# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 01:04:55 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (3S,6R,8aS)-5-oxo-1,2,3,8a-tetrahydrospiro[indolizine-6,2'-pyrrolidine]-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CC[C@H]2C=C[C@]3(CCCN3)C(=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
 2L6  2L6  '(3S,6R,8aS)-5-oxo-1,2,3,8a-tetrahydrospiro[indolizine-6,2'-pyrrolidine]-3-carboxylic acid'  L-peptide  33  17  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2L6
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
 2L6  N5   N  NH1   0  -0.626  -2.8839   0.0339  -1.0197
 2L6  C30  C  CH2   0  -0.261  -3.5187  -1.1776  -0.4883
 2L6  C29  C  CH2   0  -0.482  -2.8402  -1.4571   0.8563
 2L6  C34  C  CH2   0  -0.434  -2.2201  -0.1135   1.2175
 2L6  C35  C  CT    0  -0.072  -1.7999   0.4551  -0.1551
 2L6  C31  C  C     0   0.578  -0.4630  -0.1767  -0.5581
 2L6  O3   O  O     0  -0.488  -0.4001  -1.1938  -1.2350
 2L6  N3   N  NT    0  -0.496   0.6427   0.4446  -0.1202
 2L6  C26  C  C1    0  -0.169  -1.6669   1.9525  -0.1021
 2L6  C28  C  C1    0  -0.264  -0.5317   2.5476   0.2357
 2L6  C27  C  CH1   0  -0.059   0.6940   1.7505   0.5242
 2L6  C24  C  CH2   0  -0.455   2.0061   2.3143  -0.0122
 2L6  C9   C  CH2   0  -0.493   2.9073   1.0847  -0.0386
 2L6  C10  C  CH1   0  -0.159   1.9523  -0.0417  -0.4862
 2L6  C20  C  C     0   0.542   2.2707  -1.3455   0.2097
 2L6  O6   O  O     0  -0.430   1.7131  -1.7529   1.1942
 2L6  H12  H  HCH2  0   0.209  -4.5907  -1.0068  -0.3499
 2L6  H13  H  HCH2  0   0.222  -3.4178  -2.0222  -1.1725
 2L6  H14  H  HCH2  0   0.244  -3.5416  -1.8093   1.6122
 2L6  H15  H  HCH2  0   0.237  -2.0654  -2.2162   0.7482
 2L6  H16  H  HCH2  0   0.249  -2.9660   0.5528   1.6582
 2L6  H17  H  HCH2  0   0.251  -1.3843  -0.1789   1.9153
 2L6  H18  H  H     0   0.253  -2.5681   2.5230  -0.2936
 2L6  H19  H  H     0   0.262  -0.4644   3.6233   0.3441
 2L6  H20  H  HCH1  0   0.267   0.7907   1.6214   1.6115
 2L6  H21  H  HCH2  0   0.248   1.8569   2.7070  -1.0210
 2L6  H22  H  HCH2  0   0.263   2.3989   3.1150   0.6128
 2L6  H23  H  HCH2  0   0.276   3.7544   1.1801  -0.7144
 2L6  H24  H  HCH2  0   0.257   3.2988   0.8904   0.9625
 2L6  H25  H  HCH1  0   0.293   2.0199  -0.1861  -1.5683
 2L6  H2   H  HNH1  0   0.350  -2.5711  -0.0961  -1.9712
 2L6  OXT  O  OH1   0  -0.593   3.2887  -1.9587  -0.3785
 2L6  HXT  H  HOH1  0   0.484   3.5254  -2.7614   0.1104

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
 2L6  N5   C30  single  1.467  0.020  1.467
 2L6  N5   C35  single  1.449  0.020  1.449
 2L6  C26  C28  double  1.325  0.020  1.325
 2L6  C26  C35  single  1.504  0.020  1.504
 2L6  C28  C27  single  1.490  0.020  1.490
 2L6  C30  C29  single  1.532  0.020  1.532
 2L6  C35  C31  single  1.533  0.020  1.533
 2L6  C35  C34  single  1.544  0.020  1.544
 2L6  C24  C27  single  1.526  0.020  1.526
 2L6  C24  C9   single  1.525  0.020  1.525
 2L6  C31  O3   double  1.223  0.020  1.223
 2L6  C31  N3   single  1.342  0.020  1.342
 2L6  C27  N3   single  1.457  0.020  1.457
 2L6  N3   C10  single  1.444  0.020  1.444
 2L6  C9   C10  single  1.543  0.020  1.543
 2L6  C10  C20  single  1.512  0.020  1.512
 2L6  C34  C29  single  1.523  0.020  1.523
 2L6  C20  O6   double  1.203  0.020  1.203
 2L6  C30  H12  single  0.970  0.020  1.090
 2L6  C30  H13  single  0.970  0.020  1.090
 2L6  C29  H14  single  0.970  0.020  1.090
 2L6  C29  H15  single  0.970  0.020  1.090
 2L6  C34  H16  single  0.970  0.020  1.090
 2L6  C34  H17  single  0.970  0.020  1.090
 2L6  C26  H18  single  0.930  0.020  1.080
 2L6  C28  H19  single  0.930  0.020  1.080
 2L6  C27  H20  single  0.970  0.020  1.090
 2L6  C24  H21  single  0.970  0.020  1.090
