# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 02:25:04 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N~5~-(N-octylcarbamimidoyl)-L-ornithine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCNC(=N)NCCC[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
 C1J  C1J  N~5~-(N-octylcarbamimidoyl)-L-ornithine  ligand  49  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C1J
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
 C1J  N    N  NH2    0  -0.786  -6.1983   2.1525  -0.0424
 C1J  CA   C  CH1    0  -0.211  -6.3756   0.7548  -0.4069
 C1J  C    C  C      0   0.383  -7.7418   0.1344  -0.0205
 C1J  O    O  O      0  -0.608  -8.4565   0.7642   0.7843
 C1J  CB   C  CH2    0  -0.422  -5.2520  -0.0906   0.1981
 C1J  CG   C  CH2    0  -0.442  -3.8575   0.3452  -0.2292
 C1J  CD   C  CH2    0  -0.272  -2.7822  -0.5615   0.3469
 C1J  NE   N  NH1    0  -0.671  -1.4662  -0.1152  -0.0567
 C1J  CZ   C  C      0   0.609  -0.3417  -0.8456   0.2556
 C1J  NH1  N  N      0  -0.733  -0.3094  -2.0386   0.7249
 C1J  NH2  N  NH1    0  -0.669   0.8246  -0.1644   0.0037
 C1J  C01  C  CH2    0  -0.450   3.2475   0.1402  -0.0118
 C1J  C02  C  CH2    0  -0.234   2.0959  -0.8515   0.0399
 C1J  C03  C  CH2    0  -0.418   4.6028  -0.5549  -0.0223
 C1J  C04  C  CH2    0  -0.412   5.7743   0.4189  -0.0452
 C1J  C05  C  CH2    0  -0.412   7.1294  -0.2770  -0.0741
 C1J  C06  C  CH2    0  -0.406   8.3044   0.6926  -0.0893
 C1J  C07  C  CH2    0  -0.419   9.6600  -0.0031  -0.1226
 C1J  C08  C  CH3    0  -0.663  10.8257   0.9762  -0.1357
 C1J  H1   H  HNH2   0   0.334  -6.8976   2.7041  -0.5250
 C1J  H2   H  HNH2   0   0.322  -6.4384   2.2518   0.9380
 C1J  H4   H  HCH1   0   0.207  -6.2815   0.6866  -1.4977
 C1J  H6   H  HCH2   0   0.208  -5.3252  -0.0555   1.2923
 C1J  H7   H  HCH2   0   0.220  -5.4104  -1.1334  -0.0862
 C1J  H8   H  HCH2   0   0.217  -3.7864   0.3359  -1.3217
 C1J  H9   H  HCH2   0   0.225  -3.6848   1.3769   0.0869
 C1J  H10  H  HCH2   0   0.215  -2.8814  -0.6035   1.4405
 C1J  H11  H  HCH2   0   0.226  -2.9413  -1.5785  -0.0219
 C1J  H12  H  HNH1   0   0.376  -1.3440   0.8865  -0.0266
 C1J  H13  H  H      0   0.329  -1.2369  -2.3757   0.9496
 C1J  H14  H  HNH1   0   0.372   0.7563   0.5450  -0.7107
 C1J  H15  H  HCH2   0   0.216   3.1572   0.7664  -0.9068
 C1J  H16  H  HCH2   0   0.220   3.1812   0.8160   0.8466
 C1J  H17  H  HCH2   0   0.226   2.1496  -1.4296   0.9628
 C1J  H18  H  HCH2   0   0.204   2.1917  -1.5729  -0.7827
 C1J  H19  H  HCH2   0   0.211   4.6880  -1.2027   0.8572
 C1J  H20  H  HCH2   0   0.212   4.6660  -1.2169  -0.8928
 C1J  H21  H  HCH2   0   0.208   5.6842   1.0753  -0.9180
 C1J  H22  H  HCH2   0   0.208   5.7189   1.0732   0.8319
 C1J  H23  H  HCH2   0   0.207   7.2167  -0.9387   0.7950
 C1J  H24  H  HCH2   0   0.207   7.1848  -0.9272  -0.9545
 C1J  H25  H  HCH2   0   0.206   8.2166   1.3564  -0.9571
 C1J  H26  H  HCH2   0   0.206   8.2515   1.3414   0.7925
 C1J  H27  H  HCH2   0   0.210   9.7466  -0.6666   0.7437
 C1J  H28  H  HCH2   0   0.210   9.7131  -0.6496  -1.0043
 C1J  H29  H  HCH3   0   0.225  11.7860   0.4598  -0.1569
 C1J  H30  H  HCH3   0   0.216  10.7814   1.6278  -1.0103
 C1J  H31  H  HCH3   0   0.216  10.8129   1.6138   0.7503
 C1J  O1   O  OC    -1  -0.625  -8.0062  -0.9708  -0.5398

