# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 04:52:18 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: (4R)-4-ethoxy-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[C@H]1CN[C@@H](C1)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
 ZNY  ZNY  "(4R)-4-ethoxy-L-proline"  L-peptide  23  11  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZNY
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
 ZNY  CB   C  CH2    0  -0.487  2.7449  12.2003  50.6079
 ZNY  CD   C  CH2    0  -0.285  1.9197  12.0891  48.3946
 ZNY  C    C  C      0   0.393  2.0552   9.8335  51.2355
 ZNY  O    O  O      0  -0.596  0.9117   9.4020  50.9816
 ZNY  CA   C  CH1    0  -0.182  2.7271  10.7278  50.1756
 ZNY  CG   C  CH1    0   0.004  2.8373  12.9333  49.2741
 ZNY  N    N  NH1    0  -0.622  2.0482  10.7135  48.8810
 ZNY  O48  O  O2     0  -0.494  4.1366  12.8939  48.7216
 ZNY  C49  C  CH2    0  -0.142  5.0520  13.7848  49.3142
 ZNY  C50  C  CH3    0  -0.684  6.3595  13.7212  48.5549
 ZNY  OXT  O  OC    -1  -0.610  2.7155   9.6450  52.2755
 ZNY  H1   H  HCH2   0   0.240  3.5458  12.4407  51.3080
 ZNY  H2   H  HCH2   0   0.225  1.7992  12.4715  51.0881
 ZNY  H3   H  HCH2   0   0.211  2.1986  12.1855  47.3408
 ZNY  H4   H  HCH2   0   0.211  0.8954  12.4648  48.4878
 ZNY  H5   H  HCH1   0   0.200  3.7638  10.3867  50.0610
 ZNY  H6   H  HCH1   0   0.220  2.4901  13.9740  49.3400
 ZNY  H7   H  HNH1   0   0.333  1.1350  10.3043  49.0340
 ZNY  H9   H  HCH2   0   0.196  5.2264  13.5375  50.3692
 ZNY  H10  H  HCH2   0   0.191  4.6557  14.8101  49.2945
 ZNY  H11  H  HCH3   0   0.227  7.0796  14.4095  48.9970
 ZNY  H12  H  HCH3   0   0.226  6.7898  12.7198  48.5893
 ZNY  H13  H  HCH3   0   0.225  6.2268  14.0020  47.5095

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
 ZNY  CD   N    single  1.473  0.014  1.473
 ZNY  CD   CG   single  1.526  0.020  1.526
 ZNY  C50  C49  single  1.513  0.020  1.513
 ZNY  O48  CG   single  1.412  0.020  1.412
 ZNY  O48  C49  single  1.408  0.020  1.408
 ZNY  N    CA   single  1.458  0.019  1.458
 ZNY  CG   CB   single  1.525  0.020  1.525
 ZNY  CA   CB   single  1.521  0.033  1.521
 ZNY  CA   C    single  1.525  0.021  1.525
 ZNY  O    C    deloc   1.231  0.020  1.231
 ZNY  C    OXT  deloc   1.246  0.020  1.246
 ZNY  CB   H1   single  0.970  0.020  1.090
 ZNY  CB   H2   single  0.970  0.020  1.090
 ZNY  CD   H3   single  0.970  0.020  1.090
 ZNY  CD   H4   single  0.970  0.020  1.090
 ZNY  CA   H5   single  0.970  0.020  1.090
 ZNY  CG   H6   single  0.970  0.020  1.090
 ZNY  N    H7   single  0.890  0.020  1.040
 ZNY  C49  H9   single  0.970  0.020  1.090
 ZNY  C49  H10  single  0.970  0.020  1.090
 ZNY  C50  H11  single  0.970  0.020  1.090
 ZNY  C50  H12  single  0.970  0.020  1.090
 ZNY  C50  H13  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
 ZNY  H2   CB   H1   107.35  3.000
 ZNY  H2   CB   CG   108.48  3.000
 ZNY  H1   CB   CG   114.27  3.000
 ZNY  H2   CB   CA   110.56  3.000
 ZNY  H1   CB   CA   113.63  3.000
 ZNY  CG   CB   CA   102.45  3.000
 ZNY  H4   CD   H3   106.87  3.000
 ZNY  H4   CD   N    112.09  3.000
 ZNY  H3   CD   N    112.34  3.000
 ZNY  H4   CD   CG   108.88  3.000
 ZNY  H3   CD   CG   110.68  3.000
 ZNY  N    CD   CG   103.20  1.500
 ZNY  OXT  C    CA   120.80  1.700
 ZNY  OXT  C    O    127.07  3.000
 ZNY  CA   C    O    120.80  1.700
 ZNY  H5   CA   N    110.08  3.000
 ZNY  H5   CA   C    107.66  3.000
 ZNY  N    CA   C    111.00  2.800
 ZNY  H5   CA   CB   108.46  3.000
 ZNY  C    CA   CB   110.50  1.500
 ZNY  N    CA   CB   110.40  1.500
 ZNY  H6   CG   O48  109.90  3.000
 ZNY  H6   CG   CD   111.62  3.000
 ZNY  O48  CG   CD   108.19  3.000
 ZNY  H6   CG   CB   112.56  3.000
 ZNY  O48  CG   CB   112.62  3.000
 ZNY  CD   CG   CB   101.64  3.000
 ZNY  H7   N    CA   106.80  3.000
 ZNY  H7   N    CD   110.53  3.000
 ZNY  CA   N    CD   109.00  3.000
 ZNY  C49  O48  CG   114.57  3.000
 ZNY  H10  C49  H9   106.54  3.000
 ZNY  H10  C49  C50  109.98  3.000
 ZNY  H9   C49  C50  109.60  3.000
 ZNY  H10  C49  O48  110.37  3.000
 ZNY  H9   C49  O48  111.42  3.000
 ZNY  C50  C49  O48  108.90  3.000
 ZNY  H13  C50  H12  108.34  3.000
 ZNY  H13  C50  H11  107.86  3.000
 ZNY  H12  C50  H11  107.85  3.000
 ZNY  H13  C50  C49  111.41  3.000
 ZNY  H12  C50  C49  111.33  3.000
 ZNY  H11  C50  C49  109.93  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
 ZNY  Var_01  CG   CD   N    CA     13.22  30.0  1
 ZNY  Var_02  H3   CD   N    CA    134.21  30.0  1
 ZNY  Var_03  H4   CD   N    CA   -105.44  30.0  1
 ZNY  Var_04  H7   N    CD   CG    130.30  30.0  1
 ZNY  Var_05  C50  C49  O48  CG   -175.31  30.0  3
 ZNY  Var_06  H9   C49  O48  CG     63.68  30.0  3
 ZNY  Var_07  H10  C49  O48  CG    -54.48  30.0  3
 ZNY  Var_08  H11  C50  C49  O48   179.70  30.0  3
 ZNY  Var_09  H12  C50  C49  O48   -60.86  30.0  3
 ZNY  Var_10  H13  C50  C49  O48    60.19  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
 ZNY  chir_01  CA  N    CB  C   negativ
 ZNY  chir_02  CG  O48  CD  CB  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
 ZNY  plan-1  C    0.020
 ZNY  plan-1  O    0.020
 ZNY  plan-1  CA   0.020
 ZNY  plan-1  OXT  0.020

