# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:05:08 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N@+]1([O-])CC[C@H](CC1)[Si](C)(C)c2ccccc2
#
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
 DP4  DP4  '(1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide'  ligand  40  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DP4
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
 DP4  C1    C   CR16   0  -0.272  -4.3740   1.7549   0.1307
 DP4  C2    C   CR16   0  -0.239  -3.9380   1.0771   1.2610
 DP4  C3    C   CR16   0  -0.304  -2.8888   0.1705   1.1655
 DP4  C4    C   CR6    0  -0.155  -2.2553  -0.0825  -0.0534
 DP4  C5    C   CR16   0  -0.316  -2.7113   0.6116  -1.1788
 DP4  C6    C   CR16   0  -0.243  -3.7569   1.5209  -1.0923
 DP4  C7    C   CH3    0  -1.000  -0.6665  -2.2844   1.3952
 DP4  C8    C   CH3    0  -0.982  -1.1000  -2.4342  -1.6587
 DP4  SI    SI  SI     0   1.064  -0.8106  -1.2855  -0.1941
 DP4  C9    C   CR16   0  -0.516   0.7684  -0.2798  -0.4959
 DP4  C10   C   C      0  -0.445   2.0095  -1.1688  -0.6108
 DP4  C11   C   C      0  -0.283   3.2660  -0.3510  -0.8277
 DP4  C12   C   C      0  -0.283   2.2785   1.5561   0.3292
 DP4  C13   C   C      0  -0.438   0.9983   0.7853   0.5773
 DP4  N1    N   N      1  -0.073   3.4633   0.6407   0.2788
 DP4  O1    O   O     -1  -0.687   3.6138   0.0015   1.4603
 DP4  C14   C   CH3    0  -0.513   4.6733   1.4442  -0.0110
 DP4  HC1   H   HCR6   0   0.256  -5.1916   2.4609   0.2003
 DP4  HC2   H   HCR6   0   0.252  -4.4152   1.2523   2.2172
 DP4  HC3   H   HCR6   0   0.247  -2.5660  -0.3460   2.0623
 DP4  HC5   H   HCR6   0   0.244  -2.2484   0.4431  -2.1454
 DP4  HC6   H   HCR6   0   0.252  -4.0915   2.0474  -1.9774
 DP4  HC71  H   HCH3   0   0.249  -1.5671  -2.8773   1.5646
 DP4  HC72  H   HCH3   0   0.249   0.1748  -2.9772   1.3400
 DP4  HC73  H   HCH3   0   0.246  -0.5165  -1.6541   2.2734
 DP4  HC81  H   HCH3   0   0.245  -1.1508  -1.8817  -2.5990
 DP4  HC82  H   HCH3   0   0.244  -0.2969  -3.1675  -1.7529
 DP4  HC83  H   HCH3   0   0.248  -2.0354  -2.9853  -1.5477
 DP4  HC9   H   HCR6   0   0.232   0.6326   0.2364  -1.4579
 DP4  H101  H   H      0   0.231   2.1336  -1.7773   0.2868
 DP4  H102  H   H      0   0.244   1.9186  -1.8612  -1.4512
 DP4  H111  H   H      0   0.264   4.1573  -0.9782  -0.8405
 DP4  H112  H   H      0   0.241   3.2135   0.1913  -1.7754
 DP4  H121  H   H      0   0.240   2.2219   2.1029  -0.6156
 DP4  H122  H   H      0   0.263   2.4759   2.2724   1.1267
 DP4  H131  H   H      0   0.245   0.1809   1.5083   0.5968
 DP4  H132  H   H      0   0.230   1.0427   0.3344   1.5707
 DP4  H141  H   HCH3   0   0.240   4.5876   1.9637  -0.9646
 DP4  H142  H   HCH3   0   0.261   4.8006   2.1696   0.7890
 DP4  H143  H   HCH3   0   0.261   5.5296   0.7747  -0.0363

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
 DP4  C1   C2    aromatic  1.388  0.020  1.388
 DP4  C1   C6    aromatic  1.390  0.020  1.390
 DP4  C1   HC1   single    0.930  0.020  1.080
 DP4  C2   C3    aromatic  1.390  0.020  1.390
 DP4  C2   HC2   single    0.930  0.020  1.080
