# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:12:27 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: (3S,8aR)-octahydropyrrolo[1,2-a]pyrazine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CN2CCC[C@@H]2CN1
#
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
 1Y4  1Y4  '(3S,8aR)-octahydropyrrolo[1,2-a]pyrazine-3-carboxylic acid'  ligand  25  12  .  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_1Y4
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
 1Y4  N19  N  NH1    0  -0.599  -0.8743   1.4767  -0.9146
 1Y4  C20  C  CH2    0  -0.275   0.2051   1.7303   0.0298
 1Y4  C21  C  CH1    0  -0.051   1.3411   0.7748  -0.2572
 1Y4  C23  C  CH2    0  -0.444   2.5129   0.7679   0.7134
 1Y4  C24  C  CH2    0  -0.472   3.0916  -0.6552   0.5623
 1Y4  C25  C  CH2    0  -0.269   2.0327  -1.4214  -0.2520
 1Y4  N26  N  NT     0  -0.433   0.8545  -0.5874  -0.1600
 1Y4  C27  C  CH2    0  -0.261  -0.1947  -0.8529  -1.1112
 1Y4  C28  C  CH1    0  -0.253  -1.3566   0.1020  -0.8657
 1Y4  C30  C  C      0   0.403  -2.1675  -0.2676   0.4057
 1Y4  O31  O  O      0  -0.610  -2.5985   0.6761   1.0985
 1Y4  H23  H  HCH2   0   0.215   0.5470   2.7616  -0.0942
 1Y4  H24  H  HCH2   0   0.184  -0.1000   1.6094   1.0786
 1Y4  H25  H  HCH1   0   0.180   1.7174   0.9801  -1.2800
 1Y4  H26  H  HCH2   0   0.229   3.2414   1.5482   0.4930
 1Y4  H27  H  HCH2   0   0.221   2.1528   0.9333   1.7316
 1Y4  H28  H  HCH2   0   0.230   4.0489  -0.6479   0.0408
 1Y4  H29  H  HCH2   0   0.234   3.2638  -1.1166   1.5347
 1Y4  H30  H  HCH2   0   0.185   2.3690  -1.5370  -1.2963
 1Y4  H31  H  HCH2   0   0.225   1.8357  -2.4247   0.1333
 1Y4  H33  H  HCH2   0   0.178   0.1708  -0.7349  -2.1482
 1Y4  H34  H  HCH2   0   0.227  -0.5445  -1.8794  -1.0045
 1Y4  H35  H  HCH1   0   0.232  -2.0516  -0.0233  -1.7076
 1Y4  OXT  O  OC    -1  -0.614  -2.3813  -1.4818   0.5987
 1Y4  H2   H  HNH1   0   0.337  -1.6488   2.0850  -0.6827

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
 1Y4  C24  C25  single  1.540  0.020  1.540
 1Y4  C24  C23  single  1.544  0.020  1.544
 1Y4  C25  N26  single  1.446  0.020  1.446
 1Y4  C23  C21  single  1.522  0.020  1.522
 1Y4  N26  C21  single  1.450  0.020  1.450
 1Y4  N26  C27  single  1.441  0.020  1.441
 1Y4  C21  C20  single  1.512  0.020  1.512
 1Y4  C27  C28  single  1.524  0.020  1.524
 1Y4  C20  N19  single  1.456  0.020  1.456
 1Y4  C28  C30  single  1.553  0.020  1.553
 1Y4  C28  N19  single  1.458  0.020  1.458
 1Y4  C30  O31  deloc   1.247  0.020  1.247
 1Y4  C20  H23  single  0.970  0.020  1.090
 1Y4  C20  H24  single  0.970  0.020  1.090
 1Y4  C21  H25  single  0.970  0.020  1.090
 1Y4  C23  H26  single  0.970  0.020  1.090
 1Y4  C23  H27  single  0.970  0.020  1.090
 1Y4  C24  H28  single  0.970  0.020  1.090
 1Y4  C24  H29  single  0.970  0.020  1.090
 1Y4  C25  H30  single  0.970  0.020  1.090
 1Y4  C25  H31  single  0.970  0.020  1.090
 1Y4  C27  H33  single  0.970  0.020  1.090
 1Y4  C27  H34  single  0.970  0.020  1.090
 1Y4  C28  H35  single  0.970  0.020  1.090
 1Y4  C30  OXT  deloc   1.248  0.020  1.248
 1Y4  N19  H2   single  0.890  0.020  1.040

