# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:32:01 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  31  17  .  2022-08-09  2022-11-17
;
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  NR15  0  -0.618   2.8119   1.0496  -0.8509
 2L9  C22  C  CH2   0  -0.277   3.8845   0.7759   0.1197
 2L9  C23  C  CH2   0  -0.478   3.4719  -0.4978   0.8615
 2L9  C8   C  CR15  0  -0.303   1.9464  -0.4507   0.8010
 2L9  C21  C  CR15  0  -0.190   1.7429   0.0978  -0.6222
 2L9  C25  C  C     0   0.561   0.3671   0.7029  -0.7362
 2L9  O7   O  O     0  -0.487   0.1672   1.9087  -0.7810
 2L9  C7   C  C1    0  -0.179   1.2640  -1.7466   1.0908
 2L9  C6   C  C1    0  -0.224   0.2222  -2.2558   0.4415
 2L9  C5   C  CR15  0  -0.139  -0.5217  -1.6427  -0.7205
 2L9  C4   C  CR15  0  -0.217  -1.9661  -2.0501  -0.7350
 2L9  C3   C  CR15  0  -0.238  -2.7821  -1.0090  -0.7041
 2L9  C2   C  CR15  0  -0.213  -2.0082   0.2778  -0.6548
 2L9  N1   N  NR5   0  -0.500  -0.6422  -0.1831  -0.7132
 2L9  C1   C  C     0   0.556  -2.2947   1.0130   0.6476
 2L9  O2   O  O     0  -0.421  -1.6366   0.9111   1.6468
 2L9  OXT  O  OH1   0  -0.589  -3.4023   1.7310   0.5427
 2L9  H26  H  HCH2  0   0.221   4.8482   0.6499  -0.3788
 2L9  H27  H  HCH2  0   0.223   3.9921   1.6070   0.8215
 2L9  H28  H  HCH2  0   0.236   3.8340  -1.3877   0.3402
 2L9  H29  H  HCH2  0   0.253   3.8535  -0.5327   1.8821
 2L9  H30  H  HCR5  0   0.263   1.6008   0.3055   1.5192
 2L9  H31  H  HCR5  0   0.260   1.8262  -0.7382  -1.3303
 2L9  H32  H  H     0   0.251   1.6693  -2.3202   1.9189
 2L9  H33  H  H     0   0.257  -0.1402  -3.2340   0.7400
 2L9  H34  H  HCR5  0   0.288  -0.0443  -1.9713  -1.6536
 2L9  H35  H  HCR5  0   0.280  -2.2597  -3.0896  -0.7751
 2L9  H36  H  HCR5  0   0.284  -3.8619  -1.0343  -0.7139
 2L9  H37  H  HCR5  0   0.307  -2.2557   0.9325  -1.4972
 2L9  H2   H  HNR5  0   0.351   2.4572   1.9885  -0.7275
 2L9  H1   H  HOH1  0   0.486  -3.6173   2.1481   1.3910

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  1.531  0.020  1.531
 2L9  C22  N2   single  1.472  0.020  1.472
 2L9  C23  C8   single  1.527  0.020  1.527
 2L9  N2   C21  single  1.450  0.020  1.450
 2L9  C8   C21  single  1.539  0.020  1.539
 2L9  C8   C7   single  1.493  0.020  1.493
 2L9  C21  C25  single  1.507  0.020  1.507
 2L9  C7   C6   double  1.329  0.020  1.329
 2L9  O7   C25  double  1.223  0.020  1.223
 2L9  C25  N1   single  1.343  0.020  1.343
 2L9  C6   C5   single  1.510  0.020  1.510
 2L9  N1   C5   single  1.465  0.020  1.465
 2L9  N1   C2   single  1.443  0.020  1.443
 2L9  C5   C4   single  1.501  0.020  1.501
 2L9  OXT  C1   single  1.324  0.020  1.324
 2L9  C2   C1   single  1.523  0.020  1.523