 DP4  C3   C4    aromatic  1.397  0.020  1.397
 DP4  C3   HC3   single    0.930  0.020  1.080
 DP4  C4   C5    aromatic  1.399  0.020  1.399
 DP4  C4   SI    single    1.885  0.020  1.885
 DP4  C5   C6    aromatic  1.388  0.020  1.388
 DP4  C5   HC5   single    0.930  0.020  1.080
 DP4  C6   HC6   single    0.930  0.020  1.080
 DP4  C7   SI    single    1.883  0.020  1.883
 DP4  C7   HC71  single    0.970  0.020  1.090
 DP4  C7   HC72  single    0.970  0.020  1.090
 DP4  C7   HC73  single    0.970  0.020  1.090
 DP4  C8   SI    single    1.884  0.020  1.884
 DP4  C8   HC81  single    0.970  0.020  1.090
 DP4  C8   HC82  single    0.970  0.020  1.090
 DP4  C8   HC83  single    0.970  0.020  1.090
 DP4  SI   C9    single    1.896  0.020  1.896
 DP4  C9   C10   single    1.531  0.020  1.531
 DP4  C9   C13   single    1.529  0.020  1.529
 DP4  C9   HC9   single    0.970  0.020  1.090
 DP4  C10  C11   single    1.515  0.020  1.515
 DP4  C10  H101  single    0.970  0.020  1.090
 DP4  C10  H102  single    0.970  0.020  1.090
 DP4  C11  N1    single    1.499  0.020  1.499
 DP4  C11  H111  single    0.970  0.020  1.090
 DP4  C11  H112  single    0.970  0.020  1.090
 DP4  C12  C13   single    1.515  0.020  1.515
 DP4  C12  N1    single    1.498  0.020  1.498
 DP4  C12  H121  single    0.970  0.020  1.090
 DP4  C12  H122  single    0.970  0.020  1.090
 DP4  C13  H131  single    0.970  0.020  1.090
 DP4  C13  H132  single    0.970  0.020  1.090
 DP4  N1   O1    single    1.352  0.020  1.352
 DP4  N1   C14   single    1.481  0.020  1.481
 DP4  C14  H141  single    0.970  0.020  1.090
 DP4  C14  H142  single    0.970  0.020  1.090
 DP4  C14  H143  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
 DP4  HC1   C1   C6    120.12  3.000
 DP4  HC1   C1   C2    120.22  3.000
 DP4  C6    C1   C2    119.67  3.000
 DP4  HC2   C2   C3    119.92  3.000
 DP4  HC2   C2   C1    120.11  3.000
 DP4  C3    C2   C1    119.97  3.000
 DP4  HC3   C3   C4    120.04  3.000
 DP4  HC3   C3   C2    118.60  3.000
 DP4  C4    C3   C2    121.36  3.000
 DP4  SI    C4   C5    120.43  3.000
 DP4  SI    C4   C3    121.88  3.000
 DP4  C5    C4   C3    117.67  3.000
 DP4  HC5   C5   C6    118.59  3.000
 DP4  HC5   C5   C4    120.05  3.000
 DP4  C6    C5   C4    121.36  3.000
 DP4  HC6   C6   C5    120.02  3.000
 DP4  HC6   C6   C1    120.02  3.000
 DP4  C5    C6   C1    119.96  3.000
 DP4  HC73  C7   HC72  107.54  3.000
 DP4  HC73  C7   HC71  107.60  3.000
 DP4  HC72  C7   HC71  107.41  3.000
 DP4  HC73  C7   SI    112.54  3.000
 DP4  HC72  C7   SI    110.68  3.000
 DP4  HC71  C7   SI    110.86  3.000
 DP4  HC83  C8   HC82  107.46  3.000
 DP4  HC83  C8   HC81  107.65  3.000
 DP4  HC82  C8   HC81  107.45  3.000
 DP4  HC83  C8   SI    111.13  3.000
 DP4  HC82  C8   SI    111.33  3.000
 DP4  HC81  C8   SI    111.61  3.000
 DP4  C9    SI   C8    109.12  3.000
 DP4  C9    SI   C7    110.61  3.000
 DP4  C8    SI   C7    110.16  3.000
 DP4  C9    SI   C4    108.15  3.000
 DP4  C8    SI   C4    109.23  3.000
 DP4  C7    SI   C4    109.53  3.000