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
 C1J  NH1  CZ   double  1.282  0.020  1.282
 C1J  CZ   NH2  single  1.374  0.020  1.374
 C1J  CZ   NE   single  1.377  0.020  1.377
 C1J  NH2  C02  single  1.446  0.020  1.446
 C1J  O    C    deloc   1.247  0.020  1.247
 C1J  CD   NE   single  1.447  0.020  1.447
 C1J  CD   CG   single  1.520  0.020  1.520
 C1J  CB   CG   single  1.522  0.020  1.522
 C1J  CB   CA   single  1.531  0.020  1.531
 C1J  C02  C01  single  1.521  0.020  1.521
 C1J  C    CA   single  1.549  0.020  1.549
 C1J  CA   N    single  1.455  0.020  1.455
 C1J  C03  C01  single  1.523  0.020  1.523
 C1J  C03  C04  single  1.523  0.020  1.523
 C1J  C04  C05  single  1.524  0.020  1.524
 C1J  C05  C06  single  1.523  0.020  1.523
 C1J  C06  C07  single  1.524  0.020  1.524
 C1J  C07  C08  single  1.522  0.020  1.522
 C1J  N    H1   single  0.890  0.020  1.040
 C1J  N    H2   single  0.890  0.020  1.040
 C1J  CA   H4   single  0.970  0.020  1.090
 C1J  CB   H6   single  0.970  0.020  1.090
 C1J  CB   H7   single  0.970  0.020  1.090
 C1J  CG   H8   single  0.970  0.020  1.090
 C1J  CG   H9   single  0.970  0.020  1.090
 C1J  CD   H10  single  0.970  0.020  1.090
 C1J  CD   H11  single  0.970  0.020  1.090
 C1J  NE   H12  single  0.890  0.020  1.040
 C1J  NH1  H13  single  0.890  0.020  1.040
 C1J  NH2  H14  single  0.890  0.020  1.040
 C1J  C01  H15  single  0.970  0.020  1.090
 C1J  C01  H16  single  0.970  0.020  1.090
 C1J  C02  H17  single  0.970  0.020  1.090
 C1J  C02  H18  single  0.970  0.020  1.090
 C1J  C03  H19  single  0.970  0.020  1.090
 C1J  C03  H20  single  0.970  0.020  1.090
 C1J  C04  H21  single  0.970  0.020  1.090
 C1J  C04  H22  single  0.970  0.020  1.090
 C1J  C05  H23  single  0.970  0.020  1.090
 C1J  C05  H24  single  0.970  0.020  1.090
 C1J  C06  H25  single  0.970  0.020  1.090
 C1J  C06  H26  single  0.970  0.020  1.090
 C1J  C07  H27  single  0.970  0.020  1.090
 C1J  C07  H28  single  0.970  0.020  1.090
 C1J  C08  H29  single  0.970  0.020  1.090
 C1J  C08  H30  single  0.970  0.020  1.090
 C1J  C08  H31  single  0.970  0.020  1.090
 C1J  C    O1   deloc   1.249  0.020  1.249

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
 C1J  H2   N    H1   104.11  3.000
 C1J  H2   N    CA   107.90  3.000
 C1J  H1   N    CA   108.63  3.000
 C1J  H4   CA   CB   107.20  3.000
 C1J  H4   CA   C    107.38  3.000
 C1J  CB   CA   C    109.12  3.000
 C1J  H4   CA   N    107.35  3.000
 C1J  C    CA   N    115.44  3.000
 C1J  CB   CA   N    110.00  3.000
 C1J  O1   C    O    126.42  3.000
 C1J  O1   C    CA   115.92  3.000
 C1J  O    C    CA   117.65  3.000
 C1J  H7   CB   H6   106.28  3.000
 C1J  H7   CB   CG   109.46  3.000
 C1J  H6   CB   CG   109.38  3.000
 C1J  H7   CB   CA   108.54  3.000
 C1J  H6   CB   CA   109.11  3.000
 C1J  CG   CB   CA   113.79  3.000
 C1J  H9   CG   H8   106.64  3.000
 C1J  H9   CG   CD   109.98  3.000
 C1J  H8   CG   CD   109.09  3.000
 C1J  H9   CG   CB   109.51  3.000
 C1J  H8   CG   CB   109.71  3.000
 C1J  CD   CG   CB   111.77  3.000
 C1J  H11  CD   H10  106.68  3.000
 C1J  H11  CD   NE   108.97  3.000
 C1J  H10  CD   NE   111.81  3.000
 C1J  H11  CD   CG   108.91  3.000
 C1J  H10  CD   CG   109.64  3.000
 C1J  NE   CD   CG   110.71  3.000
 C1J  H12  NE   CZ   114.89  3.000
 C1J  H12  NE   CD   114.06  3.000
