# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:22:35 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (3S,4R)-4-amino-1-(3-carboxypropanoyl)pyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CN(C[C@@H]1C(O)=O)C(=O)CCC(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
 AJE  AJE  '(3S,4R)-4-amino-1-(3-carboxypropanoyl)pyrrolidine-3-carboxylic acid'  L-peptide  28  16  .  2022-03-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AJE
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
 AJE  N     N  NH2    0  -0.812  -2.5459   2.4979   0.4777
 AJE  CB    C  CR15   0  -0.098  -2.0079   1.3087  -0.1513
 AJE  CG    C  CH2    0  -0.248  -0.5093   1.1582   0.0968
 AJE  NG    N  NR5    0  -0.479  -0.2885  -0.2743  -0.0250
 AJE  CD    C  CH2    0  -0.234  -1.5357  -1.0289   0.0325
 AJE  CA    C  CR15   0  -0.438  -2.5683   0.0167   0.4385
 AJE  C     C  C      0   0.439  -4.0107  -0.3306   0.0482
 AJE  O     O  O      0  -0.603  -4.7895   0.6266  -0.1493
 AJE  C1    C  C      0   0.562   0.9030  -0.8828  -0.1469
 AJE  O1    O  O      0  -0.522   0.9847  -2.1039  -0.2523
 AJE  C2    C  CH2    0  -0.581   2.1185   0.0205  -0.1467
 AJE  C3    C  CH2    0  -0.580   3.4366  -0.7299  -0.1324
 AJE  C4    C  C      0   0.417   4.6891   0.1653  -0.1385
 AJE  O41   O  OC    -1  -0.632   5.7834  -0.4366  -0.1610
 AJE  O42   O  O      0  -0.608   4.5286   1.4015  -0.1186
 AJE  OXT   O  OC    -1  -0.602  -4.2979  -1.5414  -0.0125
 AJE  H     H  HNH2   0   0.338  -2.2146   3.3203  -0.0120
 AJE  HN2   H  HNH2   0   0.345  -3.5496   2.4721   0.3426
 AJE  HB    H  HCR5   0   0.204  -2.1736   1.2880  -1.2406
 AJE  HG1C  H  HCH2   0   0.246   0.0890   1.7240  -0.6195
 AJE  HG2C  H  HCH2   0   0.223  -0.2653   1.5212   1.1020
 AJE  HA    H  HCR5   0   0.244  -2.5390   0.1278   1.5322
 AJE  HD1C  H  HCH2   0   0.223  -1.7691  -1.4630  -0.9442
 AJE  HD2C  H  HCH2   0   0.234  -1.4651  -1.8505   0.7451
 AJE  H21C  H  HCH2   0   0.256   2.0667   0.6709  -1.0257
 AJE  H22C  H  HCH2   0   0.251   2.0593   0.6997   0.7083
 AJE  H31C  H  HCH2   0   0.227   3.4897  -1.3812   0.7456
 AJE  H32C  H  HCH2   0   0.226   3.4972  -1.4056  -0.9902

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
 AJE  N   CB    single  1.449  0.020  1.449
 AJE  CB  CG    single  1.526  0.020  1.526
 AJE  CB  CA    single  1.521  0.033  1.521
 AJE  CG  NG    single  1.455  0.020  1.455
 AJE  NG  CD    single  1.459  0.020  1.459
 AJE  NG  C1    single  1.343  0.020  1.343
 AJE  CD  CA    single  1.525  0.020  1.525
 AJE  CA  C     single  1.525  0.021  1.525
 AJE  C   O     deloc   1.231  0.020  1.231
 AJE  C   OXT   deloc   1.246  0.020  1.246
 AJE  C1  O1    double  1.228  0.020  1.228
 AJE  C1  C2    single  1.514  0.020  1.514
 AJE  C2  C3    single  1.517  0.020  1.517
 AJE  C3  C4    single  1.540  0.020  1.540
 AJE  C4  O41   deloc   1.249  0.020  1.249
 AJE  C4  O42   deloc   1.247  0.020  1.247
 AJE  N   H     single  0.860  0.020  0.860
 AJE  N   HN2   single  0.890  0.020  1.040
 AJE  CB  HB    single  0.970  0.020  1.090
 AJE  CG  HG1C  single  0.970  0.020  1.090
 AJE  CG  HG2C  single  0.970  0.020  1.090
 AJE  CA  HA    single  0.970  0.020  0.970
