# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 06:25:51 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 3-[(3S)-oxolan-3-yl]-1-(pyrrolidin-1-yl)propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC[C@H]1CCOC1)N2CCCC2
#
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
 P87  P87  3-[(3S)-oxolan-3-yl]-1-(pyrrolidin-1-yl)propan-1-one  ligand  33  14  .  2021-08-19  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P87
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
 P87  O1   O  O     0  -0.515   1.2015  -1.9425   0.5510
 P87  C6   C  C     0   0.571   1.2637  -0.7751   0.1780
 P87  N    N  NT    0  -0.476   2.4382  -0.1343   0.0688
 P87  C10  C  CH2   0  -0.259   3.7043  -0.8017   0.3525
 P87  C9   C  CH2   0  -0.483   4.7461   0.1736  -0.1839
 P87  C8   C  CH2   0  -0.475   4.0787   1.5323   0.0003
 P87  C7   C  CH2   0  -0.270   2.6210   1.2528  -0.3471
 P87  C5   C  CH2   0  -0.598   0.0266   0.0247  -0.1765
 P87  C4   C  CH2   0  -0.429  -1.2448  -0.8112  -0.2049
 P87  C1   C  CH1   0  -0.271  -2.4612   0.0040  -0.6240
 P87  C2   C  CH2   0  -0.164  -2.7993   1.1388   0.3539
 P87  O    O  O2    0  -0.497  -4.2034   1.2694   0.3305
 P87  C3   C  CH2   0  -0.178  -4.7089  -0.0499   0.2756
 P87  C    C  CH2   0  -0.482  -3.7706  -0.8127  -0.6633
 P87  H1   H  HCH2  0   0.233   3.8244  -0.9580   1.4287
 P87  H2   H  HCH2  0   0.244   3.7511  -1.7780  -0.1304
 P87  H3   H  HCH2  0   0.251   5.6974   0.0871   0.3399
 P87  H4   H  HCH2  0   0.238   4.9287  -0.0170  -1.2437
 P87  H5   H  HCH2  0   0.239   4.1607   1.8553   1.0406
 P87  H6   H  HCH2  0   0.252   4.5059   2.3151  -0.6252
 P87  H7   H  HCH2  0   0.239   2.4447   1.3649  -1.4215
 P87  H8   H  HCH2  0   0.252   1.9383   1.9237   0.1751
 P87  H9   H  HCH2  0   0.270  -0.0694   0.8415   0.5476
 P87  H10  H  HCH2  0   0.261   0.1709   0.5132  -1.1459
 P87  H11  H  HCH2  0   0.236  -1.1194  -1.6464  -0.8974
 P87  H12  H  HCH2  0   0.224  -1.4296  -1.2484   0.7808
 P87  H13  H  HCH1  0   0.242  -2.2716   0.4307  -1.6135
 P87  H14  H  HCH2  0   0.196  -2.4505   0.8797   1.3666
 P87  H15  H  HCH2  0   0.234  -2.3563   2.0978   0.0820
 P87  H16  H  HCH2  0   0.202  -4.7031  -0.5065   1.2746
 P87  H17  H  HCH2  0   0.230  -5.7425  -0.0138  -0.0707
 P87  H18  H  HCH2  0   0.243  -4.1717  -0.8553  -1.6761
 P87  H19  H  HCH2  0   0.240  -3.6237  -1.8414  -0.3302

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
 P87  O    C2   single  1.410  0.020  1.410
 P87  O    C3   single  1.414  0.020  1.414
 P87  C2   C1   single  1.536  0.020  1.536
 P87  C3   C    single  1.531  0.020  1.531
 P87  C7   C8   single  1.524  0.020  1.524
 P87  C7   N    single  1.460  0.020  1.460
 P87  C8   C9   single  1.525  0.020  1.525
 P87  C1   C    single  1.544  0.020  1.544
 P87  C1   C4   single  1.523  0.020  1.523
 P87  C5   C4   single  1.522  0.020  1.522
 P87  C5   C6   single  1.515  0.020  1.515
 P87  N    C6   single  1.342  0.020  1.342
 P87  N    C10  single  1.459  0.020  1.459
 P87  C6   O1   double  1.227  0.020  1.227
 P87  C9   C10  single  1.525  0.020  1.525
 P87  C10  H1   single  0.970  0.020  1.090
 P87  C10  H2   single  0.970  0.020  1.090
 P87  C9   H3   single  0.970  0.020  1.090
 P87  C9   H4   single  0.970  0.020  1.090
 P87  C8   H5   single  0.970  0.020  1.090
 P87  C8   H6   single  0.970  0.020  1.090
 P87  C7   H7   single  0.970  0.020  1.090
 P87  C7   H8   single  0.970  0.020  1.090
 P87  C5   H9   single  0.970  0.020  1.090
 P87  C5   H10  single  0.970  0.020  1.090
 P87  C4   H11  single  0.970  0.020  1.090
 P87  C4   H12  single  0.970  0.020  1.090
 P87  C1   H13  single  0.970  0.020  1.090