 C1J  CZ   NE   CD   121.06  3.000
 C1J  NH2  CZ   NH1  120.46  3.000
 C1J  NH2  CZ   NE   112.88  3.000
 C1J  NH1  CZ   NE   126.66  3.000
 C1J  H13  NH1  CZ   111.59  3.000
 C1J  H14  NH2  C02  114.29  3.000
 C1J  H14  NH2  CZ   114.89  3.000
 C1J  C02  NH2  CZ   120.42  3.000
 C1J  H16  C01  H15  106.42  3.000
 C1J  H16  C01  C03  109.94  3.000
 C1J  H15  C01  C03  109.17  3.000
 C1J  H16  C01  C02  109.28  3.000
 C1J  H15  C01  C02  109.75  3.000
 C1J  C03  C01  C02  112.11  3.000
 C1J  H18  C02  H17  106.35  3.000
 C1J  H18  C02  C01  109.68  3.000
 C1J  H17  C02  C01  109.72  3.000
 C1J  H18  C02  NH2  111.72  3.000
 C1J  H17  C02  NH2  108.45  3.000
 C1J  C01  C02  NH2  110.80  3.000
 C1J  H20  C03  H19  106.03  3.000
 C1J  H20  C03  C04  109.27  3.000
 C1J  H19  C03  C04  109.28  3.000
 C1J  H20  C03  C01  109.42  3.000
 C1J  H19  C03  C01  109.48  3.000
 C1J  C04  C03  C01  113.12  3.000
 C1J  H22  C04  H21  106.01  3.000
 C1J  H22  C04  C05  109.44  3.000
 C1J  H21  C04  C05  109.36  3.000
 C1J  H22  C04  C03  109.32  3.000
 C1J  H21  C04  C03  109.36  3.000
 C1J  C05  C04  C03  113.10  3.000
 C1J  H24  C05  H23  105.95  3.000
 C1J  H24  C05  C06  109.31  3.000
 C1J  H23  C05  C06  109.32  3.000
 C1J  H24  C05  C04  109.34  3.000
 C1J  H23  C05  C04  109.36  3.000
 C1J  C06  C05  C04  113.30  3.000
 C1J  H26  C06  H25  105.94  3.000
 C1J  H26  C06  C07  109.31  3.000
 C1J  H25  C06  C07  109.29  3.000
 C1J  H26  C06  C05  109.36  3.000
 C1J  H25  C06  C05  109.36  3.000
 C1J  C07  C06  C05  113.31  3.000
 C1J  H28  C07  H27  106.00  3.000
 C1J  H28  C07  C08  109.62  3.000
 C1J  H27  C07  C08  109.64  3.000
 C1J  H28  C07  C06  109.29  3.000
 C1J  H27  C07  C06  109.26  3.000
 C1J  C08  C07  C06  112.80  3.000
 C1J  H31  C08  H30  107.53  3.000
 C1J  H31  C08  H29  107.62  3.000
 C1J  H30  C08  H29  107.62  3.000
 C1J  H31  C08  C07  111.08  3.000
 C1J  H30  C08  C07  111.09  3.000
 C1J  H29  C08  C07  111.70  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
 C1J  CONST_01  NH1  CZ   NE   CD      0.00   0.0  0
 C1J  CONST_02  NH2  CZ   NE   CD    180.00   0.0  0
 C1J  CONST_03  C02  NH2  CZ   NE    180.00   0.0  0
 C1J  CONST_04  C02  NH2  CZ   NH1     0.00   0.0  0
 C1J  CONST_05  H13  NH1  CZ   NE      0.00   0.0  0
 C1J  Var_01    CD   CG   CB   CA   -177.45  30.0  3
 C1J  Var_02    NE   CD   CG   CB   -179.14  30.0  1
 C1J  Var_03    CZ   NE   CD   CG   -174.66  30.0  3
 C1J  Var_04    C01  C02  NH2  CZ   -169.49  30.0  3
 C1J  Var_05    C03  C01  C02  NH2  -178.09  30.0  3
 C1J  Var_06    C05  C04  C03  C01  -179.24  30.0  3
 C1J  Var_07    C04  C03  C01  C02  -178.82  30.0  1
 C1J  Var_08    C06  C05  C04  C03  -179.68  30.0  3
 C1J  Var_09    C07  C06  C05  C04  -179.82  30.0  3
 C1J  Var_10    C08  C07  C06  C05  -179.93  30.0  3
 C1J  Var_11    H29  C08  C07  C06   179.86  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
 C1J  chir_01  CA  CB  C  N  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
 C1J  plan-1  CD   0.020
 C1J  plan-1  NE   0.020
 C1J  plan-1  CZ   0.020
 C1J  plan-1  NH1  0.020
 C1J  plan-1  NH2  0.020
 C1J  plan-1  C02  0.020
 C1J  plan-1  H12  0.020
 C1J  plan-1  H13  0.020
 C1J  plan-1  H14  0.020
 C1J  plan-2  CA   0.020
 C1J  plan-2  C    0.020
 C1J  plan-2  O    0.020
 C1J  plan-2  O1   0.020

