# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 19:57:22 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(8-amino-8-oxooctyl)nonanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCC(=O)NCCCCCCCC(N)=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
 KJ1  KJ1  N-(8-amino-8-oxooctyl)nonanamide  ligand  55  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_KJ1
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
 KJ1  C13  C  CH2   0  -0.452    1.9389  -0.0649  -0.1448
 KJ1  C15  C  CH2   0  -0.413    4.4755  -0.2607  -0.1664
 KJ1  C17  C  CH2   0  -0.415    7.0132  -0.4296  -0.1539
 KJ1  C01  C  CH3   0  -0.662  -11.6958  -0.1291  -0.2278
 KJ1  C02  C  CH2   0  -0.419  -10.3814  -0.8695  -0.0229
 KJ1  C03  C  CH2   0  -0.406   -9.1703   0.0549  -0.0646
 KJ1  C04  C  CH2   0  -0.411   -7.8463  -0.6749   0.1234
 KJ1  C05  C  CH2   0  -0.412   -6.6395   0.2548   0.0898
 KJ1  C06  C  CH2   0  -0.415   -5.3140  -0.4736   0.2728
 KJ1  C07  C  CH2   0  -0.415   -4.1153   0.4665   0.2521
 KJ1  C08  C  CH2   0  -0.576   -2.7972  -0.2748   0.4384
 KJ1  C09  C  C     0   0.554   -1.5996   0.6518   0.4824
 KJ1  O10  O  O     0  -0.510   -1.6330   1.7253   1.0723
 KJ1  N11  N  NH1   0  -0.642   -0.5022   0.1957  -0.1426
 KJ1  C12  C  CH2   0  -0.248    0.7616   0.8979  -0.1966
 KJ1  C14  C  CH2   0  -0.419    3.2705   0.6692  -0.2332
 KJ1  C16  C  CH2   0  -0.414    5.8001   0.4884  -0.2339
 KJ1  C18  C  CH2   0  -0.573    8.3192   0.3522  -0.1952
 KJ1  C19  C  C     0   0.524    9.5518  -0.5244  -0.1305
 KJ1  N20  N  NH2   0  -0.805   10.5985   0.0138   0.5149
 KJ1  O21  O  O     0  -0.500    9.5951  -1.6322  -0.6486
 KJ1  H1   H  HCH2  0   0.226    1.8930  -0.6429   0.7833
 KJ1  H2   H  HCH2  0   0.223    1.8633  -0.7850  -0.9667
 KJ1  H3   H  HCH2  0   0.211    4.4343  -0.8433   0.7606
 KJ1  H4   H  HCH2  0   0.212    4.4225  -0.9866  -0.9848
 KJ1  H5   H  HCH2  0   0.221    6.9646  -1.0152   0.7696
 KJ1  H6   H  HCH3  0   0.215  -11.7160   0.3745  -1.1964
 KJ1  H7   H  HCH3  0   0.226  -12.5503  -0.8058  -0.1904
 KJ1  H8   H  HCH3  0   0.215  -11.8439   0.6327   0.5403
 KJ1  H9   H  HCH2  0   0.210  -10.4009  -1.3963   0.9365
 KJ1  H10  H  HCH2  0   0.210  -10.2726  -1.6417  -0.7905
 KJ1  H11  H  HCH2  0   0.205   -9.1574   0.5901  -1.0210
 KJ1  H12  H  HCH2  0   0.206   -9.2756   0.8228   0.7099
 KJ1  H13  H  HCH2  0   0.206   -7.8607  -1.2154   1.0767
 KJ1  H14  H  HCH2  0   0.207   -7.7383  -1.4375  -0.6558
 KJ1  H15  H  HCH2  0   0.208   -6.6271   0.7985  -0.8617
 KJ1  H16  H  HCH2  0   0.208   -6.7464   1.0147   0.8716
 KJ1  H17  H  HCH2  0   0.210   -5.3278  -1.0219   1.2215
 KJ1  H18  H  HCH2  0   0.211   -5.2020  -1.2283  -0.5130
 KJ1  H19  H  HCH2  0   0.221   -4.0984   1.0127  -0.6965
 KJ1  H20  H  HCH2  0   0.222   -4.2286   1.2155   1.0389
 KJ1  H21  H  HCH2  0   0.263   -2.8179  -0.8235   1.3866
 KJ1  H22  H  HCH2  0   0.245   -2.6762  -1.0272  -0.3451
 KJ1  H23  H  HNH1  0   0.395   -0.5729  -0.6650  -0.6613
 KJ1  H24  H  HCH2  0   0.238    0.8103   1.5871   0.6461
 KJ1  H25  H  HCH2  0   0.227    0.8203   1.5050  -1.1067
 KJ1  H26  H  HCH2  0   0.215    3.3077   1.2448  -1.1646
 KJ1  H27  H  HCH2  0   0.214    3.3356   1.4015   0.5789
 KJ1  H28  H  HCH2  0   0.212    5.8430   1.0684  -1.1628
 KJ1  H29  H  HCH2  0   0.267    8.3756   0.9230  -1.1293
 KJ1  H30  H  HCH2  0   0.247    8.3382   1.0924   0.6087
 KJ1  H31  H  HNH2  0   0.396   11.4776  -0.4750   0.5636
 KJ1  H32  H  HNH2  0   0.405   10.5483   0.9199   0.9466
 KJ1  H33  H  HCH2  0   0.223    6.9844  -1.1474  -0.9769
