# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:36:26 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: (2~{S},4~{S})-2-azanyl-6-[[(3~{S})-3,6-bis(azanyl)hexanoyl]amino]-4-oxidanyl-hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCC[C@H](N)CC(=O)NCC[C@H](O)C[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
 KEO  KEO  '(2~{S},4~{S})-2-azanyl-6-[[(3~{S})-3,6-bis(azanyl)hexanoyl]amino]-4-oxidanyl-hexanoic acid'  L-peptide  45  20  .  2019-03-22  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_KEO
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
 KEO  CA   C  CH1    0  -0.223  176.9808  201.8905  198.2431
 KEO  N    N  NH2    0  -0.802  177.1275  201.5691  199.6546
 KEO  C    C  C      0   0.410  176.4286  200.6656  197.4580
 KEO  O    O  O      0  -0.607  176.5013  200.7247  196.2137
 KEO  CB   C  CH2    0  -0.416  178.2941  202.3975  197.6494
 KEO  CG   C  CH1    0   0.053  178.6788  203.8261  198.0083
 KEO  CD   C  CH2    0  -0.463  179.8827  204.2695  197.1757
 KEO  CE   C  CH2    0  -0.313  180.3962  205.6730  197.4702
 KEO  C05  C  C      0   0.510  178.9816  207.7265  197.9773
 KEO  C06  C  CH2    0  -0.585  179.6484  207.9757  199.3099
 KEO  C07  C  CH1    0  -0.103  180.7957  209.0112  199.2373
 KEO  C08  C  CH2    0  -0.426  180.3432  210.4099  198.8170
 KEO  C09  C  CH2    0  -0.447  179.2285  211.0355  199.6476
 KEO  C10  C  CH2    0  -0.273  179.5698  211.1909  201.1227
 KEO  NZ   N  NH1    0  -0.609  179.3817  206.6786  197.2274
 KEO  N02  N  NH2    0  -0.789  181.9123  208.6186  198.3917
 KEO  N03  N  NH2    0  -0.798  178.5024  211.8878  201.8269
 KEO  O01  O  OH1    0  -0.675  178.9540  203.9158  199.3976
 KEO  O02  O  O      0  -0.498  178.1043  208.4804  197.5673
 KEO  OXT  O  OC    -1  -0.602  175.9149  199.7473  198.1267
 KEO  H1   H  HCH1   0   0.181  176.2304  202.6867  198.0719
 KEO  H2   H  HNH2   0   0.328  177.2366  202.4200  200.1882
 KEO  H3   H  HNH2   0   0.324  176.2808  201.1176  199.9720
 KEO  H5   H  HCH2   0   0.203  179.1066  201.7159  197.9276
 KEO  H6   H  HCH2   0   0.222  178.2103  202.3555  196.5628
 KEO  H7   H  HCH1   0   0.196  177.8253  204.4720  197.7562
 KEO  H8   H  HCH2   0   0.233  180.7109  203.5711  197.3311
 KEO  H9   H  HCH2   0   0.228  179.6182  204.1982  196.1160
 KEO  H10  H  HCH2   0   0.250  181.2715  205.8697  196.8451
 KEO  H11  H  HCH2   0   0.244  180.7402  205.7367  198.5000
 KEO  H12  H  HCH2   0   0.265  178.8768  208.3347  199.9930
 KEO  H13  H  HCH2   0   0.259  180.0459  207.0622  199.7547
 KEO  H14  H  HCH1   0   0.237  181.1892  209.0751  200.2565
 KEO  H15  H  HCH2   0   0.222  181.2252  211.0562  198.8576
 KEO  H16  H  HCH2   0   0.222  180.0348  210.3895  197.7676
 KEO  H17  H  HCH2   0   0.222  179.0150  212.0263  199.2325
 KEO  H18  H  HCH2   0   0.218  178.3045  210.4618  199.5455
 KEO  H19  H  HCH2   0   0.213  179.6845  210.2056  201.5830
 KEO  H20  H  HCH2   0   0.186  180.5501  211.6836  201.2096
 KEO  H21  H  HNH1   0   0.383  178.9126  206.6104  196.3339
