# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:58:38 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 1-[[(3~{S})-1,4-dioxaspiro[4.5]decan-3-yl]methyl]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCN(CC1)C[C@H]2COC3(CCCCC3)O2
#
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
 LOE  LOE  1-[[(3~{S})-1,4-dioxaspiro[4.5]decan-3-yl]methyl]piperidine  ligand  42  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LOE
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
 LOE  C4   C  CH2   0  -0.470  -2.7270   1.4807  -0.4220
 LOE  C5   C  CH2   0  -0.442  -4.2284   1.2302  -0.3019
 LOE  C6   C  CH2   0  -0.218  -1.0006  -1.4443  -1.4287
 LOE  C7   C  CH1   0  -0.024   0.1134  -0.4584  -1.0751
 LOE  C8   C  CH2   0  -0.279   1.2673  -1.1316  -0.3592
 LOE  C10  C  CH2   0  -0.435   4.0601   1.3862  -0.5224
 LOE  C13  C  CH2   0  -0.277   3.2235  -0.9155   0.9842
 LOE  N    N  NT    0  -0.415   2.3119  -0.2318   0.0811
 LOE  C    C  CH2   0  -0.435  -4.5810   0.5877   1.0359
 LOE  O    O  O2    0  -0.505  -2.1699  -0.6780  -1.2618
 LOE  C1   C  CH2   0  -0.436  -3.7762  -0.6862   1.2700
 LOE  C11  C  CH2   0  -0.438   5.0333   0.7343   0.4501
 LOE  C12  C  CH2   0  -0.438   4.2598   0.0366   1.5611
 LOE  C2   C  CH2   0  -0.464  -2.2777  -0.4264   1.1497
 LOE  C3   C  CT    0   0.526  -1.9228   0.2100  -0.1952
 LOE  C9   C  CH2   0  -0.286   3.0348   0.3788  -1.0221
 LOE  O1   O  O2    0  -0.520  -0.5375   0.4941  -0.2505
 LOE  H1   H  HCH2  0   0.238  -2.4774   1.8964  -1.4017
 LOE  H2   H  HCH2  0   0.228  -2.4211   2.2174   0.3270
 LOE  H3   H  HCH2  0   0.233  -4.7639   2.1746  -0.4217
 LOE  H4   H  HCH2  0   0.218  -4.5632   0.5849  -1.1195
 LOE  H5   H  HCH2  0   0.253  -0.9464  -1.7995  -2.4575
 LOE  H6   H  HCH2  0   0.213  -0.9893  -2.3179  -0.7624
 LOE  H7   H  HCH1  0   0.234   0.4605   0.0430  -1.9858
 LOE  H8   H  HCH2  0   0.229   0.8651  -1.6418   0.5217
 LOE  H9   H  HCH2  0   0.197   1.6569  -1.9255  -1.0237
 LOE  H11  H  HCH2  0   0.229   4.5891   1.8121  -1.3777
 LOE  H12  H  HCH2  0   0.232   2.6410  -1.3607   1.7948
 LOE  H13  H  HCH2  0   0.181   3.7422  -1.7489   0.4748
 LOE  H15  H  HCH2  0   0.212  -4.3768   1.2994   1.8432
 LOE  H16  H  HCH2  0   0.230  -5.6510   0.3712   1.0780
 LOE  H17  H  HCH2  0   0.231  -3.9982  -1.0969   2.2575
 LOE  H18  H  HCH2  0   0.217  -4.0754  -1.4488   0.5448
 LOE  H19  H  HCH2  0   0.210   5.6435  -0.0009  -0.0859
 LOE  H20  H  HCH2  0   0.230   5.7229   1.4727   0.8652
 LOE  H21  H  HCH2  0   0.214   3.7541   0.7814   2.1833
 LOE  H22  H  HCH2  0   0.229   4.9342  -0.5202   2.2155
 LOE  H23  H  HCH2  0   0.226  -1.9577   0.2555   1.9438
 LOE  H24  H  HCH2  0   0.236  -1.7140  -1.3536   1.2951
 LOE  H25  H  HCH2  0   0.238   2.3303   0.8888  -1.6811
 LOE  H26  H  HCH2  0   0.182   3.5445  -0.3861  -1.6376
 LOE  H10  H  HCH2  0   0.214   3.5382   2.2101  -0.0262

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
