# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:18:42 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (3S,7R,8aR)-7-ethoxyoctahydropyrrolo[1,2-a]pyrazine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[C@@H]1C[C@@H]2CN[C@@H](CN2C1)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
 1Y3  1Y3  '(3S,7R,8aR)-7-ethoxyoctahydropyrrolo[1,2-a]pyrazine-3-carboxylic acid'  ligand  32  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1Y3
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
 1Y3  C1   C  CH3    0  -0.687   4.7768  -1.4833   0.7167
 1Y3  C2   C  CH2    0  -0.150   3.9991  -0.6172  -0.2491
 1Y3  O3   O  O2     0  -0.499   2.9044  -0.0409   0.4270
 1Y3  C4   C  CR15   0   0.058   2.1543   0.8585  -0.3578
 1Y3  C6   C  CH2    0  -0.483   1.2239   1.6675   0.5655
 1Y3  C7   C  CR15   0  -0.054  -0.1546   1.5054  -0.0574
 1Y3  C9   C  CH2    0  -0.278  -1.3470   1.5619   0.8702
 1Y3  N10  N  NH1    0  -0.598  -2.5447   1.2623   0.0982
 1Y3  C11  C  CH1    0  -0.254  -2.4855  -0.0410  -0.5522
 1Y3  C13  C  CH2    0  -0.263  -1.2468  -0.1109  -1.4388
 1Y3  N14  N  NR5    0  -0.430  -0.0762   0.1838  -0.6498
 1Y3  C15  C  CH2    0  -0.301   1.1902   0.1709  -1.3435
 1Y3  C16  C  C      0   0.405  -2.5986  -1.2601   0.4022
 1Y3  O17  O  O      0  -0.610  -3.0120  -1.0399   1.5583
 1Y3  H1   H  HCH3   0   0.228   4.1621  -2.2943   1.1088
 1Y3  H2   H  HCH3   0   0.229   5.6311  -1.9286   0.2071
 1Y3  H3   H  HCH3   0   0.227   5.1546  -0.9001   1.5573
 1Y3  H4   H  HCH2   0   0.197   4.6487   0.1693  -0.6588
 1Y3  H5   H  HCH2   0   0.198   3.6634  -1.2208  -1.1026
 1Y3  H6   H  HCR5   0   0.211   2.8380   1.5172  -0.9089
 1Y3  H7   H  HCH2   0   0.233   1.2409   1.2321   1.5676
 1Y3  H8   H  HCH2   0   0.241   1.5236   2.7116   0.6514
 1Y3  H9   H  HCR5   0   0.186  -0.2936   2.2712  -0.8465
 1Y3  H10  H  HCH2   0   0.186  -1.1792   0.8621   1.7010
 1Y3  H11  H  HCH2   0   0.217  -1.4418   2.5634   1.2982
 1Y3  H12  H  HCH1   0   0.233  -3.3544  -0.1050  -1.2215
 1Y3  H13  H  HCH2   0   0.229  -1.1666  -1.1084  -1.8703
 1Y3  H14  H  HCH2   0   0.181  -1.3470   0.6050  -2.2750
 1Y3  H16  H  HCH2   0   0.190   1.1488   0.7573  -2.2781
 1Y3  H17  H  HCH2   0   0.238   1.4963  -0.8439  -1.6115
 1Y3  H18  H  HNH1   0   0.338  -3.3384   1.2630   0.7254
 1Y3  OXT  O  OC    -1  -0.614  -2.3270  -2.3765  -0.0842

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
 1Y3  C9   C7   single  1.512  0.020  1.512
 1Y3  C9   N10  single  1.456  0.020  1.456
 1Y3  C7   C6   single  1.521  0.020  1.521
 1Y3  C7   N14  single  1.450  0.020  1.450
 1Y3  C6   C4   single  1.540  0.020  1.540
 1Y3  N10  C11  single  1.458  0.020  1.458
 1Y3  C4   C15  single  1.541  0.020  1.541
 1Y3  C4   O3   single  1.410  0.020  1.410
 1Y3  C13  C11  single  1.525  0.020  1.525
 1Y3  C13  N14  single  1.442  0.020  1.442
 1Y3  C11  C16  single  1.552  0.020  1.552
 1Y3  N14  C15  single  1.444  0.020  1.444
 1Y3  C2   C1   single  1.513  0.020  1.513
 1Y3  C2   O3   single  1.410  0.020  1.410
 1Y3  C16  O17  deloc   1.247  0.020  1.247
 1Y3  C1   H1   single  0.970  0.020  1.090
 1Y3  C1   H2   single  0.970  0.020  1.090
 1Y3  C1   H3   single  0.970  0.020  1.090
 1Y3  C2   H4   single  0.970  0.020  1.090
 1Y3  C2   H5   single  0.970  0.020  1.090
 1Y3  C4   H6   single  0.970  0.020  1.090
 1Y3  C6   H7   single  0.970  0.020  1.090