 DP4  HC9   C9   C13   107.78  3.000
 DP4  HC9   C9   C10   107.87  3.000
 DP4  C13   C9   C10   109.59  3.000
 DP4  HC9   C9   SI    106.57  3.000
 DP4  C13   C9   SI    112.51  3.000
 DP4  C10   C9   SI    112.27  3.000
 DP4  H102  C10  H101  106.78  3.000
 DP4  H102  C10  C11   107.52  3.000
 DP4  H101  C10  C11   108.93  3.000
 DP4  H102  C10  C9    111.00  3.000
 DP4  H101  C10  C9    110.75  3.000
 DP4  C11   C10  C9    111.69  3.000
 DP4  H112  C11  H111  108.34  3.000
 DP4  H112  C11  N1    108.55  3.000
 DP4  H111  C11  N1    106.37  3.000
 DP4  H112  C11  C10   110.62  3.000
 DP4  H111  C11  C10   111.67  3.000
 DP4  N1    C11  C10   111.14  3.000
 DP4  H122  C12  H121  108.24  3.000
 DP4  H122  C12  N1    106.44  3.000
 DP4  H121  C12  N1    108.51  3.000
 DP4  H122  C12  C13   111.57  3.000
 DP4  H121  C12  C13   110.63  3.000
 DP4  N1    C12  C13   111.28  3.000
 DP4  H132  C13  H131  106.72  3.000
 DP4  H132  C13  C12   108.95  3.000
 DP4  H131  C13  C12   107.38  3.000
 DP4  H132  C13  C9    110.91  3.000
 DP4  H131  C13  C9    111.18  3.000
 DP4  C12   C13  C9    111.50  3.000
 DP4  C14   N1   O1    109.67  3.000
 DP4  C14   N1   C12   108.74  3.000
 DP4  O1    N1   C12   110.34  3.000
 DP4  C14   N1   C11   108.78  3.000
 DP4  O1    N1   C11   110.31  3.000
 DP4  C12   N1   C11   108.97  3.000
 DP4  H143  C14  H142  109.61  3.000
 DP4  H143  C14  H141  109.59  3.000
 DP4  H142  C14  H141  109.58  3.000
 DP4  H143  C14  N1    108.30  3.000
 DP4  H142  C14  N1    108.27  3.000
 DP4  H141  C14  N1    111.45  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
 DP4  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 DP4  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 DP4  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 DP4  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 DP4  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 DP4  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 DP4  CONST_07  SI    C4   C3   C2   180.00   0.0  0
 DP4  CONST_08  SI    C4   C5   C6   180.00   0.0  0
 DP4  CONST_09  HC3   C3   C2   C1   180.00   0.0  0
 DP4  CONST_10  HC5   C5   C6   C1   180.00   0.0  0
 DP4  CONST_11  HC6   C6   C1   C2   180.00   0.0  0
 DP4  CONST_12  HC1   C1   C2   C3   180.00   0.0  0
 DP4  CONST_13  HC2   C2   C3   C4   180.00   0.0  0
 DP4  Var_01    N1    C11  C10  C9    57.45  30.0  1
 DP4  Var_02    N1    C12  C13  C9   -57.69  30.0  1
 DP4  Var_03    C9    SI   C4   C3  -108.49  30.0  2
 DP4  Var_04    HC71  C7   SI   C4    61.79  30.0  3
 DP4  Var_05    HC81  C8   SI   C4    61.74  30.0  3

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
 DP4  chir_01  C9  SI   C10  C13  positiv
 DP4  chir_02  N1  C11  C12  C14  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
 DP4  plan-1  C1   0.020
 DP4  plan-1  C2   0.020
 DP4  plan-1  C3   0.020
 DP4  plan-1  C4   0.020
 DP4  plan-1  C5   0.020
 DP4  plan-1  C6   0.020
 DP4  plan-1  SI   0.020
 DP4  plan-1  HC1  0.020
 DP4  plan-1  HC2  0.020
 DP4  plan-1  HC3  0.020
 DP4  plan-1  HC5  0.020
 DP4  plan-1  HC6  0.020

