# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 09:04:21 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  32  17  .  2022-03-10  2022-03-10
;
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  -0.629  -2.9304   0.0965  -1.0141
 2L6  C30  C  CH2    0  -0.261  -3.5551  -1.1126  -0.4645
 2L6  C29  C  CH2    0  -0.481  -2.8312  -1.4070   0.8528
 2L6  C34  C  CH2    0  -0.431  -2.1836  -0.0729   1.1999
 2L6  C35  C  CR6    0  -0.072  -1.8121   0.5044  -0.1835
 2L6  C31  C  CR6    0   0.570  -0.4921  -0.1368  -0.6334
 2L6  O3   O  O      0  -0.509  -0.4756  -1.1561  -1.3166
 2L6  N3   N  NR6    0  -0.477   0.6237   0.4782  -0.2404
 2L6  C26  C  CR16   0  -0.172  -1.6706   2.0004  -0.1221
 2L6  C28  C  CR16   0  -0.266  -0.5217   2.5782   0.2004
 2L6  C27  C  CR16   0  -0.060   0.6912   1.7504   0.4552
 2L6  C24  C  CH2    0  -0.446   2.0167   2.3075  -0.0535
 2L6  C9   C  CH2    0  -0.500   2.8946   1.0600  -0.0912
 2L6  C10  C  CH1    0  -0.151   1.9375  -0.0703  -0.5217
 2L6  C20  C  C      0   0.402   2.2281  -1.3686   0.2553
 2L6  O6   O  O      0  -0.593   1.5599  -1.5805   1.2811
 2L6  H12  H  HCH2   0   0.205  -4.6203  -0.9342  -0.2862
 2L6  H13  H  HCH2   0   0.219  -3.4867  -1.9547  -1.1557
 2L6  H14  H  HCH2   0   0.240  -3.5085  -1.7579   1.6316
 2L6  H15  H  HCH2   0   0.236  -2.0663  -2.1709   0.7130
 2L6  H16  H  HCH2   0   0.242  -2.9009   0.5961   1.6823
 2L6  H17  H  HCH2   0   0.251  -1.3162  -0.1586   1.8555
 2L6  H18  H  HCR6   0   0.246  -2.5696   2.5812  -0.2937
 2L6  H19  H  HCR6   0   0.255  -0.4363   3.6520   0.3172
 2L6  H20  H  HCR6   0   0.252   0.7854   1.5754   1.5376
 2L6  H21  H  HCH2   0   0.235   1.8814   2.7219  -1.0561
 2L6  H22  H  HCH2   0   0.247   2.4111   3.0942   0.5897
 2L6  H23  H  HCH2   0   0.252   3.7429   1.1521  -0.7673
 2L6  H24  H  HCH2   0   0.236   3.2924   0.8661   0.9083
 2L6  H25  H  HCH1   0   0.234   2.0339  -0.2555  -1.5952
 2L6  H2   H  HNH1   0   0.346  -2.6389  -0.0469  -1.9706
 2L6  OXT  O  OC    -1  -0.619   3.1593  -2.0604  -0.2038

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  1.468  0.020  1.468
 2L6  N5   C35  single  1.452  0.020  1.452
 2L6  C26  C28  double  1.326  0.020  1.326
 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  1.535  0.020  1.535
 2L6  C35  C34  single  1.544  0.020  1.544
 2L6  C24  C27  single  1.525  0.020  1.525
 2L6  C24  C9   single  1.526  0.020  1.526
 2L6  C31  O3   double  1.227  0.020  1.227
 2L6  C31  N3   single  1.333  0.020  1.333
 2L6  C27  N3   single  1.452  0.020  1.452
 2L6  N3   C10  single  1.451  0.020  1.451
 2L6  C9   C10  single  1.542  0.020  1.542
 2L6  C10  C20  single  1.541  0.020  1.541
 2L6  C34  C29  single  1.523  0.020  1.523
 2L6  C20  O6   deloc   1.242  0.020  1.242
