# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 21:27:28 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2,9-diaminononanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCCC[C@H](N)C(O)=O
#
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
 1E3  1E3  '(2S)-2,9-diaminononanoic acid'  L-peptide  32  13  .  2016-04-22  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_1E3
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
 1E3  O    O  O      0  -0.605  -39.0067  23.4072  20.5085
 1E3  C    C  C      0   0.414  -38.3563  22.7696  21.3629
 1E3  CA   C  CH1    0  -0.220  -38.3866  23.3192  22.8141
 1E3  N    N  NH2    0  -0.816  -39.5567  24.1665  23.0099
 1E3  CB   C  CH2    0  -0.391  -38.3431  22.2114  23.8627
 1E3  CAJ  C  CH2    0  -0.427  -38.3198  22.7395  25.2927
 1E3  CAI  C  CH2    0  -0.422  -38.2013  21.6534  26.3596
 1E3  CAH  C  CH2    0  -0.420  -36.8519  20.9394  26.3650
 1E3  CAG  C  CH2    0  -0.424  -36.6195  20.0613  27.5904
 1E3  CAF  C  CH2    0  -0.428  -37.5755  18.8802  27.7054
 1E3  CAE  C  CH2    0  -0.267  -37.2614  17.9922  28.8990
 1E3  NAA  N  NH2    0  -0.798  -38.1948  16.8773  28.9836
 1E3  OXT  O  OC    -1  -0.604  -37.6529  21.7618  21.1564
 1E3  H1   H  HCH1   0   0.187  -37.4485  23.8956  22.9230
 1E3  H2   H  HNH2   0   0.329  -39.3645  24.8743  23.7061
 1E3  H3   H  HNH2   0   0.331  -39.7300  24.6513  22.1389
 1E3  H5   H  HCH2   0   0.190  -39.2155  21.5591  23.7377
 1E3  H6   H  HCH2   0   0.207  -37.4638  21.5917  23.6801
 1E3  H7   H  HCH2   0   0.197  -37.4859  23.4430  25.4084
 1E3  H8   H  HCH2   0   0.213  -39.2310  23.3153  25.4783
 1E3  H9   H  HCH2   0   0.210  -38.3586  22.1066  27.3445
 1E3  H10  H  HCH2   0   0.209  -39.0128  20.9304  26.2282
 1E3  H11  H  HCH2   0   0.211  -36.7410  20.3327  25.4610
 1E3  H12  H  HCH2   0   0.212  -36.0596  21.6940  26.3196
 1E3  H13  H  HCH2   0   0.215  -35.5924  19.6831  27.5674
 1E3  H14  H  HCH2   0   0.206  -36.6938  20.6775  28.4935
 1E3  H15  H  HCH2   0   0.214  -38.6059  19.2403  27.7924
 1E3  H16  H  HCH2   0   0.208  -37.5337  18.2797  26.7908
 1E3  H17  H  HCH2   0   0.208  -36.2526  17.5852  28.7845
 1E3  H18  H  HCH2   0   0.183  -37.2383  18.6142  29.8064
 1E3  H19  H  HNH2   0   0.342  -37.9539  16.2937  29.7746
 1E3  H20  H  HNH2   0   0.334  -39.1214  17.2345  29.1830

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
 1E3  C    O    deloc   1.231  0.020  1.231
 1E3  C    CA   single  1.525  0.021  1.525
 1E3  CA   N    single  1.458  0.019  1.458
 1E3  CA   CB   single  1.521  0.033  1.521
 1E3  CB   CAJ  single  1.525  0.020  1.525
 1E3  CAJ  CAI  single  1.527  0.020  1.527
 1E3  CAI  CAH  single  1.527  0.020  1.527
 1E3  CAH  CAG  single  1.525  0.020  1.525
 1E3  CAF  CAG  single  1.524  0.020  1.524
 1E3  CAF  CAE  single  1.520  0.020  1.520
 1E3  NAA  CAE  single  1.456  0.020  1.456
 1E3  C    OXT  deloc   1.246  0.020  1.246
 1E3  CA   H1   single  0.970  0.020  1.090
 1E3  N    H2   single  0.890  0.020  1.040
 1E3  N    H3   single  0.890  0.020  1.040
 1E3  CB   H5   single  0.970  0.020  1.090
 1E3  CB   H6   single  0.970  0.020  1.090
 1E3  CAJ  H7   single  0.970  0.020  1.090
 1E3  CAJ  H8   single  0.970  0.020  1.090
