# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:18:09 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 6-piperidin-1-yl-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN1CCCCC1)C(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
 LP6  LP6  6-piperidin-1-yl-L-norleucine  L-peptide  36  15  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_LP6
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
 LP6  N     N  NH2    0  -0.788  32.0116  0.6258  55.5897
 LP6  CA    C  CH1    0  -0.207  31.3353  1.9159  55.6434
 LP6  CB    C  CH2    0  -0.418  31.0677  2.3134  57.0991
 LP6  CG    C  CH2    0  -0.410  30.1717  1.3401  57.8574
 LP6  CD    C  CH2    0  -0.456  29.9682  1.6996  59.3280
 LP6  CE    C  CH2    0  -0.287  29.1314  2.9672  59.5225
 LP6  NZ    N  NT     0  -0.413  28.8836  3.3943  60.8858
 LP6  CM    C  CH2    0  -0.276  30.0746  3.8268  61.5909
 LP6  C     C  C      0   0.382  32.0826  3.0764  54.9351
 LP6  C13   C  CH2    0  -0.429  29.7047  4.5219  62.8943
 LP6  O     O  O      0  -0.603  33.2958  2.9114  54.6949
 LP6  CCA   C  CH2    0  -0.438  28.8443  3.6121  63.7625
 LP6  CCC   C  CH2    0  -0.428  27.6437  3.1051  62.9717
 LP6  CCD   C  CH2    0  -0.276  28.0968  2.4618  61.6682
 LP6  OXT   O  OC    -1  -0.617  31.4062  4.0984  54.6932
 LP6  HN1   H  HNH2   0   0.331  32.0042  0.2960  54.6318
 LP6  HN2   H  HNH2   0   0.320  32.9926  0.7939  55.7864
 LP6  HA    H  HCH1   0   0.200  30.3617  1.7980  55.1528
 LP6  HB1C  H  HCH2   0   0.198  32.0273  2.4022  57.6249
 LP6  HB2C  H  HCH2   0   0.216  30.6251  3.3115  57.1037
 LP6  HG1C  H  HCH2   0   0.198  29.1969  1.2825  57.3581
 LP6  HG2C  H  HCH2   0   0.218  30.6040  0.3402  57.7908
 LP6  HD1C  H  HCH2   0   0.222  29.4792  0.8616  59.8330
 LP6  HD2C  H  HCH2   0   0.211  30.9465  1.8160  59.8061
 LP6  HE1C  H  HCH2   0   0.223  29.6085  3.8032  59.0022
 LP6  HE2C  H  HCH2   0   0.215  28.1610  2.8194  59.0344
 LP6  HM1C  H  HCH2   0   0.182  30.7571  2.9887  61.8175
 LP6  HM2C  H  HCH2   0   0.225  30.6292  4.5129  60.9448
 LP6  HCD1  H  HCH2   0   0.225  27.2281  2.1569  61.0779
 LP6  HCD2  H  HCH2   0   0.181  28.6534  1.5395  61.9092
 LP6  H131  H  HCH2   0   0.224  30.6145  4.8147  63.4234
 LP6  H132  H  HCH2   0   0.210  29.1562  5.4406  62.6661
 LP6  HCA1  H  HCH2   0   0.207  29.4439  2.7561  64.0915
 LP6  HCA2  H  HCH2   0   0.227  28.5206  4.1335  64.6662
 LP6  HCC1  H  HCH2   0   0.223  27.0744  2.3798  63.5578
 LP6  HCC2  H  HCH2   0   0.210  26.9685  3.9364  62.7474

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
 LP6  N    CA    single  1.458  0.019  1.458
 LP6  CA   CB    single  1.530  0.020  1.530
 LP6  CA   C     single  1.525  0.021  1.525
 LP6  CB   CG    single  1.525  0.020  1.525
 LP6  CG   CD    single  1.528  0.020  1.528
 LP6  CD   CE    single  1.531  0.020  1.531
 LP6  CE   NZ    single  1.450  0.020  1.450
 LP6  NZ   CM    single  1.450  0.020  1.450
 LP6  NZ   CCD   single  1.449  0.020  1.449
 LP6  CM   C13   single  1.523  0.020  1.523
 LP6  C    O     deloc   1.231  0.020  1.231
 LP6  C    OXT   deloc   1.249  0.020  1.249
 LP6  C13  CCA   single  1.524  0.020  1.524
 LP6  CCA  CCC   single  1.524  0.020  1.524
 LP6  CCC  CCD   single  1.523  0.020  1.523
 LP6  N    HN1   single  0.890  0.020  1.040
 LP6  N    HN2   single  0.890  0.020  1.040
 LP6  CA   HA    single  0.970  0.020  0.970
 LP6  CB   HB1C  single  0.970  0.020  1.090
 LP6  CB   HB2C  single  0.970  0.020  1.090
 LP6  CG   HG1C  single  0.970  0.020  1.090
 LP6  CG   HG2C  single  0.970  0.020  1.090
 LP6  CD   HD1C  single  0.970  0.020  1.090
 LP6  CD   HD2C  single  0.970  0.020  1.090
 LP6  CE   HE1C  single  0.970  0.020  1.090
 LP6  CE   HE2C  single  0.970  0.020  1.090
 LP6  CM   HM1C  single  0.970  0.020  1.090
