# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:43:06 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: (2S)-2-amino-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1CCC[C@@H]1c2ccccc2)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
 M6J  M6J  '(2S)-2-amino-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]butanoic acid'  L-peptide  36  19  .  2022-07-25  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_M6J
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
 M6J  C13  C  CH2    0  -0.471  -2.3490   2.2053   0.5619
 M6J  C15  C  CR6    0   0.143  -2.3576  -0.1538  -0.3221
 M6J  C17  C  CR16   0  -0.252  -2.3912  -2.3325   0.7125
 M6J  C20  C  CR16   0  -0.319  -3.5373  -0.4746  -0.9851
 M6J  C04  C  C      0   0.389   3.9438  -0.7100   0.1227
 M6J  C06  C  CH1    0  -0.218   2.3953  -0.6470   0.0556
 M6J  C07  C  CH2    0  -0.557   1.9855   0.6153  -0.7177
 M6J  C11  C  CH2    0  -0.270   0.0098   2.2309   0.8111
 M6J  C12  C  CH2    0  -0.468  -1.1967   3.1556   0.8562
 M6J  C14  C  CH1    0  -0.098  -1.7764   1.2292  -0.4812
 M6J  C16  C  CR16   0  -0.321  -1.7874  -1.0957   0.5309
 M6J  C18  C  CR16   0  -0.272  -3.5731  -2.6455   0.0512
 M6J  C19  C  CR16   0  -0.246  -4.1455  -1.7100  -0.7996
 M6J  N10  N  NT     0  -0.475  -0.3358   1.3025  -0.2579
 M6J  N21  N  NH2    0  -0.763   1.7077  -0.6902   1.3345
 M6J  O09  O  O      0  -0.516   0.0865  -0.0924  -1.9565
 M6J  H1   H  HCH2   0   0.240  -2.6233   1.6624   1.4693
 M6J  H2   H  HCH2   0   0.256  -3.2466   2.7015   0.1942
 M6J  H3   H  HCR6   0   0.247  -1.9322  -3.0592   1.3714
 M6J  H4   H  HCR6   0   0.242  -3.9880   0.2468  -1.6574
 M6J  H9   H  HCH1   0   0.228   2.0577  -1.5096  -0.5280
 M6J  H10  H  HCH2   0   0.243   2.2973   1.4983  -0.1569
 M6J  H11  H  HCH2   0   0.257   2.5201   0.6328  -1.6672
 M6J  H12  H  HCH2   0   0.252   0.9324   2.7654   0.5954
 M6J  H13  H  HCH2   0   0.235   0.1410   1.7007   1.7582
 M6J  H14  H  HCH2   0   0.237  -1.1127   3.9171   0.0777
 M6J  H15  H  HCH2   0   0.250  -1.2949   3.6630   1.8152
 M6J  H16  H  HCH1   0   0.255  -2.0062   1.5911  -1.4894
 M6J  H17  H  HCR6   0   0.276  -0.8497  -0.8752   1.0316
 M6J  H18  H  HCR6   0   0.249  -4.0387  -3.6125   0.1932
 M6J  H19  H  HCR6   0   0.250  -5.0637  -1.9420  -1.3243
 M6J  H30  H  HNH2   0   0.339   1.8381  -1.6075   1.7426
 M6J  H5   H  HNH2   0   0.328   2.1801  -0.0577   1.9708
 M6J  C08  C  C      0   0.550   0.5075   0.5930  -1.0286
 M6J  O05  O  O      0  -0.602   4.4765  -0.5811   1.2416
 M6J  OXT  O  OC    -1  -0.620   4.5285  -0.8720  -0.9680

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
 M6J  C13  C14  single    1.539  0.020  1.539
 M6J  C13  C12  single    1.522  0.020  1.522
 M6J  C15  C20  aromatic  1.391  0.020  1.391
 M6J  C15  C16  aromatic  1.393  0.020  1.393
 M6J  C15  C14  single    1.509  0.020  1.509