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
 1Y4  H2   N19  C28  107.82  3.000
 1Y4  H2   N19  C20  108.30  3.000
 1Y4  C28  N19  C20  112.81  3.000
 1Y4  H24  C20  H23  107.38  3.000
 1Y4  H24  C20  C21  108.68  3.000
 1Y4  H23  C20  C21  109.85  3.000
 1Y4  H24  C20  N19  113.20  3.000
 1Y4  H23  C20  N19  108.81  3.000
 1Y4  C21  C20  N19  108.88  3.000
 1Y4  H25  C21  N26  110.47  3.000
 1Y4  H25  C21  C23  109.14  3.000
 1Y4  N26  C21  C23  102.21  3.000
 1Y4  H25  C21  C20  108.24  3.000
 1Y4  N26  C21  C20  109.20  3.000
 1Y4  C23  C21  C20  117.41  3.000
 1Y4  H27  C23  H26  107.48  3.000
 1Y4  H27  C23  C24  110.75  3.000
 1Y4  H26  C23  C24  112.93  3.000
 1Y4  H27  C23  C21  109.87  3.000
 1Y4  H26  C23  C21  112.49  3.000
 1Y4  C24  C23  C21  103.32  3.000
 1Y4  H29  C24  H28  106.91  3.000
 1Y4  H29  C24  C25  111.70  3.000
 1Y4  H28  C24  C25  110.74  3.000
 1Y4  H29  C24  C23  111.23  3.000
 1Y4  H28  C24  C23  111.71  3.000
 1Y4  C25  C24  C23  104.64  3.000
 1Y4  H31  C25  H30  107.01  3.000
 1Y4  H31  C25  N26  111.11  3.000
 1Y4  H30  C25  N26  111.65  3.000
 1Y4  H31  C25  C24  113.23  3.000
 1Y4  H30  C25  C24  110.06  3.000
 1Y4  N26  C25  C24  103.86  3.000
 1Y4  C27  N26  C25  116.42  3.000
 1Y4  C27  N26  C21  111.91  3.000
 1Y4  C25  N26  C21  105.32  3.000
 1Y4  H34  C27  H33  107.36  3.000
 1Y4  H34  C27  C28  109.25  3.000
 1Y4  H33  C27  C28  109.65  3.000
 1Y4  H34  C27  N26  110.04  3.000
 1Y4  H33  C27  N26  111.02  3.000
 1Y4  C28  C27  N26  109.48  3.000
 1Y4  H35  C28  C30  105.66  3.000
 1Y4  H35  C28  C27  106.70  3.000
 1Y4  C30  C28  C27  112.40  3.000
 1Y4  H35  C28  N19  106.92  3.000
 1Y4  C30  C28  N19  115.14  3.000
 1Y4  C27  C28  N19  109.47  3.000
 1Y4  OXT  C30  O31  126.22  3.000
 1Y4  OXT  C30  C28  116.60  3.000
 1Y4  O31  C30  C28  117.07  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
 1Y4  Var_01  C25  C24  C23  C21  -11.43  30.0  1
 1Y4  Var_02  C24  C25  N26  C21   39.16  30.0  1
 1Y4  Var_03  C28  C27  N26  C21  -59.31  30.0  1
 1Y4  Var_04  C28  N19  C20  C21   57.66  30.0  1
 1Y4  Var_05  N26  C25  C24  C23  -15.85  30.0  1

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
 1Y4  chir_01  C21  C23  N26  C20  negativ
 1Y4  chir_02  C28  N19  C27  C30  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
 1Y4  plan-1  C28  0.020
 1Y4  plan-1  C30  0.020
 1Y4  plan-1  O31  0.020
 1Y4  plan-1  OXT  0.020

