# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:31:28 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (2R,4R,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-prop-2-yn-1-ylhexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC1CCCCC1)[C@H](O)C[C@@H](CC#C)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
 PCE  PCE  '(2R,4R,5S)-5-amino-6-cyclohexyl-4-hydroxy-2-prop-2-yn-1-ylhexanoic acid'  L-peptide  43  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PCE
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
 PCE  N     N  NH2    0  -0.787  -0.3127   1.5984  -0.7482
 PCE  CA    C  CH1    0  -0.143  -0.1325   0.1531  -0.8242
 PCE  CB    C  CH2    0  -0.396   0.7467  -0.3050  -1.9939
 PCE  CG    C  CH1    0  -0.231   0.3108   0.1971  -3.3702
 PCE  CD1   C  CH2    0  -0.409   1.3303  -0.2136  -4.4334
 PCE  CD2   C  CH2    0  -0.423  -1.0824  -0.2946  -3.7649
 PCE  CE1   C  CH2    0  -0.431   0.9356   0.2643  -5.8268
 PCE  CE2   C  CH2    0  -0.426  -1.4859   0.1819  -5.1572
 PCE  CZ    C  CH2    0  -0.428  -0.4581  -0.2234  -6.2076
 PCE  CH    C  CH1    0   0.068   0.4268  -0.3239   0.5280
 PCE  OH    O  OH1    0  -0.667   0.8636  -1.6691   0.4898
 PCE  CM    C  CH2    0  -0.460  -0.5741  -0.1072   1.6598
 PCE  CA2   C  CH1    0  -0.339   0.0043  -0.2940   3.0670
 PCE  CB2   C  CH2    0  -0.568   0.9144   0.8860   3.4320
 PCE  CG2   C  CSP    0   0.290   1.5405   0.7276   4.7380
 PCE  CD3   C  CSP1   0  -0.586   2.0562   0.5762   5.8149
 PCE  C     C  C      0   0.412  -1.1535  -0.4279   4.0765
 PCE  O     O  O      0  -0.615  -1.7669   0.6224   4.3565
 PCE  OXT   O  OC    -1  -0.613  -1.4096  -1.5709   4.5040
 PCE  H     H  HNH2   0   0.335   0.5850   2.0580  -0.8555
 PCE  H2    H  HNH2   0   0.347  -0.8793   1.9204  -1.5224
 PCE  HA    H  HCH1   0   0.216  -1.1336  -0.2816  -0.9428
 PCE  HB2   H  HCH2   0   0.206   1.7758   0.0304  -1.8090
 PCE  HB3   H  HCH2   0   0.209   0.7841  -1.3977  -2.0208
 PCE  HG    H  HCH1   0   0.193   0.2885   1.2952  -3.3524
 PCE  HD12  H  HCH2   0   0.220   2.3170   0.1769  -4.1672
 PCE  HD13  H  HCH2   0   0.201   1.4223  -1.3068  -4.4355
 PCE  HD23  H  HCH2   0   0.203  -1.0913  -1.3917  -3.7401
 PCE  HD22  H  HCH2   0   0.226  -1.8276   0.0340  -3.0350
 PCE  HE12  H  HCH2   0   0.206   0.9527   1.3599  -5.8503
 PCE  HE13  H  HCH2   0   0.223   1.6704  -0.0725  -6.5626
 PCE  HE23  H  HCH2   0   0.206  -1.5853   1.2731  -5.1516
 PCE  HE22  H  HCH2   0   0.223  -2.4703  -0.2151  -5.4179
 PCE  HZ2   H  HCH2   0   0.223  -0.7431   0.1681  -7.1874
 PCE  HZ3   H  HCH2   0   0.206  -0.4478  -1.3151  -6.3013
 PCE  HH    H  HCH1   0   0.208   1.3361   0.2591   0.7217
 PCE  HO    H  HOH1   0   0.438   0.0863  -2.2325   0.4078
 PCE  HM1   H  HCH2   0   0.233  -1.0062   0.8911   1.5697
 PCE  HM2   H  HCH2   0   0.225  -1.4002  -0.8148   1.5117
 PCE  HA2   H  HCH1   0   0.210   0.5974  -1.2125   3.0855