 2L6  C24  H22  single  0.970  0.020  1.090
 2L6  C9   H23  single  0.970  0.020  1.090
 2L6  C9   H24  single  0.970  0.020  1.090
 2L6  C10  H25  single  0.970  0.020  1.090
 2L6  N5   H2   single  0.890  0.020  1.040
 2L6  C20  OXT  single  1.326  0.020  1.326
 2L6  OXT  HXT  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
 2L6  H2   N5   C35  111.59  3.000
 2L6  H2   N5   C30  111.65  3.000
 2L6  C35  N5   C30  110.33  3.000
 2L6  H13  C30  H12  106.89  3.000
 2L6  H13  C30  C29  111.59  3.000
 2L6  H12  C30  C29  110.57  3.000
 2L6  H13  C30  N5   111.83  3.000
 2L6  H12  C30  N5   109.92  3.000
 2L6  C29  C30  N5   106.08  3.000
 2L6  H15  C29  H14  107.53  3.000
 2L6  H15  C29  C34  110.39  3.000
 2L6  H14  C29  C34  112.49  3.000
 2L6  H15  C29  C30  110.78  3.000
 2L6  H14  C29  C30  112.51  3.000
 2L6  C34  C29  C30  103.15  3.000
 2L6  H17  C34  H16  107.55  3.000
 2L6  H17  C34  C35  112.48  3.000
 2L6  H16  C34  C35  108.65  3.000
 2L6  H17  C34  C29  114.25  3.000
 2L6  H16  C34  C29  110.83  3.000
 2L6  C35  C34  C29  102.99  3.000
 2L6  C26  C35  C31  110.03  3.000
 2L6  C31  C35  C34  108.63  3.000
 2L6  C26  C35  C34  111.06  3.000
 2L6  C34  C35  N5   102.70  3.000
 2L6  C31  C35  N5   112.07  3.000
 2L6  C26  C35  N5   112.12  3.000
 2L6  N3   C31  O3   121.54  3.000
 2L6  N3   C31  C35  116.24  3.000
 2L6  O3   C31  C35  122.22  3.000
 2L6  C10  N3   C27  112.46  3.000
 2L6  C10  N3   C31  120.58  3.000
 2L6  C27  N3   C31  126.03  3.000
 2L6  H18  C26  C28  121.39  3.000
 2L6  H18  C26  C35  116.38  3.000
 2L6  C28  C26  C35  122.12  3.000
 2L6  H19  C28  C27  117.44  3.000
 2L6  H19  C28  C26  121.64  3.000
 2L6  C27  C28  C26  120.90  3.000
 2L6  H20  C27  C24  108.39  3.000
 2L6  H20  C27  C28  109.06  3.000
 2L6  C24  C27  C28  116.21  3.000
 2L6  H20  C27  N3   109.59  3.000
 2L6  C24  C27  N3   101.89  3.000
 2L6  C28  C27  N3   111.40  3.000
 2L6  H22  C24  H21  108.36  3.000
 2L6  H22  C24  C9   112.94  3.000
 2L6  H21  C24  C9   110.76  3.000
 2L6  H22  C24  C27  112.35  3.000
 2L6  H21  C24  C27  109.87  3.000
 2L6  C9   C24  C27  102.50  3.000
 2L6  H24  C9   H23  107.81  3.000
 2L6  H24  C9   C10  110.97  3.000
 2L6  H23  C9   C10  111.46  3.000
 2L6  H24  C9   C24  109.84  3.000
 2L6  H23  C9   C24  113.60  3.000
 2L6  C10  C9   C24  103.17  3.000
 2L6  H25  C10  C20  109.18  3.000
 2L6  H25  C10  C9   110.19  3.000
 2L6  C20  C10  C9   111.45  3.000
 2L6  H25  C10  N3   110.57  3.000
 2L6  C20  C10  N3   111.39  3.000
 2L6  C9   C10  N3   104.00  3.000
 2L6  OXT  C20  O6   124.23  3.000
 2L6  OXT  C20  C10  110.87  3.000
 2L6  O6   C20  C10  124.85  3.000
 2L6  HXT  OXT  C20  110.28  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
 2L6  CONST_01  C27  N3   C31  C35    0.00   0.0  0
 2L6  CONST_02  C10  N3   C31  C35  180.00   0.0  0
 2L6  CONST_03  C27  N3   C31  O3   180.00   0.0  0
 2L6  CONST_04  C10  N3   C31  O3     0.00   0.0  0
 2L6  CONST_05  HXT  OXT  C20  C10  180.00   0.0  0
 2L6  Var_01    C34  C29  C30  N5    19.59  30.0  1
 2L6  Var_02    C35  C34  C29  C30  -34.91  30.0  1
 2L6  Var_03    C35  N5   C30  C29    4.48  30.0  1
 2L6  Var_04    C27  C28  C26  C35    2.70  30.0  1
 2L6  Var_05    C10  C9   C24  C27   37.97  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
 2L6  chir_01  C35  C26  C31  C34  negativ
 2L6  chir_02  C27  N3   C28  C24  positiv
 2L6  chir_03  C10  N3   C9   C20  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
 2L6  plan-1  C35  0.020
 2L6  plan-1  C31  0.020
 2L6  plan-1  O3   0.020
 2L6  plan-1  N3   0.020
 2L6  plan-1  C27  0.020
 2L6  plan-1  C10  0.020
 2L6  plan-2  C10  0.020
 2L6  plan-2  C20  0.020
 2L6  plan-2  O6   0.020
 2L6  plan-2  OXT  0.020
 2L6  plan-2  HXT  0.020