 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  deloc   1.247  0.020  1.247

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  111.06  3.000
 2L6  H2   N5   C30  111.13  3.000
 2L6  C35  N5   C30  110.19  3.000
 2L6  H13  C30  H12  106.85  3.000
 2L6  H13  C30  C29  111.51  3.000
 2L6  H12  C30  C29  110.55  3.000
 2L6  H13  C30  N5   111.82  3.000
 2L6  H12  C30  N5   109.93  3.000
 2L6  C29  C30  N5   106.22  3.000
 2L6  H15  C29  H14  107.58  3.000
 2L6  H15  C29  C34  110.16  3.000
 2L6  H14  C29  C34  112.54  3.000
 2L6  H15  C29  C30  110.86  3.000
 2L6  H14  C29  C30  112.50  3.000
 2L6  C34  C29  C30  103.21  3.000
 2L6  H17  C34  H16  107.74  3.000
 2L6  H17  C34  C35  112.12  3.000
 2L6  H16  C34  C35  108.93  3.000
 2L6  H17  C34  C29  113.98  3.000
 2L6  H16  C34  C29  110.96  3.000
 2L6  C35  C34  C29  103.04  3.000
 2L6  C26  C35  C31  110.28  3.000
 2L6  C31  C35  C34  108.26  3.000
 2L6  C26  C35  C34  110.98  3.000
 2L6  C34  C35  N5   102.84  3.000
 2L6  C31  C35  N5   112.17  3.000
 2L6  C26  C35  N5   112.05  3.000
 2L6  N3   C31  O3   122.41  3.000
 2L6  N3   C31  C35  116.14  3.000
 2L6  O3   C31  C35  121.44  3.000
 2L6  C10  N3   C27  112.46  3.000
 2L6  C10  N3   C31  121.75  3.000
 2L6  C27  N3   C31  125.76  3.000
 2L6  H18  C26  C28  121.58  3.000
 2L6  H18  C26  C35  116.64  3.000
 2L6  C28  C26  C35  121.67  3.000
 2L6  H19  C28  C27  117.90  3.000
 2L6  H19  C28  C26  121.77  3.000
 2L6  C27  C28  C26  120.31  3.000
 2L6  H20  C27  C24  108.16  3.000
 2L6  H20  C27  C28  109.03  3.000
 2L6  C24  C27  C28  116.57  3.000
 2L6  H20  C27  N3   109.63  3.000
 2L6  C24  C27  N3   101.58  3.000
 2L6  C28  C27  N3   111.54  3.000
 2L6  H22  C24  H21  108.21  3.000
 2L6  H22  C24  C9   113.35  3.000
 2L6  H21  C24  C9   111.01  3.000
 2L6  H22  C24  C27  112.41  3.000
 2L6  H21  C24  C27  109.68  3.000
 2L6  C9   C24  C27  102.10  3.000
 2L6  H24  C9   H23  107.42  3.000
 2L6  H24  C9   C10  110.55  3.000
 2L6  H23  C9   C10  111.85  3.000
 2L6  H24  C9   C24  109.38  3.000
 2L6  H23  C9   C24  113.23  3.000
 2L6  C10  C9   C24  104.42  3.000
 2L6  H25  C10  C20  109.61  3.000
 2L6  H25  C10  C9   110.09  3.000
 2L6  C20  C10  C9   111.08  3.000
 2L6  H25  C10  N3   109.52  3.000
 2L6  C20  C10  N3   113.05  3.000
 2L6  C9   C10  N3   103.34  3.000
 2L6  OXT  C20  O6   127.64  3.000
 2L6  OXT  C20  C10  114.99  3.000
 2L6  O6   C20  C10  117.30  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  Var_01    C34  C29  C30  N5    19.52  30.0  1
 2L6  Var_02    C35  C34  C29  C30  -34.66  30.0  1
 2L6  Var_03    C35  N5   C30  C29    4.34  30.0  1
 2L6  Var_04    C27  C28  C26  C35    2.74  30.0  1
 2L6  Var_05    C10  C9   C24  C27   36.01  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

