.9994  86.6645  102.9118
 S9G  C14  C  CH2   0  -0.515  -14.0559  85.1493  104.3908
 S9G  C18  C  CH2   0  -0.320  -10.5430  89.1027  106.0892
 S9G  N06  N  NT    0  -0.477  -11.3607  90.2842  105.8678
 S9G  N09  N  NT    0  -0.462  -11.3639  88.1669  103.9931
 S9G  O01  O  O     0  -0.510   -9.7799  91.6638  106.6883
 S9G  O11  O  O     0  -0.487  -10.9167  85.9594  103.8467
 S9G  O16  O  O2    0  -0.490  -12.9920  85.4107  102.2866
 S9G  H1   H  HCH2  0   0.257  -14.0480  87.3134  104.7495
 S9G  H2   H  HCH2  0   0.260  -15.0931  86.7988  103.4292
 S9G  H3   H  HCH2  0   0.214  -14.4232  83.9715  102.5956
 S9G  H4   H  HCH2  0   0.220  -12.8613  83.6389  103.3514
 S9G  H5   H  HCH2  0   0.273   -9.6079  87.5446  104.9349
 S9G  H6   H  HCH2  0   0.252   -9.5299  89.1434  104.1893
 S9G  H7   H  HCH1  0   0.286  -12.7685  92.5518  105.6008
 S9G  H8   H  HCH2  0   0.261  -12.3867  94.5169  106.9975
 S9G  H9   H  HCH2  0   0.257  -10.7556  93.8846  107.5132
 S9G  H10  H  HCH2  0   0.257  -10.0059  93.8453  105.1238
 S9G  H11  H  HCH2  0   0.262  -11.6290  94.4849  104.5946
 S9G  H12  H  HCH2  0   0.278  -13.1479  90.8736  104.9164
 S9G  H13  H  HCH2  0   0.254  -13.1847  89.2984  105.6917
 S9G  H14  H  HCH2  0   0.264  -11.6451  90.0581  103.1650
 S9G  H15  H  HCH2  0   0.279  -13.1062  89.0874  103.2428
 S9G  H16  H  HCH1  0   0.276  -13.1687  87.4188  102.1396
 S9G  H17  H  HCH2  0   0.257  -15.0094  84.7650  104.7500
 S9G  H18  H  HCH2  0   0.247  -13.3305  85.0448  105.1985
 S9G  H19  H  HCH2  0   0.252  -11.1139  88.3881  106.6904
 S9G  H20  H  HCH2  0   0.275   -9.6487  89.3717  106.6432
 S9G  C02  C  C     0   0.598  -10.8869  91.5153  106.1816

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
 S9G  O16  C15  single  1.425  0.020  1.425
 S9G  O16  C12  single  1.401  0.020  1.401
 S9G  C15  C14  single  1.527  0.020  1.527
 S9G  C12  C10  single  1.534  0.020  1.534
 S9G  C12  C13  single  1.533  0.020  1.533
 S9G  C08  N09  single  1.451  0.020  1.451
 S9G  C08  C07  single  1.525  0.020  1.525
 S9G  C10  N09  single  1.352  0.020  1.352
 S9G  C10  O11  double  1.221  0.020  1.221
 S9G  N09  C17  single  1.453  0.020  1.453
 S9G  C14  C13  single  1.526  0.020  1.526
 S9G  C17  C18  single  1.523  0.020  1.523
 S9G  C07  N06  single  1.450  0.020  1.450
 S9G  C03  C02  single  1.490  0.020  1.490
 S9G  C03  C04  single  1.506  0.020  1.506
 S9G  C03  C05  single  1.510  0.020  1.510
 S9G  N06  C02  single  1.356  0.020  1.356
 S9G  N06  C18  single  1.454  0.020  1.454
 S9G  C02  O01  double  1.226  0.020  1.226
 S9G  C04  C05  single  1.484  0.020  1.484