 M6J  C17  C18  aromatic  1.390  0.020  1.390
 M6J  C17  C16  aromatic  1.388  0.020  1.388
 M6J  C20  C19  aromatic  1.389  0.020  1.389
 M6J  C04  O05  deloc     1.246  0.020  1.246
 M6J  C04  C06  single    1.551  0.020  1.551
 M6J  C06  C07  single    1.536  0.020  1.536
 M6J  C06  N21  single    1.453  0.020  1.453
 M6J  C07  C08  single    1.511  0.020  1.511
 M6J  C08  N10  single    1.345  0.020  1.345
 M6J  C08  O09  double    1.228  0.020  1.228
 M6J  C11  N10  single    1.457  0.020  1.457
 M6J  C11  C12  single    1.521  0.020  1.521
 M6J  C14  N10  single    1.460  0.020  1.460
 M6J  C18  C19  aromatic  1.388  0.020  1.388
 M6J  C13  H1   single    0.970  0.020  1.090
 M6J  C13  H2   single    0.970  0.020  1.090
 M6J  C17  H3   single    0.930  0.020  1.080
 M6J  C20  H4   single    0.930  0.020  1.080
 M6J  C06  H9   single    0.970  0.020  1.090
 M6J  C07  H10  single    0.970  0.020  1.090
 M6J  C07  H11  single    0.970  0.020  1.090
 M6J  C11  H12  single    0.970  0.020  1.090
 M6J  C11  H13  single    0.970  0.020  1.090
 M6J  C12  H14  single    0.970  0.020  1.090
 M6J  C12  H15  single    0.970  0.020  1.090
 M6J  C14  H16  single    0.970  0.020  1.090
 M6J  C16  H17  single    0.930  0.020  1.080
 M6J  C18  H18  single    0.930  0.020  1.080
 M6J  C19  H19  single    0.930  0.020  1.080
 M6J  N21  H30  single    0.890  0.020  1.040
 M6J  N21  H5   single    0.890  0.020  1.040
 M6J  C04  OXT  deloc     1.248  0.020  1.248

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
 M6J  H2   C13  H1   107.44  3.000
 M6J  H2   C13  C14  111.50  3.000
 M6J  H1   C13  C14  109.95  3.000
 M6J  H2   C13  C12  113.86  3.000
 M6J  H1   C13  C12  109.87  3.000
 M6J  C14  C13  C12  104.20  3.000
 M6J  C16  C15  C14  121.79  3.000
 M6J  C14  C15  C20  119.21  3.000
 M6J  C16  C15  C20  118.90  3.000
 M6J  H3   C17  C18  119.91  3.000
 M6J  H3   C17  C16  119.54  3.000
 M6J  C18  C17  C16  120.54  3.000
 M6J  H4   C20  C19  119.50  3.000
 M6J  H4   C20  C15  119.65  3.000
 M6J  C19  C20  C15  120.85  3.000
 M6J  OXT  C04  O05  126.72  3.000
 M6J  OXT  C04  C06  115.80  3.000
 M6J  O05  C04  C06  117.48  3.000
 M6J  H9   C06  N21  107.45  3.000
 M6J  H9   C06  C07  107.26  3.000
 M6J  N21  C06  C07  109.96  3.000
 M6J  H9   C06  C04  107.39  3.000
 M6J  N21  C06  C04  115.67  3.000
 M6J  C07  C06  C04  108.75  3.000
 M6J  H11  C07  H10  107.13  3.000
 M6J  H11  C07  C08  107.51  3.000
 M6J  H10  C07  C08  113.41  3.000
 M6J  H11  C07  C06  108.72  3.000
 M6J  H10  C07  C06  109.26  3.000
 M6J  C08  C07  C06  110.64  3.000
 M6J  H13  C11  H12  107.96  3.000
 M6J  H13  C11  N10  110.79  3.000
 M6J  H12  C11  N10  111.63  3.000
 M6J  H13  C11  C12  111.37  3.000
 M6J  H12  C11  C12  112.33  3.000
 M6J  N10  C11  C12  102.76  3.000
 M6J  H15  C12  H14  108.04  3.000
 M6J  H15  C12  C11  112.38  3.000