 PCE  HB21  H  HCH2   0   0.261   1.7032   1.0150   2.6858
 PCE  HB22  H  HCH2   0   0.257   0.3273   1.8074   3.4259
 PCE  HD31  H  H      0   0.276   2.5119   0.4443   6.7690

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
 PCE  N    CA    single  1.458  0.019  1.458
 PCE  N    H     single  0.860  0.020  0.860
 PCE  N    H2    single  0.868  0.020  1.013
 PCE  CA   CB    single  1.521  0.033  1.521
 PCE  CA   CH    single  1.539  0.020  1.539
 PCE  CA   HA    single  0.970  0.020  0.970
 PCE  CB   CG    single  1.528  0.020  1.528
 PCE  CB   HB2   single  0.939  0.020  1.096
 PCE  CB   HB3   single  0.939  0.020  1.096
 PCE  CG   CD1   single  1.529  0.020  1.529
 PCE  CG   CD2   single  1.529  0.020  1.529
 PCE  CG   HG    single  0.939  0.020  1.096
 PCE  CD1  CE1   single  1.525  0.020  1.525
 PCE  CD1  HD12  single  0.939  0.020  1.096
 PCE  CD1  HD13  single  0.939  0.020  1.096
 PCE  CD2  CE2   single  1.526  0.020  1.526
 PCE  CD2  HD23  single  0.939  0.020  1.096
 PCE  CD2  HD22  single  0.939  0.020  1.096
 PCE  CE1  CZ    single  1.525  0.020  1.525
 PCE  CE1  HE12  single  0.939  0.020  1.096
 PCE  CE1  HE13  single  0.939  0.020  1.096
 PCE  CE2  CZ    single  1.524  0.020  1.524
 PCE  CE2  HE23  single  0.939  0.020  1.096
 PCE  CE2  HE22  single  0.939  0.020  1.096
 PCE  CZ   HZ2   single  0.939  0.020  1.096
 PCE  CZ   HZ3   single  0.939  0.020  1.096
 PCE  CH   OH    single  1.415  0.020  1.415
 PCE  CH   CM    single  1.526  0.020  1.526
 PCE  CH   HH    single  0.939  0.020  1.096
 PCE  OH   HO    single  0.832  0.020  0.971
 PCE  CM   CA2   single  1.533  0.020  1.533
 PCE  CM   HM1   single  0.939  0.020  1.096
 PCE  CM   HM2   single  0.939  0.020  1.096
 PCE  CA2  CB2   single  1.534  0.020  1.534
 PCE  CA2  C     single  1.542  0.020  1.542
 PCE  CA2  HA2   single  0.939  0.020  1.096
 PCE  CB2  CG2   single  1.457  0.020  1.457
 PCE  CB2  HB21  single  0.939  0.020  1.096
 PCE  CB2  HB22  single  0.939  0.020  1.096
 PCE  CG2  CD3   triple  1.203  0.020  1.203
 PCE  CD3  HD31  single  0.913  0.020  1.066
 PCE  C    O     deloc   1.231  0.020  1.231
 PCE  C    OXT   deloc   1.247  0.020  1.247

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
 PCE  H2    N    H     105.69  3.000
 PCE  H2    N    CA    110.16  3.000
 PCE  H     N    CA    114.00  3.000
 PCE  HA    CA   CH    107.68  3.000
 PCE  HA    CA   CB    109.00  3.000
 PCE  CH    CA   CB    111.67  3.000
 PCE  HA    CA   N     110.00  3.000
 PCE  CH    CA   N     107.83  3.000
 PCE  CB    CA   N     110.40  1.500
 PCE  HB3   CB   HB2   106.10  3.000
 PCE  HB3   CB   CG    108.41  3.000
 PCE  HB2   CB   CG    108.57  3.000
 PCE  HB3   CB   CA    109.69  3.000
 PCE  HB2   CB   CA    108.52  3.000
 PCE  CG    CB   CA    115.17  3.000
 PCE  HG    CG   CD2   107.88  3.000
 PCE  HG    CG   CD1   107.06  3.000
 PCE  CD2   CG   CD1   109.97  3.000
 PCE  HG    CG   CB    108.64  3.000
