# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 08:49:27 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  44  19  .  2022-03-23  2022-11-17
;
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  -0.790  -0.2829   1.6371  -0.7444
 PCE  CA    C  CH1   0  -0.147  -0.1211   0.1890  -0.7956
 PCE  CB    C  CH2   0  -0.401   0.7437  -0.3038  -1.9614
 PCE  CG    C  CH1   0  -0.230   0.3020   0.1744  -3.3440
 PCE  CD1   C  CH2   0  -0.410   1.3096  -0.2684  -4.4056
 PCE  CD2   C  CH2   0  -0.424  -1.0988  -0.3117  -3.7195
 PCE  CE1   C  CH2   0  -0.431   0.9107   0.1892  -5.8045
 PCE  CE2   C  CH2   0  -0.427  -1.5073   0.1435  -5.1176
 PCE  CZ    C  CH2   0  -0.428  -0.4907  -0.2900  -6.1677
 PCE  CH    C  CH1   0   0.068   0.4445  -0.2710   0.5595
 PCE  OH    O  OH1   0  -0.663   0.8448  -1.6252   0.5573
 PCE  CM    C  CH2   0  -0.463  -0.5468  -0.0002   1.6895
 PCE  CA2   C  CH1   0  -0.377   0.0580  -0.1969   3.0909
 PCE  CB2   C  CH2   0  -0.574   0.9845   0.9634   3.4638
 PCE  CG2   C  CSP   0   0.293   1.6337   0.7747   4.7543
 PCE  CD3   C  CSP1  0  -0.566   2.1686   0.5964   5.8163
 PCE  C     C  C     0   0.557  -1.0670  -0.3209   4.0907
 PCE  O     O  O     0  -0.438  -1.4988   0.5854   4.7584
 PCE  OXT   O  OH1   0  -0.591  -1.5655  -1.5513   4.1242
 PCE  H     H  HNH2  0   0.339   0.6099   2.0873  -0.9126
 PCE  H2    H  HNH2  0   0.351  -0.8936   1.9481  -1.4885
 PCE  HA    H  HCH1  0   0.222  -1.1279  -0.2358  -0.8974
 PCE  HB2   H  HCH2  0   0.210   1.7775   0.0242  -1.7914
 PCE  HB3   H  HCH2  0   0.212   0.7693  -1.3972  -1.9653
 PCE  HG    H  HCH1  0   0.195   0.2902   1.2726  -3.3497
 PCE  HD12  H  HCH2  0   0.221   2.3028   0.1153  -4.1533
 PCE  HD13  H  HCH2  0   0.202   1.3887  -1.3624  -4.3879
 PCE  HD23  H  HCH2  0   0.203  -1.1175  -1.4080  -3.6745
 PCE  HD22  H  HCH2  0   0.226  -1.8358   0.0375  -2.9908
 PCE  HE12  H  HCH2  0   0.206   0.9393   1.2841  -5.8468
 PCE  HE13  H  HCH2  0   0.223   1.6370  -0.1678  -6.5392
 PCE  HE23  H  HCH2  0   0.206  -1.5968   1.2355  -5.1305
 PCE  HE22  H  HCH2  0   0.224  -2.4971  -0.2490  -5.3643
 PCE  HZ2   H  HCH2  0   0.224  -0.7784   0.0886  -7.1518
 PCE  HZ3   H  HCH2  0   0.206  -0.4926  -1.3831  -6.2436
 PCE  HH    H  HCH1  0   0.220   1.3675   0.2952   0.7333
 PCE  HO    H  HOH1  0   0.442   0.0623  -2.1716   0.4236
 PCE  HM1   H  HCH2  0   0.254  -0.9343   1.0155   1.5958
 PCE  HM2   H  HCH2  0   0.251  -1.4001  -0.6738   1.5546
 PCE  HA2   H  HCH1  0   0.281   0.6269  -1.1303   3.0978
 PCE  HB21  H  HCH2  0   0.288   1.7565   1.0712   2.6988
 PCE  HB22  H  HCH2  0   0.277   0.4254   1.9019   3.4687
 PCE  HD31  H  H     0   0.278   2.6362   0.4445   6.7618
 PCE  HXT   H  HOH1  0   0.481  -2.3254  -1.5866   4.7247

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  1.530  0.020  1.530
 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  1.525  0.020  1.525
 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  1.412  0.020  1.412
 PCE  CH   CM    single  1.527  0.020  1.527
 PCE  CH   HH    single  0.939  0.020  1.096
 PCE  OH   HO    single  0.832  0.020  0.971
 PCE  CM   CA2   single  1.539  0.020  1.539
 PCE  CM   HM1   single  0.939  0.020  1.096
 PCE  CM   HM2   single  0.939  0.020  1.096
 PCE  CA2  CB2   single  1.531  0.020  1.531
 PCE  CA2  C     single  1.510  0.020  1.510
 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  1.202  0.020  1.202
 PCE  CD3  HD31  single  0.913  0.020  1.066
 PCE  C    O     double  1.231  0.020  1.231
 PCE  C    OXT   single  1.328  0.020  1.328
