# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:21:06 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  30  16  .  2022-03-11  2022-11-17
;
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  -0.800  -2.6087   2.4906   0.4810
 AJE  CB    C  CH1   0  -0.100  -2.0646   1.3095  -0.1549
 AJE  CG    C  CH2   0  -0.258  -0.5705   1.1621   0.1186
 AJE  NG    N  NT    0  -0.488  -0.3412  -0.2677  -0.0152
 AJE  CD    C  CH2   0  -0.234  -1.5748  -1.0388   0.0219
 AJE  CA    C  CH1   0  -0.437  -2.6138   0.0112   0.4266
 AJE  C     C  C     0   0.570  -4.0123  -0.3268  -0.0088
 AJE  O     O  O     0  -0.436  -4.7410   0.4147  -0.6200
 AJE  C1    C  C     0   0.583   0.8525  -0.8717  -0.1378
 AJE  O1    O  O     0  -0.507   0.9456  -2.0879  -0.2542
 AJE  C2    C  CH2   0  -0.597   2.0611   0.0397  -0.1231
 AJE  C3    C  CH2   0  -0.575   3.3631  -0.7373  -0.1279
 AJE  C4    C  C     0   0.556   4.5697   0.1595  -0.1255
 AJE  O41   O  OH1   0  -0.597   5.6987  -0.5418  -0.1532
 AJE  O42   O  O     0  -0.444   4.5457   1.3650  -0.1015
 AJE  OXT   O  OH1   0  -0.589  -4.3645  -1.5471   0.3721
 AJE  H     H  HNH2  0   0.353  -2.1606   3.3136   0.0966
 AJE  HN2   H  HNH2  0   0.351  -3.5866   2.5802   0.2351
 AJE  HB    H  HCH1  0   0.233  -2.2131   1.2914  -1.2447
 AJE  HG1C  H  HCH2  0   0.263   0.0282   1.7379  -0.5876
 AJE  HG2C  H  HCH2  0   0.241  -0.3412   1.5158   1.1298
 AJE  HA    H  HCH1  0   0.306  -2.6215   0.1013   1.5203
 AJE  HD1C  H  HCH2  0   0.248  -1.7936  -1.4675  -0.9606
 AJE  HD2C  H  HCH2  0   0.262  -1.5123  -1.8579   0.7373
 AJE  HXT   H  HOH1  0   0.484  -5.2720  -1.7394   0.0898
 AJE  H21C  H  HCH2  0   0.282   2.0121   0.7013  -0.9929
 AJE  H22C  H  HCH2  0   0.277   2.0098   0.6958   0.7497
 AJE  H31C  H  HCH2  0   0.287   3.4295  -1.3963   0.7418
 AJE  H32C  H  HCH2  0   0.286   3.4271  -1.3937  -0.9990
 AJE  H41   H  HOH1  0   0.479   6.4601   0.0572  -0.1485

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  1.448  0.020  1.448
 AJE  CB   CG    single  1.526  0.020  1.526
 AJE  CB   CA    single  1.521  0.033  1.521
 AJE  CG   NG    single  1.454  0.020  1.454
 AJE  NG   CD    single  1.455  0.020  1.455
 AJE  NG   C1    single  1.343  0.020  1.343
 AJE  CD   CA    single  1.532  0.020  1.532
 AJE  CA   C     single  1.525  0.021  1.525
 AJE  C    O     double  1.231  0.020  1.231
 AJE  C    OXT   single  1.326  0.020  1.326
 AJE  C1   O1    double  1.225  0.020  1.225
 AJE  C1   C2    single  1.514  0.020  1.514
 AJE  C2   C3    single  1.516  0.020  1.516
 AJE  C3   C4    single  1.503  0.020  1.503
 AJE  C4   O41   single  1.329  0.020  1.329
 AJE  C4   O42   double  1.206  0.020  1.206
 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  OXT  HXT   single  0.850  0.020  0.980
 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
 AJE  O41  H41   single  0.850  0.020  0.980

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     105.27  3.000
 AJE  HN2   N    CB    109.19  3.000
 AJE  H     N    CB    109.26  3.000
 AJE  HB    CB   CA    108.37  3.000
 AJE  HB    CB   CG    107.95  3.000
 AJE  CA    CB   CG    101.66  3.000
 AJE  HB    CB   N     113.44  3.000
 AJE  CA    CB   N     110.40  1.500
 AJE  CG    CB   N     111.60  3.000
 AJE  HG2C  CG   HG1C  108.20  3.000
 AJE  HG2C  CG   NG    111.67  3.000
 AJE  HG1C  CG   NG    111.91  3.000
 AJE  HG2C  CG   CB    109.83  3.000
 AJE  HG1C  CG   CB    111.75  3.000
 AJE  NG    CG   CB    103.47  3.000
 AJE  C1    NG   CD    121.15  3.000
 AJE  C1    NG   CG    126.20  3.000
 AJE  CD    NG   CG    112.64  3.000
 AJE  HD2C  CD   HD1C  107.86  3.000
 AJE  HD2C  CD   CA    112.39  3.000
 AJE  HD1C  CD   CA    111.73  3.000
 AJE  HD2C  CD   NG    111.50  3.000
 AJE  HD1C  CD   NG    110.75  3.000
 AJE  CA    CD   NG    102.62  3.000
 AJE  HA    CA   C     110.00  3.000
 AJE  HA    CA   CD    108.93  3.000
 AJE  C     CA   CD    113.61  3.000
 AJE  HA    CA   CB    109.00  3.000
 AJE  C     CA   CB    110.50  1.500
 AJE  CD    CA   CB    103.80  3.000
 AJE  OXT   C    O     123.43  3.000
 AJE  OXT   C    CA    120.80  1.700
 AJE  O     C    CA    120.80  1.700
 AJE  C2    C1   O1    122.54  3.000
 AJE  C2    C1   NG    115.97  3.000
 AJE  O1    C1   NG    121.50  3.000
 AJE  H22C  C2   H21C  105.65  3.000
 AJE  H22C  C2   C3    110.51  3.000
 AJE  H21C  C2   C3    110.24  3.000
 AJE  H22C  C2   C1    109.37  3.000
 AJE  H21C  C2   C1    108.70  3.000
 AJE  C3    C2   C1    112.15  3.000
 AJE  H32C  C3   H31C  105.58  3.000
 AJE  H32C  C3   C4    108.22  3.000
 AJE  H31C  C3   C4    108.03  3.000
 AJE  H32C  C3   C2    111.14  3.000
 AJE  H31C  C3   C2    111.01  3.000
 AJE  C4    C3   C2    112.55  3.000
 AJE  O42   C4   O41   122.99  3.000
 AJE  O42   C4   C3    125.48  3.000
 AJE  O41   C4   C3    111.53  3.000
 AJE  H41   O41  C4    109.96  3.000
 AJE  HXT   OXT  C     110.33  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  CONST_05  HXT  OXT  C   CA   180.00   0.0  0
 AJE  CONST_06  H41  O41  C4  C3   180.00   0.0  0
 AJE  Var_01    CD   NG   CG  CB   -15.75  30.0  1
 AJE  Var_02    CA   CD   NG  CG    -9.05  30.0  1
 AJE  Var_03    C3   C2   C1  NG   174.32  30.0  3
 AJE  Var_04    C4   C3   C2  C1   179.50  30.0  3
 AJE  Var_05    O41  C4   C3  C2  -178.91  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-2  HXT  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
 AJE  plan-3  H41  0.020