 P87  C2   H14  single  0.970  0.020  1.090
 P87  C2   H15  single  0.970  0.020  1.090
 P87  C3   H16  single  0.970  0.020  1.090
 P87  C3   H17  single  0.970  0.020  1.090
 P87  C    H18  single  0.970  0.020  1.090
 P87  C    H19  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
 P87  C5   C6   N    116.32  3.000
 P87  N    C6   O1   121.55  3.000
 P87  C5   C6   O1   122.14  3.000
 P87  C7   N    C10  112.42  3.000
 P87  C10  N    C6   121.67  3.000
 P87  C7   N    C6   125.90  3.000
 P87  H2   C10  H1   107.64  3.000
 P87  H2   C10  C9   112.82  3.000
 P87  H1   C10  C9   111.25  3.000
 P87  H2   C10  N    111.14  3.000
 P87  H1   C10  N    110.60  3.000
 P87  C9   C10  N    103.41  3.000
 P87  H4   C9   H3   107.86  3.000
 P87  H4   C9   C8   110.24  3.000
 P87  H3   C9   C8   113.26  3.000
 P87  H4   C9   C10  110.12  3.000
 P87  H3   C9   C10  112.13  3.000
 P87  C8   C9   C10  103.20  3.000
 P87  H6   C8   H5   107.76  3.000
 P87  H6   C8   C7   112.08  3.000
 P87  H5   C8   C7   110.06  3.000
 P87  H6   C8   C9   113.53  3.000
 P87  H5   C8   C9   110.22  3.000
 P87  C7   C8   C9   103.15  3.000
 P87  H8   C7   H7   107.83  3.000
 P87  H8   C7   C8   112.13  3.000
 P87  H7   C7   C8   111.04  3.000
 P87  H8   C7   N    111.71  3.000
 P87  H7   C7   N    110.91  3.000
 P87  C8   C7   N    103.25  3.000
 P87  H10  C5   H9   105.31  3.000
 P87  H10  C5   C4   109.79  3.000
 P87  H9   C5   C4   110.40  3.000
 P87  H10  C5   C6   109.57  3.000
 P87  H9   C5   C6   108.08  3.000
 P87  C4   C5   C6   113.36  3.000
 P87  H12  C4   H11  106.56  3.000
 P87  H12  C4   C1   109.08  3.000
 P87  H11  C4   C1   109.05  3.000
 P87  H12  C4   C5   110.11  3.000
 P87  H11  C4   C5   109.63  3.000
 P87  C1   C4   C5   112.23  3.000
 P87  H13  C1   C    109.29  3.000
 P87  H13  C1   C2   109.02  3.000
 P87  C    C1   C2   102.73  3.000
 P87  H13  C1   C4   108.62  3.000
 P87  C    C1   C4   113.66  3.000
 P87  C2   C1   C4   113.33  3.000
 P87  H15  C2   H14  107.89  3.000
 P87  H15  C2   O    108.59  3.000
 P87  H14  C2   O    110.62  3.000
 P87  H15  C2   C1   113.67  3.000
 P87  H14  C2   C1   109.98  3.000
 P87  O    C2   C1   106.08  3.000
 P87  C3   O    C2   105.67  3.000
 P87  H17  C3   H16  107.91  3.000
 P87  H17  C3   C    113.74  3.000
 P87  H16  C3   C    110.33  3.000
 P87  H17  C3   O    108.68  3.000
 P87  H16  C3   O    110.53  3.000
 P87  C    C3   O    105.64  3.000
 P87  H19  C    H18  107.23  3.000
 P87  H19  C    C3   111.41  3.000
 P87  H18  C    C3   111.33  3.000
 P87  H19  C    C1   112.13  3.000
 P87  H18  C    C1   110.88  3.000
 P87  C3   C    C1   103.93  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
 P87  CONST_01  C7   N   C6   O1    180.00   0.0  0
 P87  CONST_02  C10  N   C6   O1      0.00   0.0  0
 P87  CONST_03  C5   C6  N    C10   180.00   0.0  0
 P87  CONST_04  C5   C6  N    C7      0.00   0.0  0
 P87  Var_01    C9   C8  C7   N      31.33  30.0  1
 P87  Var_02    C8   C9  C10  N      30.40  30.0  1
 P87  Var_03    C8   C7  N    C10   -12.76  30.0  1
 P87  Var_04    C7   C8  C9   C10   -38.43  30.0  1
 P87  Var_05    C7   N   C10  C9    -11.14  30.0  1
 P87  Var_06    O    C3  C    C1     22.62  30.0  1
 P87  Var_07    C    C3  O    C2    -39.16  30.0  1
 P87  Var_08    H14  C2  O    C3    -79.40  30.0  1
 P87  Var_09    C1   C4  C5   C6   -177.45  30.0  3
 P87  Var_10    C4   C5  C6   N     172.50  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
 P87  chir_01  C1  C2  C  C4  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
 P87  plan-1  O1   0.020
 P87  plan-1  C6   0.020
 P87  plan-1  N    0.020
 P87  plan-1  C10  0.020
 P87  plan-1  C7   0.020
 P87  plan-1  C5   0.020