 AJE  CD  HD1C  single  0.970  0.020  1.090
 AJE  CD  HD2C  single  0.970  0.020  1.090
 AJE  C2  H21C  single  0.970  0.020  1.090
 AJE  C2  H22C  single  0.970  0.020  1.090
 AJE  C3  H31C  single  0.970  0.020  1.090
 AJE  C3  H32C  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
 AJE  HN2   N   H     106.27  3.000
 AJE  HN2   N   CB    106.80  3.000
 AJE  H     N   CB    109.58  3.000
 AJE  HB    CB  CA    108.10  3.000
 AJE  HB    CB  CG    107.84  3.000
 AJE  CA    CB  CG    102.37  3.000
 AJE  HB    CB  N     112.87  3.000
 AJE  CA    CB  N     110.40  1.500
 AJE  CG    CB  N     112.02  3.000
 AJE  HG2C  CG  HG1C  107.95  3.000
 AJE  HG2C  CG  NG    111.66  3.000
 AJE  HG1C  CG  NG    111.87  3.000
 AJE  HG2C  CG  CB    109.56  3.000
 AJE  HG1C  CG  CB    112.36  3.000
 AJE  NG    CG  CB    103.44  3.000
 AJE  C1    NG  CD    121.84  3.000
 AJE  C1    NG  CG    126.04  3.000
 AJE  CD    NG  CG    112.11  3.000
 AJE  HD2C  CD  HD1C  107.36  3.000
 AJE  HD2C  CD  CA    112.75  3.000
 AJE  HD1C  CD  CA    111.43  3.000
 AJE  HD2C  CD  NG    111.12  3.000
 AJE  HD1C  CD  NG    110.64  3.000
 AJE  CA    CD  NG    103.58  3.000
 AJE  HA    CA  C     110.00  3.000
 AJE  HA    CA  CD    108.43  3.000
 AJE  C     CA  CD    114.44  3.000
 AJE  HA    CA  CB    109.00  3.000
 AJE  C     CA  CB    110.50  1.500
 AJE  CD    CA  CB    103.23  3.000
 AJE  OXT   C   O     126.37  3.000
 AJE  OXT   C   CA    120.80  1.700
 AJE  O     C   CA    120.80  1.700
 AJE  C2    C1  O1    122.66  3.000
 AJE  C2    C1  NG    116.21  3.000
 AJE  O1    C1  NG    121.14  3.000
 AJE  H22C  C2  H21C  104.84  3.000
 AJE  H22C  C2  C3    110.30  3.000
 AJE  H21C  C2  C3    110.03  3.000
 AJE  H22C  C2  C1    109.10  3.000
 AJE  H21C  C2  C1    108.44  3.000
 AJE  C3    C2  C1    113.73  3.000
 AJE  H32C  C3  H31C  105.01  3.000
 AJE  H32C  C3  C4    108.13  3.000
 AJE  H31C  C3  C4    108.04  3.000
 AJE  H32C  C3  C2    110.27  3.000
 AJE  H31C  C3  C2    110.12  3.000
 AJE  C4    C3  C2    114.79  3.000
 AJE  O42   C4  O41   126.22  3.000
 AJE  O42   C4  C3    118.15  3.000
 AJE  O41   C4  C3    115.63  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
 AJE  CONST_01  O1   C1  NG  CG   180.00   0.0  0
 AJE  CONST_02  C2   C1  NG  CG     0.00   0.0  0
 AJE  CONST_03  O1   C1  NG  CD     0.00   0.0  0
 AJE  CONST_04  C2   C1  NG  CD   180.00   0.0  0
 AJE  Var_01    CD   NG  CG  CB   -15.23  30.0  1
 AJE  Var_02    CA   CD  NG  CG    -9.24  30.0  1
 AJE  Var_03    C3   C2  C1  NG   173.61  30.0  3
 AJE  Var_04    C4   C3  C2  C1   179.73  30.0  3
 AJE  Var_05    O41  C4  C3  C2  -178.27  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
 AJE  chir_01  CB  N   CG  CA  negativ
 AJE  chir_02  CA  CB  CD  C   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
 AJE  plan-1  CG   0.020
 AJE  plan-1  NG   0.020
 AJE  plan-1  CD   0.020
 AJE  plan-1  C1   0.020
 AJE  plan-1  O1   0.020
 AJE  plan-1  C2   0.020
 AJE  plan-2  CA   0.020
 AJE  plan-2  C    0.020
 AJE  plan-2  O    0.020
 AJE  plan-2  OXT  0.020
 AJE  plan-3  C3   0.020
 AJE  plan-3  C4   0.020
 AJE  plan-3  O41  0.020
 AJE  plan-3  O42  0.020