 S9G  C13  H1   single  0.970  0.020  1.090
 S9G  C13  H2   single  0.970  0.020  1.090
 S9G  C15  H3   single  0.970  0.020  1.090
 S9G  C15  H4   single  0.970  0.020  1.090
 S9G  C17  H5   single  0.970  0.020  1.090
 S9G  C17  H6   single  0.970  0.020  1.090
 S9G  C03  H7   single  0.970  0.020  1.090
 S9G  C04  H8   single  0.970  0.020  1.090
 S9G  C04  H9   single  0.970  0.020  1.090
 S9G  C05  H10  single  0.970  0.020  1.090
 S9G  C05  H11  single  0.970  0.020  1.090
 S9G  C07  H12  single  0.970  0.020  1.090
 S9G  C07  H13  single  0.970  0.020  1.090
 S9G  C08  H14  single  0.970  0.020  1.090
 S9G  C08  H15  single  0.970  0.020  1.090
 S9G  C12  H16  single  0.970  0.020  1.090
 S9G  C14  H17  single  0.970  0.020  1.090
 S9G  C14  H18  single  0.970  0.020  1.090
 S9G  C18  H19  single  0.970  0.020  1.090
 S9G  C18  H20  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
 S9G  O11  C10  N09  122.53  3.000
 S9G  O11  C10  C12  119.85  3.000
 S9G  N09  C10  C12  117.60  3.000
 S9G  H2   C13  H1   107.66  3.000
 S9G  H2   C13  C14  111.16  3.000
 S9G  H1   C13  C14  112.95  3.000
 S9G  H2   C13  C12  109.68  3.000
 S9G  H1   C13  C12  114.00  3.000
 S9G  C14  C13  C12  101.34  3.000
 S9G  H4   C15  H3   107.84  3.000
 S9G  H4   C15  O16  110.03  3.000
 S9G  H3   C15  O16  108.49  3.000
 S9G  H4   C15  C14  112.22  3.000
 S9G  H3   C15  C14  111.33  3.000
 S9G  O16  C15  C14  106.88  3.000
 S9G  H6   C17  H5   108.12  3.000
 S9G  H6   C17  N09  109.19  3.000
 S9G  H5   C17  N09  109.75  3.000
 S9G  H6   C17  C18  109.65  3.000
 S9G  H5   C17  C18  110.09  3.000
 S9G  N09  C17  C18  110.01  3.000
 S9G  H7   C03  C05  115.31  3.000
 S9G  H7   C03  C04  114.91  3.000
 S9G  C05  C03  C04   58.95  3.000
 S9G  H7   C03  C02  119.09  3.000
 S9G  C05  C03  C02  116.94  3.000
 S9G  C04  C03  C02  117.57  3.000
 S9G  H9   C04  H8   114.96  3.000
 S9G  H9   C04  C05  118.21  3.000
 S9G  H8   C04  C05  118.39  3.000
 S9G  H9   C04  C03  117.59  3.000
 S9G  H8   C04  C03  116.32  3.000
 S9G  C05  C04  C03   60.67  3.000
 S9G  H11  C05  H10  114.82  3.000
 S9G  H11  C05  C04  118.80  3.000
 S9G  H10  C05  C04  118.10  3.000
 S9G  H11  C05  C03  116.71  3.000
 S9G  H10  C05  C03  117.28  3.000
 S9G  C04  C05  C03   60.38  3.000
 S9G  H13  C07  H12  107.38  3.000
 S9G  H13  C07  N06  108.89  3.000
 S9G  H12  C07  N06  111.82  3.000
 S9G  H13  C07  C08  109.59  3.000
 S9G  H12  C07  C08  108.82  3.000
 S9G  N06  C07  C08  110.29  3.000
 S9G  H15  C08  H14  107.27  3.000
 S9G  H15  C08  N09  111.64  3.000
 S9G  H14  C08  N09  109.07  3.000
 S9G  H15  C08  C07  109.09  3.000
 S9G  H14  C08  C07  109.24  3.000
