# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 13:26:02 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (2R,3S)-3-amino-4-cyclohexyl-1-(pyridin-4-yloxy)butan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1CCCCC1)[C@@H](O)COc2ccncc2
#
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
 PCH  PCH  (2R,3S)-3-amino-4-cyclohexyl-1-(pyridin-4-yloxy)butan-2-ol  ligand  43  19  .  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_PCH
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
 PCH  N     N  NH2   0  -0.824   0.0082   1.8907  -1.0038
 PCH  CA    C  CH1   0  -0.126   0.1950   0.4396  -0.9740
 PCH  CB    C  CH2   0  -0.433   0.9041  -0.1090  -2.2108
 PCH  CG    C  CH1   0  -0.228   0.2087   0.1746  -3.5418
 PCH  CD1   C  CH2   0  -0.410   1.0690  -0.3239  -4.7044
 PCH  CD2   C  CH2   0  -0.423  -1.1858  -0.4483  -3.6146
 PCH  CE1   C  CH2   0  -0.432   0.4091  -0.0790  -6.0574
 PCH  CE2   C  CH2   0  -0.427  -1.8503  -0.2157  -4.9690
 PCH  CZ    C  CH2   0  -0.427  -0.9781  -0.7097  -6.1175
 PCH  CH    C  CH1   0   0.019   0.9674   0.0879   0.3129
 PCH  OH    O  OH1   0  -0.669   2.0506   0.9615   0.5007
 PCH  CM    C  CH2   0  -0.199   0.0129   0.1152   1.4955
 PCH  O1    O  O2    0  -0.459   0.7458  -0.2117   2.6683
 PCH  C1    C  CR6   0   0.470   0.1122  -0.2433   3.8402
 PCH  C2    C  CR16  0  -0.413   0.8641  -0.5999   4.9626
 PCH  C3    C  CR16  0  -0.065   0.2395  -0.6429   6.1923
 PCH  N4    N  N     0  -0.423  -1.0486  -0.3635   6.3880
 PCH  C5    C  CR16  0  -0.067  -1.7509  -0.0264   5.3151
 PCH  C6    C  CR16  0  -0.439  -1.2371   0.0509   4.0286
 PCH  HN1   H  HNH2  0   0.357   0.5934   2.3142  -1.7124
 PCH  HN2   H  HNH2  0   0.363  -0.9424   2.1277  -1.2497
 PCH  HA    H  HCH1  0   0.238  -0.7896  -0.0317  -0.9002
 PCH  HB1   H  HCH2  0   0.224   1.9221   0.2970  -2.2453
 PCH  HB2   H  HCH2  0   0.221   1.0150  -1.1929  -2.0944
 PCH  HG    H  HCH1  0   0.201   0.0994   1.2617  -3.6588
 PCH  HD11  H  HCH2  0   0.222   2.0504   0.1579  -4.6693
 PCH  HD12  H  HCH2  0   0.203   1.2463  -1.3994  -4.5791
 PCH  HD21  H  HCH2  0   0.204  -1.1000  -1.5256  -3.4263
 PCH  HD22  H  HCH2  0   0.226  -1.8271  -0.0464  -2.8256
 PCH  HE11  H  HCH2  0   0.207   0.3224   0.9996  -6.2285
 PCH  HE12  H  HCH2  0   0.224   1.0398  -0.4711  -6.8594
 PCH  HE21  H  HCH2  0   0.207  -2.0376   0.8563  -5.0973
 PCH  HE22  H  HCH2  0   0.224  -2.8273  -0.7048  -4.9941
 PCH  HCZ1  H  HCH2  0   0.223  -1.4529  -0.4869  -7.0765
 PCH  HCZ2  H  HCH2  0   0.206  -0.8839  -1.7997  -6.0620
 PCH  HH    H  HCH1  0   0.233   1.3799  -0.9231   0.2253
 PCH  HO    H  HOH1  0   0.438   1.6894   1.8470   0.3446
 PCH  HM1   H  HCH2  0   0.230  -0.4432   1.1075   1.5903
 PCH  HM2   H  HCH2  0   0.233  -0.7887  -0.6140   1.3362
 PCH  HC2   H  HCR6  0   0.275   1.9159  -0.8363   4.8701
 PCH  HC3   H  HCR6  0   0.264   0.8133  -0.9197   7.0700
 PCH  HC5   H  HCR6  0   0.264  -2.7999   0.1993   5.4743
 PCH  HC6   H  HCR6  0   0.288  -1.8922   0.3343   3.2167

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
 PCH  N    CA    single    1.463  0.020  1.463
 PCH  N    HN1   single    0.890  0.020  1.040
 PCH  N    HN2   single    0.890  0.020  1.040
 PCH  CA   CB    single    1.528  0.020  1.528
