# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 13:10:40 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S,4E)-2-amino-5-phenylpent-4-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C\C=C\c1ccccc1)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
 P4E  P4E  '(2S,4E)-2-amino-5-phenylpent-4-enoic acid'  L-peptide  27  14  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_P4E
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
 P4E  C01   C  CR16  0  -0.273   4.9631   0.2927   0.2959
 P4E  C02   C  CR16  0  -0.240   4.5446  -0.9256  -0.2195
 P4E  C03   C  CR16  0  -0.320   3.1969  -1.1521  -0.4621
 P4E  C04   C  CR6   0   0.148   2.2387  -0.1695  -0.2008
 P4E  C05   C  CR16  0  -0.331   2.6762   1.0525   0.3221
 P4E  C06   C  CR16  0  -0.234   4.0204   1.2795   0.5660
 P4E  C07   C  C1    0  -0.306   0.8306  -0.4638  -0.4861
 P4E  C08   C  C1    0  -0.177  -0.1985   0.3775  -0.3834
 P4E  C09   C  CH2   0  -0.509  -1.6052   0.0246  -0.7321
 P4E  C10   C  CH1   0  -0.207  -2.5664   0.2782   0.4427
 P4E  C11   C  C     0   0.521  -3.9936  -0.0068  -0.0063
 P4E  O12   O  O     0  -0.438  -4.6630  -0.9312   0.3813
 P4E  N32   N  NH2   0  -0.769  -2.1553  -0.4745   1.5994
 P4E  H01   H  HCR6  0   0.256   6.0125   0.4752   0.4869
 P4E  H02   H  HCR6  0   0.255   5.2673  -1.7025  -0.4342
 P4E  H03   H  HCR6  0   0.251   2.8795  -2.1064  -0.8660
 P4E  H05   H  HCR6  0   0.250   1.9636   1.8370   0.5451
 P4E  H06   H  HCR6  0   0.257   4.3367   2.2319   0.9716
 P4E  H109  H  HCH2  0   0.265  -1.9250   0.6255  -1.5877
 P4E  H209  H  HCH2  0   0.254  -1.6679  -1.0234  -1.0399
 P4E  H10   H  HCH1  0   0.273  -2.5163   1.3442   0.6902
 P4E  HN32  H  HNH2  0   0.353  -2.7937  -0.3191   2.3691
 P4E  H107  H  H     0   0.239   0.6318  -1.4777  -0.8241
 P4E  H108  H  H     0   0.248  -0.0394   1.4010  -0.0535
 P4E  OXT   O  OH1   0  -0.594  -4.4245   0.8857  -0.8905
 P4E  HXT   H  HOH1  0   0.482  -5.3246   0.6671  -1.1751
 P4E  H2    H  HNH2  0   0.344  -2.1817  -1.4677   1.4028

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
 P4E  C01  C02   aromatic  1.387  0.020  1.387
 P4E  C01  H01   single    0.930  0.020  1.080
 P4E  C02  C03   aromatic  1.388  0.020  1.388
 P4E  C02  H02   single    0.930  0.020  1.080
 P4E  C03  H03   single    0.930  0.020  1.080
 P4E  C04  C07   single    1.466  0.020  1.466
 P4E  C04  C03   aromatic  1.397  0.020  1.397
 P4E  C05  C04   aromatic  1.399  0.020  1.399
 P4E  C05  H05   single    0.930  0.020  1.080
 P4E  C06  C05   aromatic  1.385  0.020  1.385
 P4E  C06  C01   aromatic  1.391  0.020  1.391
 P4E  C06  H06   single    0.930  0.020  1.080
 P4E  C08  C07   double    1.333  0.020  1.333
 P4E  C08  C09   single    1.492  0.020  1.492
 P4E  C09  C10   single    1.539  0.020  1.539
 P4E  C09  H109  single    0.970  0.020  1.090
 P4E  C09  H209  single    0.970  0.020  1.090
 P4E  C10  H10   single    0.970  0.020  1.090
 P4E  C11  C10   single    1.523  0.020  1.523
 P4E  O12  C11   double    1.205  0.020  1.205
 P4E  N32  C10   single    1.440  0.020  1.440
 P4E  N32  HN32  single    0.890  0.020  1.040
 P4E  C07  H107  single    0.930  0.020  1.080
 P4E  C08  H108  single    0.930  0.020  1.080
 P4E  C11  OXT   single    1.328  0.020  1.328
 P4E  OXT  HXT   single    0.850  0.020  0.980
 P4E  N32  H2    single    0.890  0.020  1.040