 LOE  C    C1   single  1.525  0.020  1.525
 LOE  C    C5   single  1.525  0.020  1.525
 LOE  C1   C2   single  1.526  0.020  1.526
 LOE  C5   C4   single  1.527  0.020  1.527
 LOE  C12  C11  single  1.523  0.020  1.523
 LOE  C12  C13  single  1.521  0.020  1.521
 LOE  C2   C3   single  1.530  0.020  1.530
 LOE  C4   C3   single  1.521  0.020  1.521
 LOE  C11  C10  single  1.522  0.020  1.522
 LOE  C13  N    single  1.454  0.020  1.454
 LOE  C3   O1   single  1.415  0.020  1.415
 LOE  C3   O    single  1.410  0.020  1.410
 LOE  O1   C7   single  1.418  0.020  1.418
 LOE  N    C9   single  1.453  0.020  1.453
 LOE  N    C8   single  1.447  0.020  1.447
 LOE  C10  C9   single  1.522  0.020  1.522
 LOE  C7   C8   single  1.516  0.020  1.516
 LOE  C7   C6   single  1.529  0.020  1.529
 LOE  O    C6   single  1.408  0.020  1.408
 LOE  C4   H1   single  0.970  0.020  1.090
 LOE  C4   H2   single  0.970  0.020  1.090
 LOE  C5   H3   single  0.970  0.020  1.090
 LOE  C5   H4   single  0.970  0.020  1.090
 LOE  C6   H5   single  0.970  0.020  1.090
 LOE  C6   H6   single  0.970  0.020  1.090
 LOE  C7   H7   single  0.970  0.020  1.090
 LOE  C8   H8   single  0.970  0.020  1.090
 LOE  C8   H9   single  0.970  0.020  1.090
 LOE  C10  H10  single  0.970  0.020  1.090
 LOE  C10  H11  single  0.970  0.020  1.090
 LOE  C13  H12  single  0.970  0.020  1.090
 LOE  C13  H13  single  0.970  0.020  1.090
 LOE  C    H15  single  0.970  0.020  1.090
 LOE  C    H16  single  0.970  0.020  1.090
 LOE  C1   H17  single  0.970  0.020  1.090
 LOE  C1   H18  single  0.970  0.020  1.090
 LOE  C11  H19  single  0.970  0.020  1.090
 LOE  C11  H20  single  0.970  0.020  1.090
 LOE  C12  H21  single  0.970  0.020  1.090
 LOE  C12  H22  single  0.970  0.020  1.090
 LOE  C2   H23  single  0.970  0.020  1.090
 LOE  C2   H24  single  0.970  0.020  1.090
 LOE  C9   H25  single  0.970  0.020  1.090
 LOE  C9   H26  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
 LOE  H2   C4   H1   107.07  3.000
 LOE  H2   C4   C3   108.22  3.000
 LOE  H1   C4   C3   109.30  3.000
 LOE  H2   C4   C5   109.36  3.000
 LOE  H1   C4   C5   110.94  3.000
 LOE  C3   C4   C5   111.79  3.000
 LOE  H4   C5   H3   106.14  3.000
 LOE  H4   C5   C    109.65  3.000
 LOE  H3   C5   C    110.31  3.000
 LOE  H4   C5   C4   109.81  3.000
 LOE  H3   C5   C4   109.36  3.000
 LOE  C    C5   C4   111.43  3.000
 LOE  H6   C6   H5   108.23  3.000
 LOE  H6   C6   O    111.68  3.000
 LOE  H5   C6   O    109.30  3.000
 LOE  H6   C6   C7   111.41  3.000
 LOE  H5   C6   C7   113.09  3.000
 LOE  O    C6   C7   103.10  3.000
 LOE  H7   C7   O1   108.74  3.000
 LOE  H7   C7   C8   110.77  3.000
 LOE  O1   C7   C8   111.91  3.000
 LOE  H7   C7   C6   109.48  3.000
 LOE  C8   C7   C6   112.17  3.000
 LOE  O1   C7   C6   103.48  3.000
 LOE  H9   C8   H8   106.16  3.000
 LOE  H9   C8   N    112.01  3.000
 LOE  H8   C8   N    108.07  3.000
 LOE  H9   C8   C7   107.65  3.000