 PCE  OXT  HXT   single  0.832  0.020  0.971

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     105.85  3.000
 PCE  H2    N    CA    110.27  3.000
 PCE  H     N    CA    114.00  3.000
 PCE  HA    CA   CH    107.65  3.000
 PCE  HA    CA   CB    109.00  3.000
 PCE  CH    CA   CB    111.48  3.000
 PCE  HA    CA   N     110.00  3.000
 PCE  CH    CA   N     107.86  3.000
 PCE  CB    CA   N     110.40  1.500
 PCE  HB3   CB   HB2   106.09  3.000
 PCE  HB3   CB   CG    108.45  3.000
 PCE  HB2   CB   CG    108.59  3.000
 PCE  HB3   CB   CA    109.71  3.000
 PCE  HB2   CB   CA    108.51  3.000
 PCE  CG    CB   CA    115.11  3.000
 PCE  HG    CG   CD2   107.86  3.000
 PCE  HG    CG   CD1   107.04  3.000
 PCE  CD2   CG   CD1   109.94  3.000
 PCE  HG    CG   CB    108.71  3.000
 PCE  CD2   CG   CB    112.79  3.000
 PCE  CD1   CG   CB    110.30  3.000
 PCE  HD13  CD1  HD12  106.29  3.000
 PCE  HD13  CD1  CE1   109.45  3.000
 PCE  HD12  CD1  CE1   110.10  3.000
 PCE  HD13  CD1  CG    108.97  3.000
 PCE  HD12  CD1  CG    109.66  3.000
 PCE  CE1   CD1  CG    112.18  3.000
 PCE  HD22  CD2  HD23  106.27  3.000
 PCE  HD22  CD2  CE2   109.56  3.000
 PCE  HD23  CD2  CE2   109.33  3.000
 PCE  HD22  CD2  CG    110.62  3.000
 PCE  HD23  CD2  CG    108.85  3.000
 PCE  CE2   CD2  CG    112.04  3.000
 PCE  HE13  CE1  HE12  106.44  3.000
 PCE  HE13  CE1  CZ    110.36  3.000
 PCE  HE12  CE1  CZ    109.19  3.000
 PCE  HE13  CE1  CD1   110.17  3.000
 PCE  HE12  CE1  CD1   109.17  3.000
 PCE  CZ    CE1  CD1   111.38  3.000
 PCE  HE22  CE2  HE23  106.33  3.000
 PCE  HE22  CE2  CZ    110.26  3.000
 PCE  HE23  CE2  CZ    109.25  3.000
 PCE  HE22  CE2  CD2   110.01  3.000
 PCE  HE23  CE2  CD2   109.27  3.000
 PCE  CZ    CE2  CD2   111.58  3.000
 PCE  HZ3   CZ   HZ2   106.42  3.000
 PCE  HZ3   CZ   CE2   109.28  3.000
 PCE  HZ2   CZ   CE2   110.26  3.000
 PCE  HZ3   CZ   CE1   109.37  3.000
 PCE  HZ2   CZ   CE1   110.34  3.000
 PCE  CE2   CZ   CE1   111.06  3.000
 PCE  HH    CH   CM    109.72  3.000
 PCE  HH    CH   OH    104.88  3.000
 PCE  CM    CH   OH    110.80  3.000
 PCE  HH    CH   CA    107.13  3.000
 PCE  CM    CH   CA    111.10  3.000
 PCE  OH    CH   CA    112.93  3.000
 PCE  HO    OH   CH    108.29  3.000
 PCE  HM2   CM   HM1   106.57  3.000
 PCE  HM2   CM   CA2   109.86  3.000
 PCE  HM1   CM   CA2   109.68  3.000
 PCE  HM2   CM   CH    107.78  3.000
 PCE  HM1   CM   CH    109.38  3.000
 PCE  CA2   CM   CH    113.33  3.000
 PCE  HA2   CA2  C     108.26  3.000
 PCE  HA2   CA2  CB2   109.31  3.000
 PCE  C     CA2  CB2   110.60  3.000
 PCE  HA2   CA2  CM    108.63  3.000
 PCE  C     CA2  CM    108.70  3.000
 PCE  CB2   CA2  CM    111.28  3.000
 PCE  HB22  CB2  HB21  106.26  3.000
 PCE  HB22  CB2  CG2   109.60  3.000
 PCE  HB21  CB2  CG2   108.56  3.000
 PCE  HB22  CB2  CA2   110.02  3.000
 PCE  HB21  CB2  CA2   109.38  3.000
 PCE  CG2   CB2  CA2   112.79  3.000
 PCE  CD3   CG2  CB2   180.00  3.000
 PCE  HD31  CD3  CG2   180.00  3.000
 PCE  OXT   C    O     123.23  3.000
 PCE  OXT   C    CA2   111.86  3.000
 PCE  O     C    CA2   124.87  3.000
 PCE  HXT   OXT  C     110.11  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  CONST_01  HXT   OXT  C    CA2  180.00   0.0  0
 PCE  Var_01    CZ    CE1  CD1  CG   -55.62  30.0  1
 PCE  Var_02    CZ    CE2  CD2  CG    55.41  30.0  1
 PCE  Var_03    CE1   CZ   CE2  CD2  -54.60  30.0  1
 PCE  Var_04    HB21  CB2  CG2  CD3  -92.29  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
 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
 PCE  plan-1  HXT  0.020