 S9G  N09  C08  C07  110.46  3.000
 S9G  H16  C12  O16  107.65  3.000
 S9G  H16  C12  C13  112.47  3.000
 S9G  O16  C12  C13  105.27  3.000
 S9G  H16  C12  C10  110.73  3.000
 S9G  C13  C12  C10  110.67  3.000
 S9G  O16  C12  C10  109.84  3.000
 S9G  H18  C14  H17  107.71  3.000
 S9G  H18  C14  C15  111.15  3.000
 S9G  H17  C14  C15  112.06  3.000
 S9G  H18  C14  C13  110.67  3.000
 S9G  H17  C14  C13  112.63  3.000
 S9G  C15  C14  C13  102.63  3.000
 S9G  H20  C18  H19  108.12  3.000
 S9G  H20  C18  N06  109.85  3.000
 S9G  H19  C18  N06  108.71  3.000
 S9G  H20  C18  C17  110.22  3.000
 S9G  H19  C18  C17  109.43  3.000
 S9G  N06  C18  C17  110.45  3.000
 S9G  C18  N06  C07  112.10  3.000
 S9G  C18  N06  C02  120.40  3.000
 S9G  C07  N06  C02  126.73  3.000
 S9G  C08  N09  C17  112.82  3.000
 S9G  C17  N09  C10  121.02  3.000
 S9G  C08  N09  C10  126.03  3.000
 S9G  C12  O16  C15  110.58  3.000
 S9G  O01  C02  N06  121.39  3.000
 S9G  O01  C02  C03  119.90  3.000
 S9G  N06  C02  C03  118.70  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
 S9G  CONST_01  C12  C10  N09  C17   180.00   0.0  0
 S9G  CONST_02  C07  N06  C02  C03     0.00   0.0  0
 S9G  CONST_03  C18  N06  C02  C03   180.00   0.0  0
 S9G  CONST_04  C12  C10  N09  C08     0.00   0.0  0
 S9G  CONST_05  O11  C10  N09  C17     0.00   0.0  0
 S9G  CONST_06  O01  C02  N06  C07   180.00   0.0  0
 S9G  CONST_07  O11  C10  N09  C08   180.00   0.0  0
 S9G  CONST_08  O01  C02  N06  C18     0.00   0.0  0
 S9G  Var_01    O16  C15  C14  C13    20.41  30.0  1
 S9G  Var_02    C12  C13  C14  C15   -33.04  30.0  1
 S9G  Var_03    C07  C08  N09  C17   -55.77  30.0  1
 S9G  Var_04    C07  N06  C18  C17    57.21  30.0  1
 S9G  Var_05    C18  C17  N09  C08    55.91  30.0  1
 S9G  Var_06    C18  N06  C07  C08   -56.72  30.0  1
 S9G  Var_07    C14  C15  O16  C12     2.21  30.0  1
 S9G  Var_08    N09  C08  C07  N06    54.90  30.0  1
 S9G  Var_09    N09  C17  C18  N06   -55.41  30.0  1
 S9G  Var_10    C05  C04  C03  C02   106.39  30.0  1
 S9G  Var_11    N06  C02  C03  C04   154.88  30.0  3
 S9G  Var_12    H10  C05  C04  C03  -107.11  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
 S9G  chir_02  C12  O16  C10  C13  positiv
 S9G  chir_03  C03  C02  C04  C05  both

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
 S9G  plan-1  C10  0.020
 S9G  plan-1  C17  0.020
 S9G  plan-1  C08  0.020
 S9G  plan-1  C12  0.020
 S9G  plan-1  N09  0.020
 S9G  plan-1  O11  0.020
 S9G  plan-2  C03  0.020
 S9G  plan-2  C07  0.020
 S9G  plan-2  C18  0.020
 S9G  plan-2  N06  0.020
 S9G  plan-2  O01  0.020
 S9G  plan-2  C02  0.020