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
 P4E  H01   C01  C06   120.21  3.000
 P4E  C06   C01  C02   119.38  3.000
 P4E  H01   C01  C02   120.41  3.000
 P4E  H02   C02  C03   119.76  3.000
 P4E  H02   C02  C01   120.16  3.000
 P4E  C03   C02  C01   120.07  3.000
 P4E  H03   C03  C04   119.22  3.000
 P4E  C04   C03  C02   121.23  3.000
 P4E  H03   C03  C02   119.55  3.000
 P4E  C07   C04  C05   123.24  3.000
 P4E  C05   C04  C03   118.01  3.000
 P4E  C07   C04  C03   118.75  3.000
 P4E  H05   C05  C06   118.93  3.000
 P4E  C06   C05  C04   120.82  3.000
 P4E  H05   C05  C04   120.25  3.000
 P4E  H06   C06  C05   119.59  3.000
 P4E  H06   C06  C01   119.92  3.000
 P4E  C05   C06  C01   120.49  3.000
 P4E  H107  C07  C08   118.12  3.000
 P4E  H107  C07  C04   115.04  3.000
 P4E  C08   C07  C04   126.84  3.000
 P4E  H108  C08  C09   115.57  3.000
 P4E  H108  C08  C07   120.30  3.000
 P4E  C09   C08  C07   124.10  3.000
 P4E  H209  C09  H109  106.83  3.000
 P4E  H209  C09  C10   109.68  3.000
 P4E  H109  C09  C10   108.91  3.000
 P4E  H209  C09  C08   110.27  3.000
 P4E  H109  C09  C08   109.20  3.000
 P4E  C10   C09  C08   111.81  3.000
 P4E  H10   C10  N32   108.31  3.000
 P4E  N32   C10  C11   113.99  3.000
 P4E  H10   C10  C11   106.95  3.000
 P4E  N32   C10  C09   110.41  3.000
 P4E  C11   C10  C09   109.23  3.000
 P4E  H10   C10  C09   107.71  3.000
 P4E  OXT   C11  O12   123.31  3.000
 P4E  OXT   C11  C10   112.00  3.000
 P4E  O12   C11  C10   124.69  3.000
 P4E  H2    N32  HN32  106.37  3.000
 P4E  H2    N32  C10   110.44  3.000
 P4E  HN32  N32  C10   110.52  3.000
 P4E  HXT   OXT  C11   110.20  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
 P4E  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 P4E  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 P4E  CONST_03  C05  C06  C01  C02     0.00   0.0  0
 P4E  CONST_04  C05  C04  C03  C02     0.00   0.0  0
 P4E  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 P4E  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 P4E  CONST_07  C07  C04  C03  C02   180.00   0.0  0
 P4E  CONST_08  C07  C04  C05  C06   180.00   0.0  0
 P4E  CONST_09  H03  C03  C02  C01   180.00   0.0  0
 P4E  CONST_10  H05  C05  C06  C01   180.00   0.0  0
 P4E  CONST_11  H06  C06  C01  C02   180.00   0.0  0
 P4E  CONST_12  H01  C01  C02  C03   180.00   0.0  0
 P4E  CONST_13  H02  C02  C03  C04   180.00   0.0  0
 P4E  CONST_14  HXT  OXT  C11  C10   180.00   0.0  0
 P4E  Var_01    C08  C07  C04  C03  -175.24  30.0  2
 P4E  Var_02    C09  C08  C07  C04   177.96   0.0  2
 P4E  Var_03    C10  C09  C08  C07   124.60  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
 P4E  chir_01  C10  C09  C11  N32  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
 P4E  plan-1  C01   0.020
 P4E  plan-1  C02   0.020
 P4E  plan-1  C03   0.020
 P4E  plan-1  C04   0.020
 P4E  plan-1  C05   0.020
 P4E  plan-1  C06   0.020
 P4E  plan-1  C07   0.020
 P4E  plan-1  H01   0.020
 P4E  plan-1  H02   0.020
 P4E  plan-1  H03   0.020
 P4E  plan-1  H05   0.020
 P4E  plan-1  H06   0.020
 P4E  plan-2  C10   0.020
 P4E  plan-2  C11   0.020
 P4E  plan-2  O12   0.020
 P4E  plan-2  OXT   0.020
 P4E  plan-2  HXT   0.020
 P4E  plan-3  C04   0.020
 P4E  plan-3  C07   0.020
 P4E  plan-3  C08   0.020
 P4E  plan-3  C09   0.020
 P4E  plan-3  H107  0.020
 P4E  plan-3  H108  0.020

