# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:35:35 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-N-tert-butylpiperidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)[C@@H]1CCCCN1
#
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
 PPL  PPL  (2S)-N-tert-butylpiperidine-2-carboxamide  ligand  33  13  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PPL
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
 PPL  N1    N  NH1   0  -0.600  -1.2107  -0.1110  -2.0274
 PPL  C2    C  CH1   0  -0.179  -0.1171  -0.3103  -1.1025
 PPL  C3    C  CH2   0  -0.419   1.1263   0.4270  -1.6122
 PPL  C4    C  CH2   0  -0.446   1.4871  -0.0366  -3.0185
 PPL  C5    C  CH2   0  -0.426   0.2842   0.0798  -3.9472
 PPL  C6    C  CH2   0  -0.295  -0.9140  -0.6401  -3.3490
 PPL  C     C  C     0   0.542  -0.4827   0.2266   0.2789
 PPL  O     O  O     0  -0.492  -1.2578   1.1598   0.4283
 PPL  N     N  NH1   0  -0.652   0.1591  -0.3945   1.2810
 PPL  C1'   C  CT    0   0.102   0.1077  -0.0598   2.7079
 PPL  C2'   C  CH3   0  -0.680   1.0472  -1.0400   3.4086
 PPL  C3'   C  CH3   0  -0.640  -1.3081  -0.2446   3.2571
 PPL  C4'   C  CH3   0  -0.642   0.5977   1.3673   2.9548
 PPL  HN1   H  HNH1  0   0.349  -2.0471  -0.5557  -1.6714
 PPL  H2    H  HCH1  0   0.217   0.1484  -1.3786  -1.0039
 PPL  H31   H  HCH2  0   0.224   0.9197   1.5015  -1.6155
 PPL  H32   H  HCH2  0   0.236   1.9606   0.2593  -0.9275
 PPL  H41   H  HCH2  0   0.236   2.3298   0.5435  -3.4005
 PPL  H42   H  HCH2  0   0.215   1.8172  -1.0803  -2.9810
 PPL  H51   H  HCH2  0   0.215   0.0328   1.1337  -4.0985
 PPL  H52   H  HCH2  0   0.229   0.5132  -0.3397  -4.9291
 PPL  H61   H  HCH2  0   0.233  -1.7937  -0.5009  -3.9807
 PPL  H62   H  HCH2  0   0.187  -0.7037  -1.7227  -3.3307
 PPL  HN    H  HNH1  0   0.397   0.7440  -1.1761   1.0297
 PPL  H2'1  H  HCH3  0   0.241   1.0403  -0.8621   4.4838
 PPL  H2'2  H  HCH3  0   0.237   0.7398  -2.0742   3.2394
 PPL  H2'3  H  HCH3  0   0.237   2.0753  -0.9277   3.0580
 PPL  H3'1  H  HCH3  0   0.225  -1.6593  -1.2636   3.0860
 PPL  H3'2  H  HCH3  0   0.224  -1.3182  -0.0619   4.3329
 PPL  H3'3  H  HCH3  0   0.239  -2.0137   0.4427   2.7943
 PPL  H4'1  H  HCH3  0   0.226   1.6083   1.5040   2.5666
 PPL  H4'2  H  HCH3  0   0.238  -0.0516   2.1053   2.4879
 PPL  H4'3  H  HCH3  0   0.224   0.6214   1.5693   4.0270

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
 PPL  N1   C2    single  1.446  0.020  1.446
 PPL  N1   C6    single  1.454  0.020  1.454
 PPL  N1   HN1   single  0.890  0.020  1.040
 PPL  C2   C3    single  1.533  0.020  1.533
 PPL  C2   C     single  1.527  0.020  1.527
 PPL  C2   H2    single  0.970  0.020  1.090
 PPL  C3   C4    single  1.524  0.020  1.524
 PPL  C3   H31   single  0.970  0.020  1.090
 PPL  C3   H32   single  0.970  0.020  1.090
 PPL  C4   C5    single  1.524  0.020  1.524
 PPL  C4   H41   single  0.970  0.020  1.090
 PPL  C4   H42   single  0.970  0.020  1.090
 PPL  C5   C6    single  1.520  0.020  1.520
 PPL  C5   H51   single  0.970  0.020  1.090
 PPL  C5   H52   single  0.970  0.020  1.090
 PPL  C6   H61   single  0.970  0.020  1.090
 PPL  C6   H62   single  0.970  0.020  1.090
 PPL  C    O     double  1.222  0.020  1.222
 PPL  C    N     single  1.342  0.020  1.342
 PPL  N    C1'   single  1.466  0.020  1.466
 PPL  N    HN    single  0.860  0.020  1.020
 PPL  C1'  C2'   single  1.528  0.020  1.528
 PPL  C1'  C3'   single  1.530  0.020  1.530
 PPL  C1'  C4'   single  1.529  0.020  1.529
 PPL  C2'  H2'1  single  0.970  0.020  1.090
 PPL  C2'  H2'2  single  0.970  0.020  1.090
