# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 23:11:43 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (3R)-1-acetyl-3-methylpiperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCCN(C1)C(C)=O
#
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
 1P3  1P3  (3R)-1-acetyl-3-methylpiperidine  ligand  25  10  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_1P3
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
 1P3  C2    C  CH3   0  -0.657   1.3454   0.0710   2.8806
 1P3  C3    C  CH1   0  -0.241   0.4659   0.3323   1.6665
 1P3  C20   C  CH2   0  -0.281   0.8296  -0.6125   0.5217
 1P3  C4    C  CH2   0  -0.426  -1.0164   0.1839   2.0033
 1P3  C5    C  CH2   0  -0.428  -1.8952   0.3429   0.7676
 1P3  N1    N  NT    0  -0.439  -0.0330  -0.4047  -0.6289
 1P3  C6    C  CH2   0  -0.316  -1.4415  -0.6038  -0.3367
 1P3  C7    C  CH3   0  -0.806  -0.5300   0.3444  -2.9050
 1P3  C10   C  C     0   0.512   0.4534   0.1032  -1.7819
 1P3  O11   O  O     0  -0.513   1.6448   0.3508  -1.9361
 1P3  H2C1  H  HCH3  0   0.229   2.4037   0.1989   2.6464
 1P3  H2C2  H  HCH3  0   0.231   1.1002   0.7565   3.6933
 1P3  H2C3  H  HCH3  0   0.216   1.2068  -0.9459   3.2554
 1P3  H3    H  HCH1  0   0.224   0.6438   1.3573   1.3191
 1P3  H201  H  HCH2  0   0.258   1.8661  -0.4789   0.2212
 1P3  H202  H  HCH2  0   0.228   0.7161  -1.6509   0.8576
 1P3  H4C1  H  HCH2  0   0.211  -1.1817  -0.8131   2.4299
 1P3  H4C2  H  HCH2  0   0.235  -1.3018   0.9053   2.7730
 1P3  H5C1  H  HCH2  0   0.238  -2.9394   0.1343   1.0111
 1P3  H5C2  H  HCH2  0   0.223  -1.8506   1.3724   0.3997
 1P3  H6C1  H  HCH2  0   0.239  -1.5844  -1.6401  -0.0118
 1P3  H6C2  H  HCH2  0   0.272  -2.0441  -0.4700  -1.2303
 1P3  H7C1  H  HCH3  0   0.266   0.0109   0.7126  -3.7730
 1P3  H7C2  H  HCH3  0   0.264  -1.0550  -0.5683  -3.1891
 1P3  H7C3  H  HCH3  0   0.262  -1.2852   1.0838  -2.6354

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
 1P3  C2   C3    single  1.522  0.020  1.522
 1P3  C2   H2C1  single  0.970  0.020  1.090
 1P3  C2   H2C2  single  0.970  0.020  1.090
 1P3  C2   H2C3  single  0.970  0.020  1.090
 1P3  C3   C20   single  1.528  0.020  1.528
 1P3  C3   C4    single  1.527  0.020  1.527
 1P3  C3   H3    single  0.970  0.020  1.090
 1P3  C20  N1    single  1.453  0.020  1.453
 1P3  C20  H201  single  0.970  0.020  1.090
 1P3  C20  H202  single  0.970  0.020  1.090
 1P3  C4   C5    single  1.525  0.020  1.525
 1P3  C4   H4C1  single  0.970  0.020  1.090
 1P3  C4   H4C2  single  0.970  0.020  1.090
 1P3  C5   C6    single  1.524  0.020  1.524
 1P3  C5   H5C1  single  0.970  0.020  1.090
 1P3  C5   H5C2  single  0.970  0.020  1.090
 1P3  N1   C6    single  1.452  0.020  1.452
 1P3  N1   C10   single  1.351  0.020  1.351
 1P3  C6   H6C1  single  0.970  0.020  1.090
 1P3  C6   H6C2  single  0.970  0.020  1.090
 1P3  C7   C10   single  1.512  0.020  1.512
 1P3  C7   H7C1  single  0.970  0.020  1.090
 1P3  C7   H7C2  single  0.970  0.020  1.090
 1P3  C7   H7C3  single  0.970  0.020  1.090
 1P3  C10  O11   double  1.227  0.020  1.227

