# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 06:16:01 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (2S)-1-acetylpiperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCCC[C@H]1C(O)=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
 APP  APP  '(2S)-1-acetylpiperidine-2-carboxylic acid'  L-peptide  24  12  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_APP
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
 APP  N1   N  NT     0  -0.465   0.5913   0.0505  -0.4582
 APP  C    C  C      0   0.525   1.6523   0.2560   0.3651
 APP  O    O  O      0  -0.499   1.5140   0.5848   1.5358
 APP  CM   C  CH3    0  -0.803   3.0387   0.0618  -0.2072
 APP  C2   C  CH1    0  -0.140  -0.7327   0.3098   0.1092
 APP  C'   C  C      0   0.411  -0.9477  -0.4011   1.4695
 APP  O1   O  O      0  -0.617  -0.5399  -1.5730   1.5614
 APP  O2   O  OC    -1  -0.619  -1.6132   0.2324   2.3119
 APP  C3   C  CH2    0  -0.461  -1.8556  -0.1975  -0.8019
 APP  C4   C  CH2    0  -0.441  -1.6766   0.1740  -2.2623
 APP  C5   C  CH2    0  -0.441  -0.3412  -0.3730  -2.7284
 APP  C6   C  CH2    0  -0.289   0.7872   0.2079  -1.8996
 APP  HM1  H  HCH3   0   0.263   3.7621   0.1000   0.6035
 APP  HM2  H  HCH3   0   0.259   3.1420  -0.8931  -0.7230
 APP  HM3  H  HCH3   0   0.263   3.2904   0.8481  -0.9210
 APP  H2   H  HCH1   0   0.205  -0.8608   1.3918   0.2428
 APP  H31  H  HCH2   0   0.238  -2.7969   0.1921  -0.4090
 APP  H32  H  HCH2   0   0.219  -1.9060  -1.2877  -0.7255
 APP  H41  H  HCH2   0   0.213  -1.7011   1.2617  -2.3887
 APP  H42  H  HCH2   0   0.235  -2.4955  -0.2340  -2.8587
 APP  H51  H  HCH2   0   0.240  -0.1503  -0.1325  -3.7761
 APP  H52  H  HCH2   0   0.222  -0.3404  -1.4640  -2.6450
 APP  H61  H  HCH2   0   0.222   0.8910   1.2732  -2.1456
 APP  H62  H  HCH2   0   0.261   1.7188  -0.2728  -2.1907

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
 APP  N1  C    single  1.359  0.020  1.359
 APP  N1  C2   single  1.464  0.020  1.464
 APP  N1  C6   single  1.463  0.020  1.463
 APP  C   O    double  1.231  0.020  1.231
 APP  C   CM   single  1.512  0.020  1.512
 APP  CM  HM1  single  0.970  0.020  1.090
 APP  CM  HM2  single  0.970  0.020  1.090
 APP  CM  HM3  single  0.970  0.020  1.090
 APP  C2  C'   single  1.550  0.020  1.550
 APP  C2  C3   single  1.532  0.020  1.532
 APP  C2  H2   single  0.970  0.020  1.090
 APP  C'  O1   deloc   1.244  0.020  1.244
 APP  C'  O2   deloc   1.246  0.020  1.246
 APP  C3  C4   single  1.517  0.020  1.517
 APP  C3  H31  single  0.970  0.020  1.090
 APP  C3  H32  single  0.970  0.020  1.090
 APP  C4  C5   single  1.517  0.020  1.517
 APP  C4  H41  single  0.970  0.020  1.090
 APP  C4  H42  single  0.970  0.020  1.090
 APP  C5  C6   single  1.516  0.020  1.516
 APP  C5  H51  single  0.970  0.020  1.090
 APP  C5  H52  single  0.970  0.020  1.090
 APP  C6  H61  single  0.970  0.020  1.090
 APP  C6  H62  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
 APP  C6   N1  C2   118.94  3.000
 APP  C6   N1  C    118.44  3.000
 APP  C2   N1  C    116.41  3.000
 APP  CM   C   O    120.01  3.000
 APP  CM   C   N1   117.85  3.000
 APP  O    C   N1   122.15  3.000
 APP  HM3  CM  HM2  107.45  3.000
 APP  HM3  CM  HM1  107.99  3.000
 APP  HM2  CM  HM1  108.70  3.000
 APP  HM3  CM  C    111.49  3.000
 APP  HM2  CM  C    112.23  3.000
 APP  HM1  CM  C    108.86  3.000
 APP  H2   C2  C3   108.25  3.000
 APP  H2   C2  C'   109.21  3.000
 APP  C3   C2  C'   105.57  3.000
 APP  H2   C2  N1   109.11  3.000
 APP  C3   C2  N1   111.95  3.000
 APP  C'   C2  N1   112.61  3.000
 APP  O2   C'  O1   127.14  3.000
 APP  O2   C'  C2   115.73  3.000
 APP  O1   C'  C2   116.83  3.000
 APP  H32  C3  H31  106.89  3.000
 APP  H32  C3  C4   108.46  3.000
 APP  H31  C3  C4   111.14  3.000
 APP  H32  C3  C2   108.79  3.000
 APP  H31  C3  C2   107.44  3.000
 APP  C4   C3  C2   113.88  3.000
 APP  H42  C4  H41  106.94  3.000
 APP  H42  C4  C5   110.95  3.000
 APP  H41  C4  C5   110.02  3.000
 APP  H42  C4  C3   110.22  3.000
 APP  H41  C4  C3   110.58  3.000
 APP  C5   C4  C3   108.14  3.000
 APP  H52  C5  H51  107.02  3.000
 APP  H52  C5  C6   109.87  3.000
 APP  H51  C5  C6   108.07  3.000
 APP  H52  C5  C4   109.68  3.000
 APP  H51  C5  C4   111.68  3.000
 APP  C6   C5  C4   110.44  3.000
 APP  H62  C6  H61  106.72  3.000
 APP  H62  C6  C5   108.77  3.000
 APP  H61  C6  C5   108.64  3.000
 APP  H62  C6  N1   109.31  3.000
 APP  H61  C6  N1   109.73  3.000
 APP  C5   C6  N1   113.44  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
 APP  CONST_01  C2   N1  C   O      0.00   0.0  0
 APP  CONST_03  C2   N1  C   CM   180.00   0.0  0
 APP  Var_01    C4   C5  C6  N1    52.72  30.0  1
 APP  Var_02    C5   C6  N1  C2   -43.12  30.0  1
 APP  Var_03    C5   C4  C3  C2    57.33  30.0  1
 APP  Var_04    C6   C5  C4  C3   -59.40  30.0  1
 APP  Var_05    HM1  CM  C   N1  -170.74  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
 APP  chir_01  C2  N1  C'  C3  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
 APP  plan-1  N1  0.020
 APP  plan-1  C   0.020
 APP  plan-1  O   0.020
 APP  plan-1  CM  0.020
 APP  plan-1  C2  0.020
 APP  plan-1  C6  0.020
 APP  plan-2  C2  0.020
 APP  plan-2  C'  0.020
 APP  plan-2  O1  0.020
 APP  plan-2  O2  0.020