 KEO  H22  H  HNH2   0   0.349  182.2693  207.7129  198.6697
 KEO  H23  H  HNH2   0   0.342  181.6135  208.5245  197.4278
 KEO  H25  H  HNH2   0   0.343  178.7345  211.9577  202.8095
 KEO  H26  H  HNH2   0   0.335  178.4503  212.8423  201.4917
 KEO  H28  H  HOH1   0   0.450  178.8032  204.8200  199.6865

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
 KEO  O    C    deloc   1.231  0.020  1.231
 KEO  C    CA   single  1.525  0.021  1.525
 KEO  O02  C05  double  1.227  0.020  1.227
 KEO  N02  C07  single  1.455  0.020  1.455
 KEO  C05  NZ   single  1.349  0.020  1.349
 KEO  C05  C06  single  1.511  0.020  1.511
 KEO  NZ   CE   single  1.449  0.020  1.449
 KEO  CB   CA   single  1.530  0.020  1.530
 KEO  CB   CG   single  1.522  0.020  1.522
 KEO  CA   N    single  1.458  0.019  1.458
 KEO  CG   CD   single  1.529  0.020  1.529
 KEO  CG   O01  single  1.419  0.020  1.419
 KEO  C08  C07  single  1.529  0.020  1.529
 KEO  C08  C09  single  1.524  0.020  1.524
 KEO  C07  C06  single  1.547  0.020  1.547
 KEO  CD   CE   single  1.523  0.020  1.523
 KEO  C09  C10  single  1.522  0.020  1.522
 KEO  C10  N03  single  1.456  0.020  1.456
 KEO  C    OXT  deloc   1.247  0.020  1.247
 KEO  CA   H1   single  0.970  0.020  1.090
 KEO  N    H2   single  0.890  0.020  1.040
 KEO  N    H3   single  0.890  0.020  1.040
 KEO  CB   H5   single  0.970  0.020  1.090
 KEO  CB   H6   single  0.970  0.020  1.090
 KEO  CG   H7   single  0.970  0.020  1.090
 KEO  CD   H8   single  0.970  0.020  1.090
 KEO  CD   H9   single  0.970  0.020  1.090
 KEO  CE   H10  single  0.970  0.020  1.090
 KEO  CE   H11  single  0.970  0.020  1.090
 KEO  C06  H12  single  0.970  0.020  1.090
 KEO  C06  H13  single  0.970  0.020  1.090
 KEO  C07  H14  single  0.970  0.020  1.090
 KEO  C08  H15  single  0.970  0.020  1.090
 KEO  C08  H16  single  0.970  0.020  1.090
 KEO  C09  H17  single  0.970  0.020  1.090
 KEO  C09  H18  single  0.970  0.020  1.090
 KEO  C10  H19  single  0.970  0.020  1.090
 KEO  C10  H20  single  0.970  0.020  1.090
 KEO  NZ   H21  single  0.860  0.020  1.020
 KEO  N02  H22  single  0.890  0.020  1.040
 KEO  N02  H23  single  0.890  0.020  1.040
 KEO  N03  H25  single  0.890  0.020  1.040
 KEO  N03  H26  single  0.890  0.020  1.040
 KEO  O01  H28  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
 KEO  H1   CA   CB   106.49  3.000
 KEO  H1   CA   C    104.33  3.000
 KEO  CB   CA   C    110.10  1.900
 KEO  H1   CA   N    112.15  3.000
 KEO  CB   CA   N    110.50  1.700
 KEO  C    CA   N    111.00  2.800
 KEO  H3   N    H2   107.51  3.000
 KEO  H3   N    CA   108.59  3.000
 KEO  H2   N    CA   109.71  3.000
 KEO  OXT  C    O    126.42  3.000
 KEO  OXT  C    CA   117.09  3.000
 KEO  O    C    CA   120.80  1.700
 KEO  H6   CB   H5   106.60  3.000
 KEO  H6   CB   CG   106.88  3.000
 KEO  H5   CB   CG   109.65  3.000
 KEO  H6   CB   CA   107.96  3.000
 KEO  H5   CB   CA   109.40  3.000
 KEO  CG   CB   CA   115.91  3.000
 KEO  H7   CG   O01  109.74  3.000
 KEO  H7   CG   CD   108.41  3.000
 KEO  O01  CG   CD   111.22  3.000
