# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:46:35 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (3aR,5aS,8S,10aS)-10-oxo-1,2,3,3a,5a,8,10,10a-octahydrodipyrrolo[1,2-a:3',2'-e]azepine-8-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C=C[C@@H]2C=C[C@H]3CCN[C@@H]3C(=O)N12
#
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
 2L9  2L9  '(3aR,5aS,8S,10aS)-10-oxo-1,2,3,3a,5a,8,10,10a-octahydrodipyrrolo[1,2-a:3',2'-e]azepine-8-carboxylic acid'  L-peptide  30  17  .  2022-08-09  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_2L9
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
 2L9  N2   N  NH1    0  -0.624   2.8685   0.9535  -0.8995
 2L9  C22  C  CH2    0  -0.277   3.8332   0.8335   0.2034
 2L9  C23  C  CH2    0  -0.473   3.4307  -0.4306   0.9575
 2L9  C8   C  CH1    0  -0.300   1.9123  -0.4352   0.8053
 2L9  C21  C  CH1    0  -0.182   1.7667   0.0405  -0.6506
 2L9  C25  C  C      0   0.547   0.4059   0.6738  -0.8257
 2L9  O7   O  O      0  -0.503   0.2590   1.8834  -0.9586
 2L9  C7   C  C1     0  -0.190   1.2421  -1.7365   1.0992
 2L9  C6   C  C1     0  -0.218   0.2042  -2.2449   0.4433
 2L9  C5   C  CR15   0  -0.135  -0.5394  -1.6368  -0.7222
 2L9  C4   C  CR15   0  -0.241  -1.9954  -2.0095  -0.6953
 2L9  C3   C  CR15   0  -0.246  -2.7762  -0.9405  -0.6564
 2L9  C2   C  CR15   0  -0.207  -1.9802   0.3246  -0.6295
 2L9  N1   N  NR5    0  -0.486  -0.6254  -0.1766  -0.7667
 2L9  C1   C  C      0   0.421  -2.2379   1.0891   0.6994
 2L9  O2   O  O      0  -0.576  -1.3932   0.9819   1.5989
 2L9  OXT  O  OC    -1  -0.615  -3.3198   1.7070   0.7261
 2L9  H26  H  HCH2   0   0.219   4.8586   0.7736  -0.1693
 2L9  H27  H  HCH2   0   0.215   3.7843   1.6986   0.8720
 2L9  H28  H  HCH2   0   0.231   3.8554  -1.3193   0.4823
 2L9  H29  H  HCH2   0   0.248   3.7568  -0.4214   1.9981
 2L9  H30  H  HCH1   0   0.262   1.4954   0.3352   1.4679
 2L9  H31  H  HCH1   0   0.248   1.8428  -0.8346  -1.3109
 2L9  H32  H  H      0   0.244   1.6471  -2.3089   1.9285
 2L9  H33  H  H      0   0.248  -0.1569  -3.2255   0.7372
 2L9  H34  H  HCR5   0   0.270  -0.0819  -2.0116  -1.6492
 2L9  H35  H  HCR5   0   0.262  -2.3150  -3.0425  -0.7012
 2L9  H36  H  HCR5   0   0.259  -3.8564  -0.9422  -0.6292
 2L9  H37  H  HCR5   0   0.250  -2.2443   0.9791  -1.4671
 2L9  H2   H  HNH1   0   0.348   2.5127   1.8982  -0.9608

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
 2L9  C22  C23  single  1.526  0.020  1.526
 2L9  C22  N2   single  1.470  0.020  1.470
 2L9  C23  C8   single  1.526  0.020  1.526
 2L9  N2   C21  single  1.452  0.020  1.452
 2L9  C8   C21  single  1.539  0.020  1.539
 2L9  C8   C7   single  1.493  0.020  1.493
 2L9  C21  C25  single  1.511  0.020  1.511
 2L9  C7   C6   double  1.329  0.020  1.329
 2L9  O7   C25  double  1.226  0.020  1.226
 2L9  C25  N1   single  1.338  0.020  1.338
 2L9  C6   C5   single  1.510  0.020  1.510
 2L9  N1   C5   single  1.463  0.020  1.463
 2L9  N1   C2   single  1.451  0.020  1.451
 2L9  C5   C4   single  1.503  0.020  1.503
 2L9  OXT  C1   deloc   1.246  0.020  1.246
 2L9  C2   C1   single  1.555  0.020  1.555
 2L9  C2   C3   single  1.495  0.020  1.495
 2L9  C1   O2   deloc   1.239  0.020  1.239
 2L9  C4   C3   double  1.324  0.020  1.324
 2L9  C22  H26  single  0.970  0.020  1.090
 2L9  C22  H27  single  0.970  0.020  1.090