 PCE  CD2   CG   CB    112.74  3.000
 PCE  CD1   CG   CB    110.35  3.000
 PCE  HD13  CD1  HD12  106.28  3.000
 PCE  HD13  CD1  CE1   109.41  3.000
 PCE  HD12  CD1  CE1   110.11  3.000
 PCE  HD13  CD1  CG    108.96  3.000
 PCE  HD12  CD1  CG    109.64  3.000
 PCE  CE1   CD1  CG    112.25  3.000
 PCE  HD22  CD2  HD23  106.25  3.000
 PCE  HD22  CD2  CE2   109.57  3.000
 PCE  HD23  CD2  CE2   109.31  3.000
 PCE  HD22  CD2  CG    110.60  3.000
 PCE  HD23  CD2  CG    108.85  3.000
 PCE  CE2   CD2  CG    112.09  3.000
 PCE  HE13  CE1  HE12  106.44  3.000
 PCE  HE13  CE1  CZ    110.35  3.000
 PCE  HE12  CE1  CZ    109.18  3.000
 PCE  HE13  CE1  CD1   110.16  3.000
 PCE  HE12  CE1  CD1   109.20  3.000
 PCE  CZ    CE1  CD1   111.38  3.000
 PCE  HE22  CE2  HE23  106.34  3.000
 PCE  HE22  CE2  CZ    110.27  3.000
 PCE  HE23  CE2  CZ    109.23  3.000
 PCE  HE22  CE2  CD2   110.02  3.000
 PCE  HE23  CE2  CD2   109.28  3.000
 PCE  CZ    CE2  CD2   111.55  3.000
 PCE  HZ3   CZ   HZ2   106.42  3.000
 PCE  HZ3   CZ   CE2   109.28  3.000
 PCE  HZ2   CZ   CE2   110.28  3.000
 PCE  HZ3   CZ   CE1   109.35  3.000
 PCE  HZ2   CZ   CE1   110.34  3.000
 PCE  CE2   CZ   CE1   111.05  3.000
 PCE  HH    CH   CM    109.70  3.000
 PCE  HH    CH   OH    104.71  3.000
 PCE  CM    CH   OH    110.94  3.000
 PCE  HH    CH   CA    106.95  3.000
 PCE  CM    CH   CA    111.67  3.000
 PCE  OH    CH   CA    112.53  3.000
 PCE  HO    OH   CH    108.01  3.000
 PCE  HM2   CM   HM1   106.29  3.000
 PCE  HM2   CM   CA2   109.22  3.000
 PCE  HM1   CM   CA2   109.68  3.000
 PCE  HM2   CM   CH    107.57  3.000
 PCE  HM1   CM   CH    109.16  3.000
 PCE  CA2   CM   CH    114.58  3.000
 PCE  HA2   CA2  C     108.86  3.000
 PCE  HA2   CA2  CB2   108.68  3.000
 PCE  C     CA2  CB2   110.88  3.000
 PCE  HA2   CA2  CM    108.82  3.000
 PCE  C     CA2  CM    109.16  3.000
 PCE  CB2   CA2  CM    110.39  3.000
 PCE  HB22  CB2  HB21  106.52  3.000
 PCE  HB22  CB2  CG2   109.12  3.000
 PCE  HB21  CB2  CG2   108.33  3.000
 PCE  HB22  CB2  CA2   109.18  3.000
 PCE  HB21  CB2  CA2   110.87  3.000
 PCE  CG2   CB2  CA2   112.61  3.000
 PCE  CD3   CG2  CB2   180.00  3.000
 PCE  HD31  CD3  CG2   180.00  3.000
 PCE  OXT   C    O     126.40  3.000
 PCE  OXT   C    CA2   117.28  3.000
 PCE  O     C    CA2   116.29  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
 PCE  Var_01  CZ    CE1  CD1  CG   -55.54  30.0  1
 PCE  Var_02  CZ    CE2  CD2  CG    55.43  30.0  1
 PCE  Var_03  CE1   CZ   CE2  CD2  -54.70  30.0  1
 PCE  Var_04  HB21  CB2  CG2  CD3  -96.62  30.0  2

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
 PCE  chir_01  CA   N   CB   CH   negativ
 PCE  chir_02  CG   CB  CD1  CD2  negativ
 PCE  chir_03  CH   OH  CA   CM   negativ
 PCE  chir_04  CA2  CM  CB2  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
 PCE  plan-1  CA2  0.020
 PCE  plan-1  C    0.020
 PCE  plan-1  O    0.020
 PCE  plan-1  OXT  0.020

