# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 08:25:03 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S,3aS,7aS)-octahydro-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@@H]2CCCC[C@@H]2N1
#
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
 OIC  OIC  '(2S,3aS,7aS)-octahydro-1H-indole-2-carboxylic acid'  L-peptide  26  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OIC
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
 OIC  N    N  NH1    0  -0.591  -0.0160  4.8721  3.3884
 OIC  CA   C  CH1    0  -0.256  -0.0723  4.6737  4.8420
 OIC  C    C  C      0   0.420  -1.2140  3.6970  5.2450
 OIC  O    O  O      0  -0.602  -2.0495  4.0824  6.0885
 OIC  OXT  O  OC    -1  -0.616  -1.1709  2.5730  4.7072
 OIC  CB   C  CH2    0  -0.434  -0.1485  6.0832  5.4419
 OIC  CG   C  CH1    0  -0.228  -0.8142  6.9549  4.3623
 OIC  CD   C  CH1    0  -0.090  -0.8346  6.0481  3.0938
 OIC  C4   C  CH2    0  -0.443  -2.2027  7.4739  4.7305
 OIC  C5   C  CH2    0  -0.438  -2.9068  8.0197  3.4938
 OIC  C6   C  CH2    0  -0.433  -3.0989  6.9264  2.4210
 OIC  C7   C  CH2    0  -0.442  -2.2602  5.6775  2.7003
 OIC  H    H  HNH1   0   0.335   0.9412  5.0940  3.1450
 OIC  HA   H  HCH1   0   0.221   0.8560  4.1780  5.1469
 OIC  HB2  H  HCH2   0   0.219  -0.6920  6.1041  6.3860
 OIC  HB3  H  HCH2   0   0.211   0.8617  6.4476  5.6439
 OIC  HG   H  HCH1   0   0.214  -0.1857  7.8260  4.1541
 OIC  HD   H  HCH1   0   0.216  -0.3888  6.5754  2.2442
 OIC  H41  H  HCH2   0   0.212  -2.7947  6.6734  5.1827
 OIC  H42  H  HCH2   0   0.220  -2.1133  8.2531  5.4921
 OIC  H51  H  HCH2   0   0.222  -3.8691  8.4596  3.7641
 OIC  H52  H  HCH2   0   0.210  -2.3056  8.8396  3.0900
 OIC  H61  H  HCH2   0   0.221  -4.1515  6.6411  2.3581
 OIC  H62  H  HCH2   0   0.214  -2.8363  7.3252  1.4378
 OIC  H71  H  HCH2   0   0.220  -2.2430  5.0346  1.8170
 OIC  H72  H  HCH2   0   0.218  -2.7261  5.0928  3.4974

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
 OIC  N   CA   single  1.458  0.019  1.458
 OIC  N   CD   single  1.473  0.014  1.473
 OIC  N   H    single  0.860  0.020  0.860
 OIC  CA  C    single  1.525  0.021  1.525
 OIC  CA  CB   single  1.521  0.033  1.521
 OIC  CA  HA   single  0.970  0.020  0.970
 OIC  C   O    deloc   1.231  0.020  1.231
 OIC  C   OXT  deloc   1.247  0.020  1.247
 OIC  CB  CG   single  1.539  0.020  1.539
 OIC  CB  HB2  single  0.970  0.020  1.090
 OIC  CB  HB3  single  0.970  0.020  1.090
 OIC  CG  CD   single  1.559  0.020  1.559
 OIC  CG  C4   single  1.527  0.020  1.527
 OIC  CG  HG   single  0.970  0.020  1.090
 OIC  CD  C7   single  1.525  0.020  1.525
 OIC  CD  HD   single  0.970  0.020  1.090
 OIC  C4  C5   single  1.524  0.020  1.524
 OIC  C4  H41  single  0.970  0.020  1.090