 PCH  CA   CH    single    1.542  0.020  1.542
 PCH  CA   HA    single    0.970  0.020  1.090
 PCH  CB   CG    single    1.528  0.020  1.528
 PCH  CB   HB1   single    0.970  0.020  1.090
 PCH  CB   HB2   single    0.970  0.020  1.090
 PCH  CG   CD1   single    1.530  0.020  1.530
 PCH  CG   CD2   single    1.529  0.020  1.529
 PCH  CG   HG    single    0.970  0.020  1.090
 PCH  CD1  CE1   single    1.525  0.020  1.525
 PCH  CD1  HD11  single    0.970  0.020  1.090
 PCH  CD1  HD12  single    0.970  0.020  1.090
 PCH  CD2  CE2   single    1.526  0.020  1.526
 PCH  CD2  HD21  single    0.970  0.020  1.090
 PCH  CD2  HD22  single    0.970  0.020  1.090
 PCH  CE1  CZ    single    1.525  0.020  1.525
 PCH  CE1  HE11  single    0.970  0.020  1.090
 PCH  CE1  HE12  single    0.970  0.020  1.090
 PCH  CE2  CZ    single    1.524  0.020  1.524
 PCH  CE2  HE21  single    0.970  0.020  1.090
 PCH  CE2  HE22  single    0.970  0.020  1.090
 PCH  CZ   HCZ1  single    0.970  0.020  1.090
 PCH  CZ   HCZ2  single    0.970  0.020  1.090
 PCH  CH   OH    single    1.404  0.020  1.404
 PCH  CH   CM    single    1.520  0.020  1.520
 PCH  CH   HH    single    0.970  0.020  1.090
 PCH  OH   HO    single    0.850  0.020  0.980
 PCH  CM   O1    single    1.421  0.020  1.421
 PCH  CM   HM1   single    0.970  0.020  1.090
 PCH  CM   HM2   single    0.970  0.020  1.090
 PCH  O1   C1    single    1.333  0.020  1.333
 PCH  C1   C2    aromatic  1.397  0.020  1.397
 PCH  C1   C6    aromatic  1.394  0.020  1.394
 PCH  C2   C3    aromatic  1.380  0.020  1.380
 PCH  C2   HC2   single    0.930  0.020  1.080
 PCH  C3   N4    aromatic  1.332  0.020  1.332
 PCH  C3   HC3   single    0.930  0.020  1.080
 PCH  N4   C5    aromatic  1.326  0.020  1.326
 PCH  C5   C6    aromatic  1.387  0.020  1.387
 PCH  C5   HC5   single    0.930  0.020  1.080
 PCH  C6   HC6   single    0.930  0.020  1.080

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
 PCH  HN2   N    HN1   106.00  3.000
 PCH  HN2   N    CA    110.96  3.000
 PCH  HN1   N    CA    110.82  3.000
 PCH  HA    CA   CH    107.24  3.000
 PCH  HA    CA   CB    108.52  3.000
 PCH  CH    CA   CB    111.18  3.000
 PCH  HA    CA   N     108.28  3.000
 PCH  CH    CA   N     107.89  3.000
 PCH  CB    CA   N     113.51  3.000
 PCH  HB2   CB   HB1   106.00  3.000
 PCH  HB2   CB   CG    108.79  3.000
 PCH  HB1   CB   CG    109.04  3.000
 PCH  HB2   CB   CA    108.43  3.000
 PCH  HB1   CB   CA    108.88  3.000
 PCH  CG    CB   CA    115.29  3.000
 PCH  HG    CG   CD2   107.89  3.000
 PCH  HG    CG   CD1   107.30  3.000
 PCH  CD2   CG   CD1   110.12  3.000
 PCH  HG    CG   CB    108.76  3.000
 PCH  CD2   CG   CB    112.39  3.000
 PCH  CD1   CG   CB    110.22  3.000
 PCH  HD12  CD1  HD11  106.44  3.000
 PCH  HD12  CD1  CE1   109.19  3.000
 PCH  HD11  CD1  CE1   110.24  3.000
 PCH  HD12  CD1  CG    108.87  3.000
 PCH  HD11  CD1  CG    109.67  3.000
 PCH  CE1   CD1  CG    112.25  3.000
 PCH  HD22  CD2  HD21  106.43  3.000
 PCH  HD22  CD2  CE2   109.21  3.000
 PCH  HD21  CD2  CE2   109.63  3.000
 PCH  HD22  CD2  CG    110.54  3.000
 PCH  HD21  CD2  CG    108.70  3.000
 PCH  CE2   CD2  CG    112.16  3.000
 PCH  HE12  CE1  HE11  106.51  3.000