 1E3  CAI  H9   single  0.970  0.020  1.090
 1E3  CAI  H10  single  0.970  0.020  1.090
 1E3  CAH  H11  single  0.970  0.020  1.090
 1E3  CAH  H12  single  0.970  0.020  1.090
 1E3  CAG  H13  single  0.970  0.020  1.090
 1E3  CAG  H14  single  0.970  0.020  1.090
 1E3  CAF  H15  single  0.970  0.020  1.090
 1E3  CAF  H16  single  0.970  0.020  1.090
 1E3  CAE  H17  single  0.970  0.020  1.090
 1E3  CAE  H18  single  0.970  0.020  1.090
 1E3  NAA  H19  single  0.890  0.020  1.040
 1E3  NAA  H20  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
 1E3  OXT  C    CA   120.80  1.700
 1E3  OXT  C    O    126.40  3.000
 1E3  CA   C    O    120.80  1.700
 1E3  H1   CA   CB   106.64  3.000
 1E3  H1   CA   N    111.38  3.000
 1E3  CB   CA   N    110.40  1.500
 1E3  H1   CA   C    105.07  3.000
 1E3  CB   CA   C    110.50  1.500
 1E3  N    CA   C    111.00  2.800
 1E3  H3   N    H2   106.85  3.000
 1E3  H3   N    CA   107.48  3.000
 1E3  H2   N    CA   110.28  3.000
 1E3  H6   CB   H5   106.51  3.000
 1E3  H6   CB   CAJ  109.97  3.000
 1E3  H5   CB   CAJ  108.97  3.000
 1E3  H6   CB   CA   108.68  3.000
 1E3  H5   CB   CA   109.32  3.000
 1E3  CAJ  CB   CA   113.17  3.000
 1E3  H8   CAJ  H7   106.13  3.000
 1E3  H8   CAJ  CAI  108.70  3.000
 1E3  H7   CAJ  CAI  108.87  3.000
 1E3  H8   CAJ  CB   109.20  3.000
 1E3  H7   CAJ  CB   109.42  3.000
 1E3  CAI  CAJ  CB   114.21  3.000
 1E3  H10  CAI  H9   105.94  3.000
 1E3  H10  CAI  CAH  110.29  3.000
 1E3  H9   CAI  CAH  108.50  3.000
 1E3  H10  CAI  CAJ  109.17  3.000
 1E3  H9   CAI  CAJ  108.82  3.000
 1E3  CAH  CAI  CAJ  113.81  3.000
 1E3  H12  CAH  H11  105.93  3.000
 1E3  H12  CAH  CAG  108.66  3.000
 1E3  H11  CAH  CAG  109.21  3.000
 1E3  H12  CAH  CAI  108.48  3.000
 1E3  H11  CAH  CAI  110.24  3.000
 1E3  CAG  CAH  CAI  114.00  3.000
 1E3  H14  CAG  H13  105.97  3.000
 1E3  H14  CAG  CAF  109.34  3.000
 1E3  H13  CAG  CAF  108.81  3.000
 1E3  H14  CAG  CAH  109.15  3.000
 1E3  H13  CAG  CAH  108.96  3.000
 1E3  CAF  CAG  CAH  114.29  3.000
 1E3  H16  CAF  H15  106.42  3.000
 1E3  H16  CAF  CAE  109.12  3.000
 1E3  H15  CAF  CAE  108.91  3.000
 1E3  H16  CAF  CAG  109.76  3.000
 1E3  H15  CAF  CAG  109.96  3.000
 1E3  CAE  CAF  CAG  112.48  3.000
 1E3  H18  CAE  H17  106.10  3.000
 1E3  H18  CAE  NAA  113.47  3.000
 1E3  H17  CAE  NAA  108.20  3.000
 1E3  H18  CAE  CAF  108.76  3.000
 1E3  H17  CAE  CAF  109.01  3.000
 1E3  NAA  CAE  CAF  111.11  3.000
 1E3  H20  NAA  H19  105.49  3.000
 1E3  H20  NAA  CAE  109.13  3.000
 1E3  H19  NAA  CAE  109.53  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
 1E3  Var_01  CAI  CAJ  CB   CA   -176.92  30.0  3
 1E3  Var_02  CAH  CAI  CAJ  CB     68.13  30.0  3
 1E3  Var_03  CAG  CAH  CAI  CAJ   168.27  30.0  3
 1E3  Var_04  CAF  CAG  CAH  CAI    64.46  30.0  3
 1E3  Var_05  CAE  CAF  CAG  CAH   176.97  30.0  1
 1E3  Var_06  NAA  CAE  CAF  CAG   179.78  30.0  3
 1E3  Var_07  H19  NAA  CAE  CAF   178.97  30.0  3

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
 1E3  chir_01  CA  C  N  CB  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
 1E3  plan-1  O    0.020
 1E3  plan-1  C    0.020
 1E3  plan-1  CA   0.020
 1E3  plan-1  OXT  0.020