 KEO  H7   CG   CB   107.52  3.000
 KEO  O01  CG   CB   109.82  3.000
 KEO  CD   CG   CB   110.04  3.000
 KEO  H9   CD   H8   106.19  3.000
 KEO  H9   CD   CE   109.19  3.000
 KEO  H8   CD   CE   107.78  3.000
 KEO  H9   CD   CG   108.54  3.000
 KEO  H8   CD   CG   109.48  3.000
 KEO  CE   CD   CG   115.29  3.000
 KEO  H11  CE   H10  106.11  3.000
 KEO  H11  CE   NZ   109.85  3.000
 KEO  H10  CE   NZ   109.87  3.000
 KEO  H11  CE   CD   110.10  3.000
 KEO  H10  CE   CD   108.97  3.000
 KEO  NZ   CE   CD   111.78  3.000
 KEO  O02  C05  NZ   120.23  3.000
 KEO  NZ   C05  C06  119.17  3.000
 KEO  O02  C05  C06  120.59  3.000
 KEO  H13  C06  H12  106.13  3.000
 KEO  H13  C06  C07  108.02  3.000
 KEO  H12  C06  C07  109.48  3.000
 KEO  H13  C06  C05  112.48  3.000
 KEO  H12  C06  C05  107.12  3.000
 KEO  C07  C06  C05  113.35  3.000
 KEO  H14  C07  N02  106.33  3.000
 KEO  H14  C07  C08  108.00  3.000
 KEO  N02  C07  C08  108.32  3.000
 KEO  H14  C07  C06  105.19  3.000
 KEO  C08  C07  C06  113.93  3.000
 KEO  N02  C07  C06  114.57  3.000
 KEO  H16  C08  H15  105.89  3.000
 KEO  H16  C08  C09  108.92  3.000
 KEO  H15  C08  C09  109.07  3.000
 KEO  H16  C08  C07  109.27  3.000
 KEO  H15  C08  C07  106.95  3.000
 KEO  C09  C08  C07  116.24  3.000
 KEO  H18  C09  H17  105.96  3.000
 KEO  H18  C09  C10  109.51  3.000
 KEO  H17  C09  C10  108.59  3.000
 KEO  H18  C09  C08  110.61  3.000
 KEO  H17  C09  C08  107.89  3.000
 KEO  C10  C09  C08  113.95  3.000
 KEO  H20  C10  H19  106.07  3.000
 KEO  H20  C10  N03  113.60  3.000
 KEO  H19  C10  N03  107.73  3.000
 KEO  H20  C10  C09  108.78  3.000
 KEO  H19  C10  C09  109.85  3.000
 KEO  N03  C10  C09  110.67  3.000
 KEO  H21  NZ   C05  113.94  3.000
 KEO  H21  NZ   CE   115.21  3.000
 KEO  C05  NZ   CE   130.81  3.000
 KEO  H23  N02  H22  106.38  3.000
 KEO  H23  N02  C07  110.59  3.000
 KEO  H22  N02  C07  110.64  3.000
 KEO  H26  N03  H25  105.54  3.000
 KEO  H26  N03  C10  109.19  3.000
 KEO  H25  N03  C10  109.54  3.000
 KEO  H28  O01  CG   108.87  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
 KEO  CONST_01  O02  C05  NZ   CE   180.00   0.0  0
 KEO  CONST_02  C06  C05  NZ   CE     0.00   0.0  0
 KEO  CONST_03  H21  NZ   C05  C06  180.00   0.0  0
 KEO  Var_01    NZ   CE   CD   CG   -60.20  30.0  3
 KEO  Var_02    C05  NZ   CE   CD   133.14  30.0  1
 KEO  Var_03    C10  C09  C08  C07   59.27  30.0  3
 KEO  Var_04    O02  C05  C06  C07  -82.85  30.0  1
 KEO  Var_05    N03  C10  C09  C08  175.55  30.0  3
 KEO  Var_06    H25  N03  C10  C09  178.36  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
 KEO  chir_01  CA   C    CB   N    positiv
 KEO  chir_02  CG   O01  CD   CB   negativ
 KEO  chir_03  C07  N02  C08  C06  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
 KEO  plan-1  CE   0.020
 KEO  plan-1  C05  0.020
 KEO  plan-1  C06  0.020
 KEO  plan-1  NZ   0.020
 KEO  plan-1  O02  0.020
 KEO  plan-1  H21  0.020
 KEO  plan-2  CA   0.020
 KEO  plan-2  C    0.020
 KEO  plan-2  O    0.020
 KEO  plan-2  OXT  0.020