 2L9  C23  H28  single  0.970  0.020  1.090
 2L9  C23  H29  single  0.970  0.020  1.090
 2L9  C8   H30  single  0.970  0.020  1.090
 2L9  C21  H31  single  0.970  0.020  1.090
 2L9  C7   H32  single  0.930  0.020  1.080
 2L9  C6   H33  single  0.930  0.020  1.080
 2L9  C5   H34  single  0.970  0.020  1.090
 2L9  C4   H35  single  0.930  0.020  1.080
 2L9  C3   H36  single  0.930  0.020  1.080
 2L9  C2   H37  single  0.970  0.020  1.090
 2L9  N2   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
 2L9  H2   N2   C21  109.31  3.000
 2L9  H2   N2   C22  110.64  3.000
 2L9  C21  N2   C22  108.54  3.000
 2L9  H27  C22  H26  107.08  3.000
 2L9  H27  C22  C23  109.94  3.000
 2L9  H26  C22  C23  111.76  3.000
 2L9  H27  C22  N2   111.37  3.000
 2L9  H26  C22  N2   111.37  3.000
 2L9  C23  C22  N2   105.38  3.000
 2L9  H29  C23  H28  107.78  3.000
 2L9  H29  C23  C8   113.13  3.000
 2L9  H28  C23  C8   109.91  3.000
 2L9  H29  C23  C22  112.69  3.000
 2L9  H28  C23  C22  110.86  3.000
 2L9  C8   C23  C22  102.45  3.000
 2L9  H30  C8   C7   108.80  3.000
 2L9  H30  C8   C21  108.55  3.000
 2L9  C7   C8   C21  114.41  3.000
 2L9  H30  C8   C23  108.38  3.000
 2L9  C7   C8   C23  115.44  3.000
 2L9  C21  C8   C23  100.81  3.000
 2L9  H31  C21  C25  109.06  3.000
 2L9  H31  C21  C8   108.41  3.000
 2L9  C25  C21  C8   108.93  3.000
 2L9  H31  C21  N2   110.18  3.000
 2L9  C25  C21  N2   113.57  3.000
 2L9  C8   C21  N2   106.55  3.000
 2L9  N1   C25  O7   122.66  3.000
 2L9  N1   C25  C21  115.00  3.000
 2L9  O7   C25  C21  122.28  3.000
 2L9  H32  C7   C6   117.81  3.000
 2L9  H32  C7   C8   116.25  3.000
 2L9  C6   C7   C8   125.94  3.000
 2L9  H33  C6   C5   114.13  3.000
 2L9  H33  C6   C7   118.15  3.000
 2L9  C5   C6   C7   127.69  3.000
 2L9  H34  C5   N1   109.81  3.000
 2L9  H34  C5   C4   109.48  3.000
 2L9  N1   C5   C4   101.01  3.000
 2L9  H34  C5   C6   107.97  3.000
 2L9  C4   C5   C6   111.30  3.000
 2L9  N1   C5   C6   117.01  3.000
 2L9  H35  C4   C3   126.66  3.000
 2L9  H35  C4   C5   121.54  3.000
 2L9  C3   C4   C5   111.80  3.000
 2L9  H36  C3   C2   122.22  3.000
 2L9  H36  C3   C4   126.08  3.000
 2L9  C2   C3   C4   111.70  3.000
 2L9  H37  C2   C1   108.66  3.000
 2L9  H37  C2   N1   111.05  3.000
 2L9  C1   C2   N1   113.92  3.000
 2L9  H37  C2   C3   111.31  3.000
 2L9  C1   C2   C3   110.08  3.000
 2L9  N1   C2   C3   101.72  3.000
 2L9  C2   N1   C5   113.37  3.000
 2L9  C2   N1   C25  120.28  3.000
 2L9  C5   N1   C25  126.18  3.000
 2L9  OXT  C1   O2   128.28  3.000
 2L9  O2   C1   C2   117.72  3.000
 2L9  OXT  C1   C2   113.95  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
 2L9  Var_01  C8   C23  C22  N2   -33.54  30.0  1
 2L9  Var_02  C21  N2   C22  C23   13.24  30.0  1
 2L9  Var_03  C2   C3   C4   C5    -0.88  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
 2L9  chir_01  C8   C23  C21  C7   negativ
 2L9  chir_02  C21  N2   C8   C25  negativ
 2L9  chir_03  C5   N1   C6   C4   negativ
 2L9  chir_04  C2   N1   C1   C3   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
 2L9  plan-1  C21  0.020
 2L9  plan-1  C25  0.020
 2L9  plan-1  O7   0.020
 2L9  plan-1  C5   0.020
 2L9  plan-1  C2   0.020
 2L9  plan-1  N1   0.020
 2L9  plan-2  C2   0.020
 2L9  plan-2  C1   0.020
 2L9  plan-2  O2   0.020
 2L9  plan-2  OXT  0.020

