# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 10:57:56 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: (1aS,4S,6aR,7aS)-octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CN2[C@@H](CN1)C[C@@H]3C[C@H]23
#
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
 1XW  1XW  '(1aS,4S,6aR,7aS)-octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxylic acid'  L-peptide  26  13  .  2022-03-10  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_1XW
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
 1XW  N19  N  NH1    0  -0.601  -1.2074   1.3739  -0.9809
 1XW  C20  C  CH2    0  -0.269  -0.2165   1.7864   0.0062
 1XW  C21  C  CH1    0  -0.088   1.0230   0.9419  -0.1878
 1XW  C23  C  CH2    0  -0.414   2.1932   1.1253   0.7757
 1XW  C24  C  CH1    0  -0.298   2.8662  -0.2362   0.7542
 1XW  C26  C  CH2    0  -0.511   3.0997  -0.8878  -0.5854
 1XW  C27  C  CH1    0  -0.081   1.8565  -1.1926   0.2117
 1XW  N28  N  NT     0  -0.419   0.6545  -0.4535  -0.0219
 1XW  C29  C  CH2    0  -0.266  -0.2621  -0.8780  -1.0495
 1XW  C30  C  CH1    0  -0.247  -1.5349  -0.0469  -0.9170
 1XW  C32  C  C      0   0.406  -2.3799  -0.4668   0.3168
 1XW  O33  O  O      0  -0.611  -2.9521   0.4456   0.9470
 1XW  H23  H  HCH2   0   0.214   0.0179   2.8423  -0.1556
 1XW  H24  H  HCH2   0   0.184  -0.5615   1.6780   1.0434
 1XW  H25  H  HCH1   0   0.193   1.3806   1.1279  -1.2166
 1XW  H26  H  HCH2   0   0.231   2.8458   1.9473   0.4772
 1XW  H27  H  HCH2   0   0.225   1.8348   1.3363   1.7876
 1XW  H28  H  HCH1   0   0.251   3.5092  -0.5119   1.5813
 1XW  H29  H  HCH2   0   0.242   3.0438  -0.2944  -1.4909
 1XW  H30  H  HCH2   0   0.248   3.8573  -1.6612  -0.6193
 1XW  H31  H  HCH1   0   0.246   1.7253  -2.1881   0.6223
 1XW  H33  H  HCH2   0   0.182   0.1666  -0.7534  -2.0593
 1XW  H34  H  HCH2   0   0.228  -0.5078  -1.9312  -0.9219
 1XW  H35  H  HCH1   0   0.230  -2.1573  -0.2683  -1.7953
 1XW  OXT  O  OC    -1  -0.614  -2.4727  -1.6901   0.5431
 1XW  H2   H  HNH1   0   0.337  -2.0585   1.8908  -0.8037

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
 1XW  C26  C24  single  1.508  0.020  1.508
 1XW  C26  C27  single  1.508  0.020  1.508
 1XW  C24  C27  single  1.493  0.020  1.493
 1XW  C24  C23  single  1.519  0.020  1.519
 1XW  C27  N28  single  1.430  0.020  1.430
 1XW  C23  C21  single  1.527  0.020  1.527
 1XW  N28  C21  single  1.453  0.020  1.453
 1XW  N28  C29  single  1.441  0.020  1.441
 1XW  C21  C20  single  1.512  0.020  1.512
 1XW  C29  C30  single  1.526  0.020  1.526
 1XW  C20  N19  single  1.458  0.020  1.458
 1XW  C30  C32  single  1.553  0.020  1.553
 1XW  C30  N19  single  1.459  0.020  1.459
 1XW  C32  O33  deloc   1.248  0.020  1.248
 1XW  C20  H23  single  0.970  0.020  1.090
 1XW  C20  H24  single  0.970  0.020  1.090
 1XW  C21  H25  single  0.970  0.020  1.090
 1XW  C23  H26  single  0.970  0.020  1.090
 1XW  C23  H27  single  0.970  0.020  1.090
 1XW  C24  H28  single  0.970  0.020  1.090
 1XW  C26  H29  single  0.970  0.020  1.090