 OIC  C4  H42  single  0.970  0.020  1.090
 OIC  C5  C6   single  1.544  0.020  1.544
 OIC  C5  H51  single  0.970  0.020  1.090
 OIC  C5  H52  single  0.970  0.020  1.090
 OIC  C6  C7   single  1.530  0.020  1.530
 OIC  C6  H61  single  0.970  0.020  1.090
 OIC  C6  H62  single  0.970  0.020  1.090
 OIC  C7  H71  single  0.970  0.020  1.090
 OIC  C7  H72  single  0.970  0.020  1.090

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
 OIC  H    N   CD   107.73  3.000
 OIC  H    N   CA   114.00  3.000
 OIC  CD   N   CA   106.65  3.000
 OIC  HA   CA  CB   109.00  3.000
 OIC  HA   CA  C    110.00  3.000
 OIC  CB   CA  C    110.50  1.500
 OIC  HA   CA  N    110.00  3.000
 OIC  CB   CA  N    110.40  1.500
 OIC  C    CA  N    111.00  2.800
 OIC  OXT  C   O    126.36  3.000
 OIC  OXT  C   CA   120.80  1.700
 OIC  O    C   CA   120.80  1.700
 OIC  HB3  CB  HB2  107.13  3.000
 OIC  HB3  CB  CG   109.92  3.000
 OIC  HB2  CB  CG   112.41  3.000
 OIC  HB3  CB  CA   109.44  3.000
 OIC  HB2  CB  CA   112.41  3.000
 OIC  CG   CB  CA   105.52  3.000
 OIC  HG   CG  C4   107.31  3.000
 OIC  HG   CG  CD   108.40  3.000
 OIC  C4   CG  CD   112.45  3.000
 OIC  HG   CG  CB   109.63  3.000
 OIC  C4   CG  CB   114.62  3.000
 OIC  CD   CG  CB   104.30  3.000
 OIC  HD   CD  C7   107.31  3.000
 OIC  HD   CD  CG   110.24  3.000
 OIC  C7   CD  CG   111.32  3.000
 OIC  HD   CD  N    108.40  3.000
 OIC  C7   CD  N    112.32  3.000
 OIC  CG   CD  N    103.20  1.500
 OIC  H42  C4  H41  106.14  3.000
 OIC  H42  C4  C5   110.35  3.000
 OIC  H41  C4  C5   110.34  3.000
 OIC  H42  C4  CG   109.62  3.000
 OIC  H41  C4  CG   110.06  3.000
 OIC  C5   C4  CG   110.24  3.000
 OIC  H52  C5  H51  105.89  3.000
 OIC  H52  C5  C6   110.04  3.000
 OIC  H51  C5  C6   110.35  3.000
 OIC  H52  C5  C4   108.30  3.000
 OIC  H51  C5  C4   110.52  3.000
 OIC  C6   C5  C4   111.57  3.000
 OIC  H62  C6  H61  105.96  3.000
 OIC  H62  C6  C7   109.29  3.000
 OIC  H61  C6  C7   109.00  3.000
 OIC  H62  C6  C5   109.68  3.000
 OIC  H61  C6  C5   110.17  3.000
 OIC  C7   C6  C5   112.52  3.000
 OIC  H72  C7  H71  106.35  3.000
 OIC  H72  C7  C6   109.64  3.000
 OIC  H71  C7  C6   109.95  3.000
 OIC  H72  C7  CD   109.91  3.000
 OIC  H71  C7  CD   109.69  3.000
 OIC  C6   C7  CD   111.17  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
 OIC  Var_01  C6  C5  C4  CG   61.05  30.0  1
 OIC  Var_02  C5  C6  C7  CD  -45.27  30.0  1
 OIC  Var_03  C7  C6  C5  C4  -13.73  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
 OIC  chir_01  CA  N   C   CB  positiv
 OIC  chir_02  CG  C4  CD  CB  positiv
 OIC  chir_03  CD  N   CG  C7  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
 OIC  plan-1  CA   0.020
 OIC  plan-1  C    0.020
 OIC  plan-1  O    0.020
 OIC  plan-1  OXT  0.020