 M6J  H14  C12  C11  109.98  3.000
 M6J  H15  C12  C13  113.12  3.000
 M6J  H14  C12  C13  110.84  3.000
 M6J  C11  C12  C13  102.43  3.000
 M6J  H16  C14  N10  109.34  3.000
 M6J  H16  C14  C15  108.61  3.000
 M6J  N10  C14  C15  114.21  3.000
 M6J  H16  C14  C13  109.64  3.000
 M6J  N10  C14  C13  103.40  3.000
 M6J  C15  C14  C13  111.50  3.000
 M6J  H17  C16  C17  119.75  3.000
 M6J  H17  C16  C15  119.92  3.000
 M6J  C17  C16  C15  120.30  3.000
 M6J  H18  C18  C19  120.34  3.000
 M6J  H18  C18  C17  120.29  3.000
 M6J  C19  C18  C17  119.37  3.000
 M6J  H19  C19  C18  120.16  3.000
 M6J  H19  C19  C20  119.80  3.000
 M6J  C18  C19  C20  120.04  3.000
 M6J  C14  N10  C11  112.22  3.000
 M6J  C14  N10  C08  120.31  3.000
 M6J  C11  N10  C08  127.43  3.000
 M6J  H5   N21  H30  104.61  3.000
 M6J  H5   N21  C06  108.26  3.000
 M6J  H30  N21  C06  108.71  3.000
 M6J  O09  C08  N10  120.84  3.000
 M6J  O09  C08  C07  119.95  3.000
 M6J  N10  C08  C07  119.19  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
 M6J  CONST_01  C18  C19  C20  C15    0.00   0.0  0
 M6J  CONST_02  C18  C17  C16  C15    0.00   0.0  0
 M6J  CONST_03  C20  C19  C18  C17    0.00   0.0  0
 M6J  CONST_04  C20  C15  C16  C17    0.00   0.0  0
 M6J  CONST_05  C19  C20  C15  C16    0.00   0.0  0
 M6J  CONST_06  C19  C18  C17  C16    0.00   0.0  0
 M6J  CONST_07  C14  C15  C16  C17  180.00   0.0  0
 M6J  CONST_08  C19  C20  C15  C14  180.00   0.0  0
 M6J  CONST_09  H19  C19  C20  C15  180.00   0.0  0
 M6J  CONST_10  H3   C17  C16  C15  180.00   0.0  0
 M6J  CONST_11  H17  C16  C15  C20  180.00   0.0  0
 M6J  CONST_12  H18  C18  C19  C20  180.00   0.0  0
 M6J  CONST_13  H4   C20  C15  C14    0.00   0.0  0
 M6J  CONST_14  C11  N10  C08  C07    0.00   0.0  0
 M6J  CONST_15  C14  N10  C08  C07  180.00   0.0  0
 M6J  CONST_16  O09  C08  N10  C11  180.00   0.0  0
 M6J  CONST_17  O09  C08  N10  C14    0.00   0.0  0
 M6J  Var_01    N10  C11  C12  C13   36.42  30.0  1
 M6J  Var_02    C14  C13  C12  C11  -37.24  30.0  1
 M6J  Var_03    C14  N10  C11  C12  -22.93  30.0  1
 M6J  Var_04    N10  C08  C07  C06   99.89  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
 M6J  chir_01  C06  C04  C07  N21  positiv
 M6J  chir_02  C14  N10  C13  C15  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
 M6J  plan-1  C15  0.020
 M6J  plan-1  C17  0.020
 M6J  plan-1  C20  0.020
 M6J  plan-1  C14  0.020
 M6J  plan-1  C16  0.020
 M6J  plan-1  C18  0.020
 M6J  plan-1  C19  0.020
 M6J  plan-1  H3   0.020
 M6J  plan-1  H4   0.020
 M6J  plan-1  H17  0.020
 M6J  plan-1  H18  0.020
 M6J  plan-1  H19  0.020
 M6J  plan-2  C07  0.020
 M6J  plan-2  C11  0.020
 M6J  plan-2  C14  0.020
 M6J  plan-2  N10  0.020
 M6J  plan-2  O09  0.020
 M6J  plan-2  C08  0.020
 M6J  plan-3  C04  0.020
 M6J  plan-3  C06  0.020
 M6J  plan-3  O05  0.020
 M6J  plan-3  OXT  0.020