 LP6  CM   HM2C  single  0.970  0.020  1.090
 LP6  CCD  HCD1  single  0.970  0.020  1.090
 LP6  CCD  HCD2  single  0.970  0.020  1.090
 LP6  C13  H131  single  0.970  0.020  1.090
 LP6  C13  H132  single  0.970  0.020  1.090
 LP6  CCA  HCA1  single  0.970  0.020  1.090
 LP6  CCA  HCA2  single  0.970  0.020  1.090
 LP6  CCC  HCC1  single  0.970  0.020  1.090
 LP6  CCC  HCC2  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
 LP6  HN2   N    HN1   104.14  3.000
 LP6  HN2   N    CA    107.15  3.000
 LP6  HN1   N    CA    108.64  3.000
 LP6  HA    CA   C     109.00  3.000
 LP6  HA    CA   CB    109.00  3.000
 LP6  C     CA   CB    110.10  1.900
 LP6  HA    CA   N     110.00  3.000
 LP6  C     CA   N     111.00  2.800
 LP6  CB    CA   N     110.50  1.700
 LP6  HB2C  CB   HB1C  106.17  3.000
 LP6  HB2C  CB   CG    110.07  3.000
 LP6  HB1C  CB   CG    109.09  3.000
 LP6  HB2C  CB   CA    108.17  3.000
 LP6  HB1C  CB   CA    108.87  3.000
 LP6  CG    CB   CA    114.17  3.000
 LP6  HG2C  CG   HG1C  106.03  3.000
 LP6  HG2C  CG   CD    109.09  3.000
 LP6  HG1C  CG   CD    109.40  3.000
 LP6  HG2C  CG   CB    108.77  3.000
 LP6  HG1C  CG   CB    109.24  3.000
 LP6  CD    CG   CB    114.01  3.000
 LP6  HD2C  CD   HD1C  106.22  3.000
 LP6  HD2C  CD   CE    110.16  3.000
 LP6  HD1C  CD   CE    109.34  3.000
 LP6  HD2C  CD   CG    109.05  3.000
 LP6  HD1C  CD   CG    108.89  3.000
 LP6  CE    CD   CG    112.95  3.000
 LP6  HE2C  CE   HE1C  106.10  3.000
 LP6  HE2C  CE   NZ    107.88  3.000
 LP6  HE1C  CE   NZ    107.25  3.000
 LP6  HE2C  CE   CD    108.40  3.000
 LP6  HE1C  CE   CD    109.50  3.000
 LP6  NZ    CE   CD    117.17  3.000
 LP6  CCD   NZ   CM    112.04  3.000
 LP6  CCD   NZ   CE    114.25  3.000
 LP6  CM    NZ   CE    113.87  3.000
 LP6  HM2C  CM   HM1C  106.50  3.000
 LP6  HM2C  CM   C13   110.03  3.000
 LP6  HM1C  CM   C13   108.71  3.000
 LP6  HM2C  CM   NZ    108.44  3.000
 LP6  HM1C  CM   NZ    112.40  3.000
 LP6  C13   CM   NZ    110.66  3.000
 LP6  OXT   C    O     126.68  3.000
 LP6  OXT   C    CA    116.08  3.000
 LP6  O     C    CA    120.80  1.700
 LP6  H132  C13  H131  107.07  3.000
 LP6  H132  C13  CCA   109.70  3.000
 LP6  H131  C13  CCA   110.75  3.000
 LP6  H132  C13  CM    109.06  3.000
 LP6  H131  C13  CM    109.54  3.000
 LP6  CCA   C13  CM    110.63  3.000
 LP6  HCA2  CCA  HCA1  106.66  3.000
 LP6  HCA2  CCA  CCC   110.77  3.000
 LP6  HCA1  CCA  CCC   109.08  3.000
 LP6  HCA2  CCA  C13   110.72  3.000
 LP6  HCA1  CCA  C13   109.18  3.000
 LP6  CCC   CCA  C13   110.34  3.000
 LP6  HCC2  CCC  HCC1  107.02  3.000
 LP6  HCC2  CCC  CCD   109.22  3.000
 LP6  HCC1  CCC  CCD   109.50  3.000
 LP6  HCC2  CCC  CCA   109.85  3.000
 LP6  HCC1  CCC  CCA   110.66  3.000
 LP6  CCD   CCC  CCA   110.51  3.000
 LP6  HCD2  CCD  HCD1  106.58  3.000
 LP6  HCD2  CCD  CCC   108.43  3.000
 LP6  HCD1  CCD  CCC   110.09  3.000
 LP6  HCD2  CCD  NZ    112.44  3.000
 LP6  HCD1  CCD  NZ    108.62  3.000
 LP6  CCC   CCD  NZ    110.60  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
 LP6  Var_01  CCA  C13  CM   NZ     56.05  30.0  1
 LP6  Var_02  CCA  CCC  CCD  NZ    -56.44  30.0  1
 LP6  Var_03  CCC  CCD  NZ   CM     60.30  30.0  1
 LP6  Var_04  CCC  CCA  C13  CM    -53.09  30.0  1
 LP6  Var_05  CCD  NZ   CM   C13   -60.08  30.0  1
 LP6  Var_06  CCD  CCC  CCA  C13    53.26  30.0  1
 LP6  Var_07  CM   NZ   CE   CD     66.45  30.0  3
 LP6  Var_08  NZ   CE   CD   CG   -179.88  30.0  3
 LP6  Var_09  CD   CG   CB   CA    176.90  30.0  3
 LP6  Var_10  CE   CD   CG   CB     68.91  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
 LP6  chir_01  CA  N  CB  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
 LP6  plan-1  CA   0.020
 LP6  plan-1  C    0.020
 LP6  plan-1  O    0.020
 LP6  plan-1  OXT  0.020