 PCH  HE12  CE1  CZ    110.34  3.000
 PCH  HE11  CE1  CZ    109.21  3.000
 PCH  HE12  CE1  CD1   110.10  3.000
 PCH  HE11  CE1  CD1   109.32  3.000
 PCH  CZ    CE1  CD1   111.23  3.000
 PCH  HE22  CE2  HE21  106.40  3.000
 PCH  HE22  CE2  CZ    110.44  3.000
 PCH  HE21  CE2  CZ    109.06  3.000
 PCH  HE22  CE2  CD2   109.96  3.000
 PCH  HE21  CE2  CD2   109.11  3.000
 PCH  CZ    CE2  CD2   111.72  3.000
 PCH  HCZ2  CZ   HCZ1  106.53  3.000
 PCH  HCZ2  CZ   CE2   109.48  3.000
 PCH  HCZ1  CZ   CE2   110.27  3.000
 PCH  HCZ2  CZ   CE1   109.35  3.000
 PCH  HCZ1  CZ   CE1   110.21  3.000
 PCH  CE2   CZ   CE1   110.90  3.000
 PCH  HH    CH   CM    108.38  3.000
 PCH  HH    CH   OH    107.12  3.000
 PCH  CM    CH   OH    111.67  3.000
 PCH  HH    CH   CA    109.42  3.000
 PCH  CM    CH   CA    109.31  3.000
 PCH  OH    CH   CA    110.87  3.000
 PCH  HO    OH   CH    105.04  3.000
 PCH  HM2   CM   HM1   108.11  3.000
 PCH  HM2   CM   O1    110.14  3.000
 PCH  HM1   CM   O1    110.57  3.000
 PCH  HM2   CM   CH    109.54  3.000
 PCH  HM1   CM   CH    110.17  3.000
 PCH  O1    CM   CH    108.31  3.000
 PCH  C1    O1   CM    119.08  3.000
 PCH  C6    C1   C2    117.79  3.000
 PCH  C6    C1   O1    125.04  3.000
 PCH  C2    C1   O1    117.17  3.000
 PCH  HC2   C2   C3    120.62  3.000
 PCH  HC2   C2   C1    120.68  3.000
 PCH  C3    C2   C1    118.70  3.000
 PCH  HC3   C3   N4    116.50  3.000
 PCH  HC3   C3   C2    119.32  3.000
 PCH  N4    C3   C2    124.19  3.000
 PCH  C5    N4   C3    116.52  3.000
 PCH  HC5   C5   C6    118.86  3.000
 PCH  HC5   C5   N4    116.51  3.000
 PCH  C6    C5   N4    124.64  3.000
 PCH  HC6   C6   C5    119.12  3.000
 PCH  HC6   C6   C1    122.72  3.000
 PCH  C5    C6   C1    118.16  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
 PCH  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 PCH  CONST_02  N4   C5   C6   C1     0.00   0.0  0
 PCH  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 PCH  CONST_04  C5   N4   C3   C2     0.00   0.0  0
 PCH  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 PCH  CONST_06  C6   C5   N4   C3     0.00   0.0  0
 PCH  CONST_07  C3   C2   C1   O1   180.00   0.0  0
 PCH  CONST_08  C5   C6   C1   O1   180.00   0.0  0
 PCH  CONST_09  HC3  C3   C2   C1   180.00   0.0  0
 PCH  CONST_10  HC5  C5   C6   C1   180.00   0.0  0
 PCH  CONST_11  HC6  C6   C1   C2   180.00   0.0  0
 PCH  CONST_12  HC2  C2   C3   N4   180.00   0.0  0
 PCH  Var_01    CZ   CE1  CD1  CG   -55.88  30.0  1
 PCH  Var_02    CZ   CE2  CD2  CG    55.00  30.0  1
 PCH  Var_03    CE2  CZ   CE1  CD1   55.12  30.0  1
 PCH  Var_04    CE1  CZ   CE2  CD2  -54.82  30.0  1
 PCH  Var_05    C2   C1   O1   CM   178.54  30.0  2
 PCH  Var_06    HM1  CM   O1   C1    58.85  30.0  1

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
 PCH  chir_01  CA  N   CB   CH   negativ
 PCH  chir_02  CG  CB  CD1  CD2  negativ
 PCH  chir_03  CH  OH  CA   CM   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
 PCH  plan-1  O1   0.020
 PCH  plan-1  C1   0.020
 PCH  plan-1  C2   0.020
 PCH  plan-1  C3   0.020
 PCH  plan-1  N4   0.020
 PCH  plan-1  C5   0.020
 PCH  plan-1  C6   0.020
 PCH  plan-1  HC2  0.020
 PCH  plan-1  HC3  0.020
 PCH  plan-1  HC5  0.020
 PCH  plan-1  HC6  0.020