 1Y3  C6   H8   single  0.970  0.020  1.090
 1Y3  C7   H9   single  0.970  0.020  1.090
 1Y3  C9   H10  single  0.970  0.020  1.090
 1Y3  C9   H11  single  0.970  0.020  1.090
 1Y3  C11  H12  single  0.970  0.020  1.090
 1Y3  C13  H13  single  0.970  0.020  1.090
 1Y3  C13  H14  single  0.970  0.020  1.090
 1Y3  C15  H16  single  0.970  0.020  1.090
 1Y3  C15  H17  single  0.970  0.020  1.090
 1Y3  N10  H18  single  0.890  0.020  1.040
 1Y3  C16  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
 1Y3  H3   C1   H2   107.90  3.000
 1Y3  H3   C1   H1   108.40  3.000
 1Y3  H2   C1   H1   107.83  3.000
 1Y3  H3   C1   C2   111.35  3.000
 1Y3  H2   C1   C2   109.79  3.000
 1Y3  H1   C1   C2   111.44  3.000
 1Y3  H5   C2   H4   106.51  3.000
 1Y3  H5   C2   O3   111.10  3.000
 1Y3  H4   C2   O3   110.19  3.000
 1Y3  H5   C2   C1   109.80  3.000
 1Y3  H4   C2   C1   110.11  3.000
 1Y3  O3   C2   C1   109.10  3.000
 1Y3  C4   O3   C2   114.02  3.000
 1Y3  H6   C4   C15  109.65  3.000
 1Y3  H6   C4   C6   111.22  3.000
 1Y3  C15  C4   C6   103.88  3.000
 1Y3  H6   C4   O3   109.32  3.000
 1Y3  C15  C4   O3   113.85  3.000
 1Y3  C6   C4   O3   108.83  3.000
 1Y3  H8   C6   H7   107.77  3.000
 1Y3  H8   C6   C7   112.56  3.000
 1Y3  H7   C6   C7   110.31  3.000
 1Y3  H8   C6   C4   112.61  3.000
 1Y3  H7   C6   C4   109.33  3.000
 1Y3  C7   C6   C4   104.24  3.000
 1Y3  H9   C7   N14  110.22  3.000
 1Y3  H9   C7   C9   108.18  3.000
 1Y3  N14  C7   C9   109.10  3.000
 1Y3  H9   C7   C6   109.36  3.000
 1Y3  N14  C7   C6   102.44  3.000
 1Y3  C9   C7   C6   117.36  3.000
 1Y3  H11  C9   H10  107.49  3.000
 1Y3  H11  C9   N10  108.95  3.000
 1Y3  H10  C9   N10  113.29  3.000
 1Y3  H11  C9   C7   110.05  3.000
 1Y3  H10  C9   C7   108.64  3.000
 1Y3  N10  C9   C7   108.41  3.000
 1Y3  H18  N10  C11  108.01  3.000
 1Y3  H18  N10  C9   108.45  3.000
 1Y3  C11  N10  C9   112.77  3.000
 1Y3  H12  C11  C16  105.73  3.000
 1Y3  H12  C11  C13  106.59  3.000
 1Y3  C16  C11  C13  112.37  3.000
 1Y3  H12  C11  N10  106.96  3.000
 1Y3  C16  C11  N10  115.14  3.000
 1Y3  C13  C11  N10  109.48  3.000
 1Y3  H14  C13  H13  107.46  3.000
 1Y3  H14  C13  N14  110.80  3.000
 1Y3  H13  C13  N14  110.12  3.000
 1Y3  H14  C13  C11  109.66  3.000
 1Y3  H13  C13  C11  109.39  3.000
 1Y3  N14  C13  C11  109.38  3.000
 1Y3  C15  N14  C13  116.56  3.000
 1Y3  C15  N14  C7   104.58  3.000
 1Y3  C13  N14  C7   111.46  3.000
 1Y3  H17  C15  H16  107.21  3.000
 1Y3  H17  C15  N14  111.82  3.000
 1Y3  H16  C15  N14  111.66  3.000
 1Y3  H17  C15  C4   113.32  3.000
 1Y3  H16  C15  C4   109.15  3.000
 1Y3  N14  C15  C4   103.73  3.000
 1Y3  OXT  C16  O17  126.26  3.000
 1Y3  OXT  C16  C11  116.56  3.000
 1Y3  O17  C16  C11  117.09  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
 1Y3  Var_01  C7   N14  C15  C4   42.43  30.0  1
 1Y3  Var_02  C11  N10  C9   C7   58.17  30.0  1
 1Y3  Var_03  C11  C13  N14  C7  -59.58  30.0  1
 1Y3  Var_04  H4   C2   O3   C4   55.14  30.0  1
 1Y3  Var_05  H1   C1   C2   O3   61.05  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
 1Y3  chir_01  C4   C6   C15  O3   positiv
 1Y3  chir_02  C7   N14  C6   C9   positiv
 1Y3  chir_03  C11  N10  C16  C13  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
 1Y3  plan-1  C11  0.020
 1Y3  plan-1  C16  0.020
 1Y3  plan-1  O17  0.020
 1Y3  plan-1  OXT  0.020