 LOE  H8   C8   C7   107.91  3.000
 LOE  N    C8   C7   114.65  3.000
 LOE  H11  C10  H10  107.01  3.000
 LOE  H11  C10  C9   109.11  3.000
 LOE  H10  C10  C9   109.03  3.000
 LOE  H11  C10  C11  110.95  3.000
 LOE  H10  C10  C11  109.73  3.000
 LOE  C9   C10  C11  110.91  3.000
 LOE  H13  C13  H12  106.53  3.000
 LOE  H13  C13  C12  109.08  3.000
 LOE  H12  C13  C12  109.68  3.000
 LOE  H13  C13  N    111.25  3.000
 LOE  H12  C13  N    108.54  3.000
 LOE  C12  C13  N    111.62  3.000
 LOE  C9   N    C13  110.92  3.000
 LOE  C9   N    C8   112.90  3.000
 LOE  C13  N    C8   110.43  3.000
 LOE  H16  C    H15  106.43  3.000
 LOE  H16  C    C1   110.21  3.000
 LOE  H15  C    C1   109.35  3.000
 LOE  H16  C    C5   110.10  3.000
 LOE  H15  C    C5   109.25  3.000
 LOE  C1   C    C5   111.38  3.000
 LOE  C3   O    C6   106.68  3.000
 LOE  H18  C1   H17  106.36  3.000
 LOE  H18  C1   C2   109.58  3.000
 LOE  H17  C1   C2   109.57  3.000
 LOE  H18  C1   C    109.65  3.000
 LOE  H17  C1   C    110.22  3.000
 LOE  C2   C1   C    111.35  3.000
 LOE  H20  C11  H19  106.73  3.000
 LOE  H20  C11  C12  110.68  3.000
 LOE  H19  C11  C12  109.41  3.000
 LOE  H20  C11  C10  110.91  3.000
 LOE  H19  C11  C10  109.32  3.000
 LOE  C12  C11  C10  109.73  3.000
 LOE  H22  C12  H21  106.96  3.000
 LOE  H22  C12  C11  110.92  3.000
 LOE  H21  C12  C11  109.73  3.000
 LOE  H22  C12  C13  109.20  3.000
 LOE  H21  C12  C13  109.07  3.000
 LOE  C11  C12  C13  110.86  3.000
 LOE  H24  C2   H23  106.31  3.000
 LOE  H24  C2   C3   110.46  3.000
 LOE  H23  C2   C3   108.11  3.000
 LOE  H24  C2   C1   110.55  3.000
 LOE  H23  C2   C1   109.64  3.000
 LOE  C3   C2   C1   111.59  3.000
 LOE  O1   C3   C2   110.18  3.000
 LOE  O1   C3   O    105.57  3.000
 LOE  C2   C3   O    111.25  3.000
 LOE  O    C3   C4   108.71  3.000
 LOE  O1   C3   C4   110.13  3.000
 LOE  C2   C3   C4   110.86  3.000
 LOE  H26  C9   H25  106.54  3.000
 LOE  H26  C9   N    111.17  3.000
 LOE  H25  C9   N    109.49  3.000
 LOE  H26  C9   C10  109.27  3.000
 LOE  H25  C9   C10  108.89  3.000
 LOE  N    C9   C10  111.34  3.000
 LOE  C3   O1   C7   109.71  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
 LOE  Var_01  C1   C    C5   C4    -54.53  30.0  1
 LOE  Var_02  C1   C2   C3   C4     55.16  30.0  1
 LOE  Var_03  C2   C1   C    C5     54.75  30.0  1
 LOE  Var_04  C2   C3   C4   C5    -55.00  30.0  1
 LOE  Var_05  C13  C12  C11  C10    52.95  30.0  1
 LOE  Var_06  C13  N    C9   C10   -59.24  30.0  1
 LOE  Var_07  C11  C12  C13  N     -56.35  30.0  1
 LOE  Var_08  C11  C10  C9   N      56.78  30.0  1
 LOE  Var_09  C3   C2   C1   C     -55.22  30.0  1
 LOE  Var_10  C3   C4   C5   C      54.98  30.0  1
 LOE  Var_11  C9   C10  C11  C12   -53.23  30.0  1
 LOE  Var_12  C9   N    C13  C12    59.13  30.0  1
 LOE  Var_13  H5   C6   O    C3   -154.50  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
 LOE  chir_01  C7  O1  C8  C6  negativ