 1XW  C26  H30  single  0.970  0.020  1.090
 1XW  C27  H31  single  0.970  0.020  1.090
 1XW  C29  H33  single  0.970  0.020  1.090
 1XW  C29  H34  single  0.970  0.020  1.090
 1XW  C30  H35  single  0.970  0.020  1.090
 1XW  C32  OXT  deloc   1.248  0.020  1.248
 1XW  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
 1XW  H2   N19  C30  107.52  3.000
 1XW  H2   N19  C20  107.98  3.000
 1XW  C30  N19  C20  113.47  3.000
 1XW  H24  C20  H23  107.59  3.000
 1XW  H24  C20  C21  108.87  3.000
 1XW  H23  C20  C21  110.15  3.000
 1XW  H24  C20  N19  113.44  3.000
 1XW  H23  C20  N19  108.58  3.000
 1XW  C21  C20  N19  108.19  3.000
 1XW  H25  C21  N28  110.49  3.000
 1XW  H25  C21  C23  108.61  3.000
 1XW  N28  C21  C23  103.76  3.000
 1XW  H25  C21  C20  106.90  3.000
 1XW  N28  C21  C20  108.29  3.000
 1XW  C23  C21  C20  118.69  3.000
 1XW  H27  C23  H26  107.68  3.000
 1XW  H27  C23  C24  109.34  3.000
 1XW  H26  C23  C24  113.98  3.000
 1XW  H27  C23  C21  110.84  3.000
 1XW  H26  C23  C21  112.10  3.000
 1XW  C24  C23  C21  102.88  3.000
 1XW  H28  C24  C27  121.05  3.000
 1XW  H28  C24  C26  118.45  3.000
 1XW  C27  C24  C26   60.33  3.000
 1XW  H28  C24  C23  118.71  3.000
 1XW  C27  C24  C23  106.24  3.000
 1XW  C26  C24  C23  117.94  3.000
 1XW  H30  C26  H29  113.63  3.000
 1XW  H30  C26  C27  116.67  3.000
 1XW  H29  C26  C27  120.65  3.000
 1XW  H30  C26  C24  116.40  3.000
 1XW  H29  C26  C24  119.84  3.000
 1XW  C27  C26  C24   59.34  3.000
 1XW  H31  C27  N28  115.75  3.000
 1XW  H31  C27  C26  119.03  3.000
 1XW  N28  C27  C26  120.13  3.000
 1XW  H31  C27  C24  122.15  3.000
 1XW  N28  C27  C24  107.26  3.000
 1XW  C26  C27  C24   60.33  3.000
 1XW  C29  N28  C27  119.93  3.000
 1XW  C29  N28  C21  111.28  3.000
 1XW  C27  N28  C21  107.57  3.000
 1XW  H34  C29  H33  107.68  3.000
 1XW  H34  C29  C30  109.18  3.000
 1XW  H33  C29  C30  109.99  3.000
 1XW  H34  C29  N28  110.18  3.000
 1XW  H33  C29  N28  111.84  3.000
 1XW  C30  C29  N28  107.96  3.000
 1XW  H35  C30  C32  105.80  3.000
 1XW  H35  C30  C29  107.05  3.000
 1XW  C32  C30  C29  112.05  3.000
 1XW  H35  C30  N19  106.75  3.000
 1XW  C32  C30  N19  114.84  3.000
 1XW  C29  C30  N19  109.83  3.000
 1XW  OXT  C32  O33  126.24  3.000
 1XW  OXT  C32  C30  116.72  3.000
 1XW  O33  C32  C30  116.94  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
 1XW  Var_01  C26  C24  C23  C21   45.99  30.0  1
 1XW  Var_02  C26  C27  N28  C21  -41.75  30.0  1
 1XW  Var_03  C30  C29  N28  C21  -62.19  30.0  1
 1XW  Var_04  C30  N19  C20  C21   56.70  30.0  1
 1XW  Var_05  C27  C26  C24  C23  -93.57  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
 1XW  chir_01  C21  C23  N28  C20  negativ
 1XW  chir_04  C30  C29  C32  N19  negativ
 1XW  chir_05  C24  C26  C27  C23  both
 1XW  chir_06  C27  N28  C26  C24  both

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
 1XW  plan-1  C30  0.020
 1XW  plan-1  C32  0.020
 1XW  plan-1  O33  0.020
 1XW  plan-1  OXT  0.020