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
 1P3  H2C3  C2   H2C2  107.51  3.000
 1P3  H2C3  C2   H2C1  107.80  3.000
 1P3  H2C2  C2   H2C1  107.71  3.000
 1P3  H2C3  C2   C3    111.11  3.000
 1P3  H2C2  C2   C3    110.88  3.000
 1P3  H2C1  C2   C3    111.65  3.000
 1P3  H3    C3   C4    108.55  3.000
 1P3  H3    C3   C20   107.57  3.000
 1P3  C4    C3   C20   109.64  3.000
 1P3  H3    C3   C2    108.63  3.000
 1P3  C4    C3   C2    111.61  3.000
 1P3  C20   C3   C2    110.73  3.000
 1P3  H202  C20  H201  107.43  3.000
 1P3  H202  C20  N1    108.44  3.000
 1P3  H201  C20  N1    109.23  3.000
 1P3  H202  C20  C3    109.34  3.000
 1P3  H201  C20  C3    110.98  3.000
 1P3  N1    C20  C3    111.31  3.000
 1P3  H4C2  C4   H4C1  106.66  3.000
 1P3  H4C2  C4   C5    110.58  3.000
 1P3  H4C1  C4   C5    108.86  3.000
 1P3  H4C2  C4   C3    110.15  3.000
 1P3  H4C1  C4   C3    108.69  3.000
 1P3  C5    C4   C3    111.75  3.000
 1P3  H5C2  C5   H5C1  107.08  3.000
 1P3  H5C2  C5   C6    109.19  3.000
 1P3  H5C1  C5   C6    109.12  3.000
 1P3  H5C2  C5   C4    110.32  3.000
 1P3  H5C1  C5   C4    110.51  3.000
 1P3  C6    C5   C4    110.55  3.000
 1P3  C10   N1   C6    124.93  3.000
 1P3  C10   N1   C20   121.07  3.000
 1P3  C6    N1   C20   113.38  3.000
 1P3  H6C2  C6   H6C1  106.75  3.000
 1P3  H6C2  C6   N1    110.84  3.000
 1P3  H6C1  C6   N1    108.42  3.000
 1P3  H6C2  C6   C5    110.76  3.000
 1P3  H6C1  C6   C5    109.51  3.000
 1P3  N1    C6   C5    110.45  3.000
 1P3  H7C3  C7   H7C2  107.37  3.000
 1P3  H7C3  C7   H7C1  108.19  3.000
 1P3  H7C2  C7   H7C1  108.36  3.000
 1P3  H7C3  C7   C10   112.02  3.000
 1P3  H7C2  C7   C10   111.91  3.000
 1P3  H7C1  C7   C10   108.88  3.000
 1P3  O11   C10  C7    120.41  3.000
 1P3  O11   C10  N1    122.21  3.000
 1P3  C7    C10  N1    117.38  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
 1P3  CONST_01  C7    C10  N1   C20   180.00   0.0  0
 1P3  CONST_02  O11   C10  N1   C20     0.00   0.0  0
 1P3  CONST_03  C7    C10  N1   C6      0.00   0.0  0
 1P3  CONST_04  O11   C10  N1   C6    180.00   0.0  0
 1P3  Var_01    C6    N1   C20  C3    -58.95  30.0  1
 1P3  Var_02    C6    C5   C4   C3     53.41  30.0  1
 1P3  Var_03    N1    C6   C5   C4    -54.92  30.0  1
 1P3  Var_04    H7C1  C7   C10  N1   -177.70  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
 1P3  chir_01  C3  C2  C20  C4  negativ

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
 1P3  plan-1  C20  0.020
 1P3  plan-1  N1   0.020
 1P3  plan-1  C6   0.020
 1P3  plan-1  C7   0.020
 1P3  plan-1  C10  0.020
 1P3  plan-1  O11  0.020

