# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 19:09:25 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[(3~{R})-1-ethyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C[C@@H](SC[C@H](N)C(O)=O)C1=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
 6V1  6V1  '(2~{R})-2-azanyl-3-[(3~{R})-1-ethyl-2,5-bis(oxidanylidene)pyrrolidin-3-yl]sulfanyl-propanoic acid'  L-peptide  29  16  .  2019-03-22  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_6V1
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
 6V1  N    N  NH2    0  -0.779  18.6654  221.3053   -9.9091
 6V1  CA   C  CH1    0  -0.225  19.4985  220.5121  -10.7951
 6V1  C    C  C      0   0.393  20.8279  219.9721  -10.1930
 6V1  O    O  O      0  -0.593  21.0845  220.2778   -9.0147
 6V1  CB   C  CH2    0  -0.540  19.8072  221.3185  -12.0508
 6V1  SG   S  S2     0   0.015  18.2543  222.0143  -12.6999
 6V1  C1   C  CR15   0  -0.537  18.7674  222.5085  -14.3693
 6V1  C2   C  CR5    0   0.615  18.7393  221.3534  -15.3494
 6V1  N3   N  NR5    0  -0.521  17.9788  221.7226  -16.4352
 6V1  C4   C  CR5    0   0.559  17.4223  222.9770  -16.3115
 6V1  C5   C  CH2    0  -0.571  17.8148  223.5386  -14.9695
 6V1  C6   C  CH2    0  -0.323  17.7328  220.8509  -17.5708
 6V1  O7   O  O      0  -0.420  19.2875  220.2852  -15.2353
 6V1  O8   O  O      0  -0.425  16.7294  223.5003  -17.1484
 6V1  C3   C  CH3    0  -0.659  16.5051  219.9788  -17.3704
 6V1  O1   O  OC    -1  -0.610  21.5185  219.2714  -10.9607
 6V1  H1   H  HNH2   0   0.341  18.3688  220.7295   -9.1310
 6V1  H2   H  HNH2   0   0.329  19.2379  222.0296   -9.4901
 6V1  H4   H  HCH1   0   0.230  18.9056  219.6442  -11.1063
 6V1  H5   H  HCH2   0   0.273  20.2635  220.6839  -12.8049
 6V1  H6   H  HCH2   0   0.256  20.4937  222.1414  -11.8314
 6V1  H7   H  HCR5   0   0.338  19.7886  222.8961  -14.3252
 6V1  H8   H  HCH2   0   0.310  18.2696  224.5216  -15.0862
 6V1  H9   H  HCH2   0   0.305  16.9064  223.6742  -14.3775
 6V1  H10  H  HCH2   0   0.264  18.6214  220.2398  -17.7204
 6V1  H11  H  HCH2   0   0.264  17.6219  221.4789  -18.4530
 6V1  H12  H  HCH3   0   0.241  16.3573  219.3454  -18.2448
 6V1  H13  H  HCH3   0   0.236  16.6169  219.3305  -16.5019
 6V1  H14  H  HCH3   0   0.235  15.6072  220.5815  -17.2375

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
 6V1  C6  C3   single  1.519  0.020  1.519
 6V1  C6  N3   single  1.453  0.020  1.453
 6V1  O8  C4   double  1.206  0.020  1.206
 6V1  C4  N3   single  1.378  0.020  1.378
 6V1  C4  C5   single  1.507  0.020  1.507
 6V1  N3  C2   single  1.376  0.020  1.376
 6V1  C5  C1   single  1.526  0.020  1.526
 6V1  C2  O7   double  1.206  0.020  1.206
 6V1  C2  C1   single  1.515  0.020  1.515
 6V1  C1  SG   single  1.815  0.020  1.815
 6V1  SG  CB   single  1.821  0.020  1.821
 6V1  CB  CA   single  1.530  0.020  1.530
 6V1  CA  C    single  1.525  0.021  1.525
 6V1  CA  N    single  1.458  0.019  1.458
 6V1  C   O    deloc   1.231  0.020  1.231
 6V1  C   O1   deloc   1.248  0.020  1.248
 6V1  N   H1   single  0.890  0.020  1.040
 6V1  N   H2   single  0.890  0.020  1.040
 6V1  CA  H4   single  0.970  0.020  1.090
 6V1  CB  H5   single  0.970  0.020  1.090