 PPL  C2'  H2'3  single  0.970  0.020  1.090
 PPL  C3'  H3'1  single  0.970  0.020  1.090
 PPL  C3'  H3'2  single  0.970  0.020  1.090
 PPL  C3'  H3'3  single  0.970  0.020  1.090
 PPL  C4'  H4'1  single  0.970  0.020  1.090
 PPL  C4'  H4'2  single  0.970  0.020  1.090
 PPL  C4'  H4'3  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
 PPL  HN1   N1   C6    109.17  3.000
 PPL  HN1   N1   C2    109.85  3.000
 PPL  C6    N1   C2    112.14  3.000
 PPL  H2    C2   C     108.46  3.000
 PPL  H2    C2   C3    107.45  3.000
 PPL  C     C2   C3    109.03  3.000
 PPL  H2    C2   N1    111.84  3.000
 PPL  C     C2   N1    110.44  3.000
 PPL  C3    C2   N1    109.54  3.000
 PPL  H32   C3   H31   107.27  3.000
 PPL  H32   C3   C4    110.55  3.000
 PPL  H31   C3   C4    109.92  3.000
 PPL  H32   C3   C2    109.71  3.000
 PPL  H31   C3   C2    108.67  3.000
 PPL  C4    C3   C2    110.64  3.000
 PPL  H42   C4   H41   106.59  3.000
 PPL  H42   C4   C5    109.36  3.000
 PPL  H41   C4   C5    110.82  3.000
 PPL  H42   C4   C3    109.25  3.000
 PPL  H41   C4   C3    110.11  3.000
 PPL  C5    C4   C3    110.62  3.000
 PPL  H52   C5   H51   107.09  3.000
 PPL  H52   C5   C6    109.70  3.000
 PPL  H51   C5   C6    109.23  3.000
 PPL  H52   C5   C4    110.67  3.000
 PPL  H51   C5   C4    109.83  3.000
 PPL  C6    C5   C4    110.25  3.000
 PPL  H62   C6   H61   106.76  3.000
 PPL  H62   C6   C5    108.72  3.000
 PPL  H61   C6   C5    110.30  3.000
 PPL  H62   C6   N1    112.39  3.000
 PPL  H61   C6   N1    108.36  3.000
 PPL  C5    C6   N1    110.24  3.000
 PPL  N     C    O     124.42  3.000
 PPL  N     C    C2    113.47  3.000
 PPL  O     C    C2    122.08  3.000
 PPL  HN    N    C1'   116.09  3.000
 PPL  HN    N    C     116.75  3.000
 PPL  C1'   N    C     127.15  3.000
 PPL  C4'   C1'  C3'   110.57  3.000
 PPL  C4'   C1'  C2'   109.12  3.000
 PPL  C3'   C1'  C2'   109.08  3.000
 PPL  C4'   C1'  N     111.03  3.000
 PPL  C3'   C1'  N     110.74  3.000
 PPL  C2'   C1'  N     106.16  3.000
 PPL  H2'3  C2'  H2'2  108.22  3.000
 PPL  H2'3  C2'  H2'1  107.82  3.000
 PPL  H2'2  C2'  H2'1  107.80  3.000
 PPL  H2'3  C2'  C1'   111.45  3.000
 PPL  H2'2  C2'  C1'   111.30  3.000
 PPL  H2'1  C2'  C1'   110.11  3.000
 PPL  H3'3  C3'  H3'2  107.91  3.000
 PPL  H3'3  C3'  H3'1  108.33  3.000
 PPL  H3'2  C3'  H3'1  107.93  3.000
 PPL  H3'3  C3'  C1'   111.78  3.000
 PPL  H3'2  C3'  C1'   110.01  3.000
 PPL  H3'1  C3'  C1'   110.76  3.000
 PPL  H4'3  C4'  H4'2  107.99  3.000
 PPL  H4'3  C4'  H4'1  107.83  3.000
 PPL  H4'2  C4'  H4'1  108.36  3.000
 PPL  H4'3  C4'  C1'   109.78  3.000
 PPL  H4'2  C4'  C1'   111.87  3.000
 PPL  H4'1  C4'  C1'   110.87  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
 PPL  CONST_01  C1'   N    C    C2   180.00   0.0  0
 PPL  CONST_02  HN    N    C    C2     0.00   0.0  0
 PPL  CONST_03  C1'   N    C    O      0.00   0.0  0
 PPL  Var_01    C4    C5   C6   N1    56.58  30.0  1
 PPL  Var_02    C5    C6   N1   C2   -61.88  30.0  1
 PPL  Var_03    C5    C4   C3   C2    53.17  30.0  1
 PPL  Var_04    C6    C5   C4   C3   -53.09  30.0  1
 PPL  Var_05    C2'   C1'  N    C   -178.22  30.0  3
 PPL  Var_06    H2'1  C2'  C1'  N   -178.69  30.0  3
 PPL  Var_07    H3'1  C3'  C1'  N     56.72  30.0  3
 PPL  Var_08    H4'1  C4'  C1'  N    -56.77  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
 PPL  chir_01  C2  N1  C3  C  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
 PPL  plan-1  C2   0.020
 PPL  plan-1  C    0.020
 PPL  plan-1  O    0.020
 PPL  plan-1  N    0.020
 PPL  plan-1  C1'  0.020
 PPL  plan-1  HN   0.020