 2L9  C2   C3   single  1.502  0.020  1.502
 2L9  C1   O2   double  1.201  0.020  1.201
 2L9  C4   C3   double  1.323  0.020  1.323
 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
 2L9  OXT  H1   single  0.850  0.020  0.980

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  109.38  3.000
 2L9  H2   N2   C22  110.35  3.000
 2L9  C21  N2   C22  108.13  3.000
 2L9  H27  C22  H26  107.09  3.000
 2L9  H27  C22  C23  110.37  3.000
 2L9  H26  C22  C23  111.29  3.000
 2L9  H27  C22  N2   110.71  3.000
 2L9  H26  C22  N2   111.31  3.000
 2L9  C23  C22  N2   106.13  3.000
 2L9  H29  C23  H28  107.72  3.000
 2L9  H29  C23  C8   112.81  3.000
 2L9  H28  C23  C8   109.70  3.000
 2L9  H29  C23  C22  112.71  3.000
 2L9  H28  C23  C22  110.92  3.000
 2L9  C8   C23  C22  102.97  3.000
 2L9  H30  C8   C7   109.07  3.000
 2L9  H30  C8   C21  108.52  3.000
 2L9  C7   C8   C21  115.37  3.000
 2L9  H30  C8   C23  108.03  3.000
 2L9  C7   C8   C23  114.97  3.000
 2L9  C21  C8   C23  100.36  3.000
 2L9  H31  C21  C25  109.02  3.000
 2L9  H31  C21  C8   108.35  3.000
 2L9  C25  C21  C8   109.50  3.000
 2L9  H31  C21  N2   110.00  3.000
 2L9  C25  C21  N2   113.43  3.000
 2L9  C8   C21  N2   106.41  3.000
 2L9  N1   C25  O7   121.88  3.000
 2L9  N1   C25  C21  114.82  3.000
 2L9  O7   C25  C21  123.21  3.000
 2L9  H32  C7   C6   117.56  3.000
 2L9  H32  C7   C8   115.85  3.000
 2L9  C6   C7   C8   126.59  3.000
 2L9  H33  C6   C5   114.41  3.000
 2L9  H33  C6   C7   118.22  3.000
 2L9  C5   C6   C7   127.35  3.000
 2L9  H34  C5   N1   109.76  3.000
 2L9  H34  C5   C4   109.20  3.000
 2L9  N1   C5   C4   101.04  3.000
 2L9  H34  C5   C6   108.55  3.000
 2L9  C4   C5   C6   111.80  3.000
 2L9  N1   C5   C6   116.19  3.000
 2L9  H35  C4   C3   126.16  3.000
 2L9  H35  C4   C5   121.52  3.000
 2L9  C3   C4   C5   112.32  3.000
 2L9  H36  C3   C2   122.37  3.000
 2L9  H36  C3   C4   126.72  3.000
 2L9  C2   C3   C4   110.92  3.000
 2L9  H37  C2   C1   109.07  3.000
 2L9  H37  C2   N1   111.94  3.000
 2L9  C1   C2   N1   111.53  3.000
 2L9  H37  C2   C3   111.74  3.000
 2L9  C1   C2   C3   110.16  3.000
 2L9  N1   C2   C3   102.28  3.000
 2L9  C2   N1   C5   113.35  3.000
 2L9  C2   N1   C25  120.09  3.000
 2L9  C5   N1   C25  126.55  3.000
 2L9  OXT  C1   O2   124.78  3.000
 2L9  O2   C1   C2   124.58  3.000
 2L9  OXT  C1   C2   110.57  3.000
 2L9  H1   OXT  C1   110.45  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  CONST_01  H1   OXT  C1   C2   180.00   0.0  0
 2L9  Var_01    C8   C23  C22  N2   -28.61  30.0  1
 2L9  Var_02    C21  N2   C22  C23    5.85  30.0  1
 2L9  Var_03    C2   C3   C4   C5    -0.35  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
 2L9  plan-2  H1   0.020