 6V1  CB  H6   single  0.970  0.020  1.090
 6V1  C1  H7   single  0.970  0.020  1.090
 6V1  C5  H8   single  0.970  0.020  1.090
 6V1  C5  H9   single  0.970  0.020  1.090
 6V1  C6  H10  single  0.970  0.020  1.090
 6V1  C6  H11  single  0.970  0.020  1.090
 6V1  C3  H12  single  0.970  0.020  1.090
 6V1  C3  H13  single  0.970  0.020  1.090
 6V1  C3  H14  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
 6V1  H2   N   H1   104.72  3.000
 6V1  H2   N   CA   108.57  3.000
 6V1  H1   N   CA   109.05  3.000
 6V1  H4   CA  CB   107.13  3.000
 6V1  H4   CA  C    107.29  3.000
 6V1  CB   CA  C    110.10  1.900
 6V1  H4   CA  N    107.18  3.000
 6V1  C    CA  N    111.00  2.800
 6V1  CB   CA  N    110.50  1.700
 6V1  O1   C   O    127.34  3.000
 6V1  O1   C   CA   115.44  3.000
 6V1  O    C   CA   120.80  1.700
 6V1  H6   CB  H5   108.38  3.000
 6V1  H6   CB  SG   108.62  3.000
 6V1  H5   CB  SG   109.51  3.000
 6V1  H6   CB  CA   111.10  3.000
 6V1  H5   CB  CA   110.37  3.000
 6V1  SG   CB  CA   108.85  3.000
 6V1  C1   SG  CB   101.00  3.000
 6V1  H7   C1  C5   111.08  3.000
 6V1  H7   C1  C2   108.28  3.000
 6V1  C5   C1  C2   104.40  3.000
 6V1  H7   C1  SG   108.88  3.000
 6V1  C2   C1  SG   112.46  3.000
 6V1  C5   C1  SG   111.66  3.000
 6V1  O7   C2  N3   124.30  3.000
 6V1  O7   C2  C1   127.28  3.000
 6V1  N3   C2  C1   108.42  3.000
 6V1  C6   N3  C4   123.24  3.000
 6V1  C4   N3  C2   113.37  3.000
 6V1  C6   N3  C2   123.33  3.000
 6V1  O8   C4  C5   127.31  3.000
 6V1  C5   C4  N3   108.30  3.000
 6V1  O8   C4  N3   124.38  3.000
 6V1  H9   C5  H8   107.04  3.000
 6V1  H9   C5  C4   108.19  3.000
 6V1  H8   C5  C4   110.46  3.000
 6V1  H9   C5  C1   112.93  3.000
 6V1  H8   C5  C1   112.99  3.000
 6V1  C4   C5  C1   105.15  3.000
 6V1  H11  C6  H10  107.19  3.000
 6V1  H11  C6  C3   110.83  3.000
 6V1  H10  C6  C3   110.82  3.000
 6V1  H11  C6  N3   107.74  3.000
 6V1  H10  C6  N3   107.83  3.000
 6V1  C3   C6  N3   112.22  3.000
 6V1  H14  C3  H13  108.45  3.000
 6V1  H14  C3  H12  107.91  3.000
 6V1  H13  C3  H12  107.92  3.000
 6V1  H14  C3  C6   111.38  3.000
 6V1  H13  C3  C6   111.34  3.000
 6V1  H12  C3  C6   109.72  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
 6V1  CONST_01  C4   N3  C2  C1    0.00   0.0  0
 6V1  CONST_02  C6   N3  C2  C1  180.00   0.0  0
 6V1  CONST_03  O7   C2  N3  C4  180.00   0.0  0
 6V1  CONST_04  O7   C2  N3  C6    0.00   0.0  0
 6V1  Var_01    N3   C4  C5  C1    4.65  30.0  1
 6V1  Var_02    C5   C4  N3  C2   -1.38  30.0  1
 6V1  Var_03    C3   C6  N3  C2   88.57  30.0  2
 6V1  Var_04    H5   CB  SG  C1  -44.32  30.0  3
 6V1  Var_05    H12  C3  C6  N3  179.83  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
 6V1  chir_01  CA  CB  C   N   negativ
 6V1  chir_02  C1  SG  C5  C2  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
 6V1  plan-1  N3  0.020
 6V1  plan-1  C4  0.020
 6V1  plan-1  C5  0.020
 6V1  plan-1  O8  0.020
 6V1  plan-2  C1  0.020
 6V1  plan-2  C2  0.020
 6V1  plan-2  N3  0.020
 6V1  plan-2  C4  0.020
 6V1  plan-2  C6  0.020
 6V1  plan-2  O7  0.020
 6V1  plan-3  CA  0.020
 6V1  plan-3  C   0.020
 6V1  plan-3  O   0.020
 6V1  plan-3  O1  0.020