 KJ1  H34  H  HCH2  0   0.211    5.8426   1.2193   0.5811

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
 KJ1  C01  C02  single  1.522  0.020  1.522
 KJ1  C02  C03  single  1.524  0.020  1.524
 KJ1  C03  C04  single  1.523  0.020  1.523
 KJ1  C04  C05  single  1.524  0.020  1.524
 KJ1  C05  C06  single  1.523  0.020  1.523
 KJ1  C06  C07  single  1.523  0.020  1.523
 KJ1  C07  C08  single  1.524  0.020  1.524
 KJ1  C08  C09  single  1.515  0.020  1.515
 KJ1  C09  O10  double  1.225  0.020  1.225
 KJ1  C09  N11  single  1.343  0.020  1.343
 KJ1  N11  C12  single  1.447  0.020  1.447
 KJ1  C13  C12  single  1.522  0.020  1.522
 KJ1  C13  C14  single  1.523  0.020  1.523
 KJ1  N20  C19  single  1.342  0.020  1.342
 KJ1  C14  C15  single  1.524  0.020  1.524
 KJ1  C16  C15  single  1.523  0.020  1.523
 KJ1  C16  C17  single  1.523  0.020  1.523
 KJ1  C19  O21  double  1.224  0.020  1.224
 KJ1  C19  C18  single  1.514  0.020  1.514
 KJ1  C18  C17  single  1.523  0.020  1.523
 KJ1  C13  H1   single  0.970  0.020  1.090
 KJ1  C13  H2   single  0.970  0.020  1.090
 KJ1  C15  H3   single  0.970  0.020  1.090
 KJ1  C15  H4   single  0.970  0.020  1.090
 KJ1  C17  H5   single  0.970  0.020  1.090
 KJ1  C01  H6   single  0.970  0.020  1.090
 KJ1  C01  H7   single  0.970  0.020  1.090
 KJ1  C01  H8   single  0.970  0.020  1.090
 KJ1  C02  H9   single  0.970  0.020  1.090
 KJ1  C02  H10  single  0.970  0.020  1.090
 KJ1  C03  H11  single  0.970  0.020  1.090
 KJ1  C03  H12  single  0.970  0.020  1.090
 KJ1  C04  H13  single  0.970  0.020  1.090
 KJ1  C04  H14  single  0.970  0.020  1.090
 KJ1  C05  H15  single  0.970  0.020  1.090
 KJ1  C05  H16  single  0.970  0.020  1.090
 KJ1  C06  H17  single  0.970  0.020  1.090
 KJ1  C06  H18  single  0.970  0.020  1.090
 KJ1  C07  H19  single  0.970  0.020  1.090
 KJ1  C07  H20  single  0.970  0.020  1.090
 KJ1  C08  H21  single  0.970  0.020  1.090
 KJ1  C08  H22  single  0.970  0.020  1.090
 KJ1  N11  H23  single  0.860  0.020  1.020
 KJ1  C12  H24  single  0.970  0.020  1.090
 KJ1  C12  H25  single  0.970  0.020  1.090
 KJ1  C14  H26  single  0.970  0.020  1.090
 KJ1  C14  H27  single  0.970  0.020  1.090
 KJ1  C16  H28  single  0.970  0.020  1.090
 KJ1  C18  H29  single  0.970  0.020  1.090
 KJ1  C18  H30  single  0.970  0.020  1.090
 KJ1  N20  H31  single  0.860  0.020  1.020
 KJ1  N20  H32  single  0.860  0.020  1.020
 KJ1  C17  H33  single  0.970  0.020  1.090
 KJ1  C16  H34  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
 KJ1  H2   C13  H1   106.63  3.000
 KJ1  H2   C13  C14  109.49  3.000
 KJ1  H1   C13  C14  109.90  3.000
 KJ1  H2   C13  C12  109.70  3.000
 KJ1  H1   C13  C12  109.30  3.000
 KJ1  C14  C13  C12  111.68  3.000
 KJ1  H4   C15  H3   106.14  3.000
 KJ1  H4   C15  C16  109.57  3.000
 KJ1  H3   C15  C16  109.37  3.000
 KJ1  H4   C15  C14  109.48  3.000
 KJ1  H3   C15  C14  109.39  3.000
 KJ1  C16  C15  C14  112.68  3.000
 KJ1  H33  C17  H5   106.44  3.000
 KJ1  H33  C17  C18  109.85  3.000
 KJ1  H5   C17  C18  109.61  3.000
 KJ1  H33  C17  C16  109.60  3.000
 KJ1  H5   C17  C16  109.35  3.000
 KJ1  C18  C17  C16  111.84  3.000
 KJ1  H8   C01  H7   107.61  3.000
 KJ1  H8   C01  H6   107.45  3.000
 KJ1  H7   C01  H6   107.59  3.000
 KJ1  H8   C01  C02  111.20  3.000
 KJ1  H7   C01  C02  111.71  3.000
 KJ1  H6   C01  C02  111.08  3.000
 KJ1  H10  C02  H9   106.08  3.000
 KJ1  H10  C02  C03  109.26  3.000
 KJ1  H9   C02  C03  109.27  3.000
 KJ1  H10  C02  C01  109.55  3.000
 KJ1  H9   C02  C01  109.67  3.000
 KJ1  C03  C02  C01  112.79  3.000
 KJ1  H12  C03  H11  106.00  3.000
 KJ1  H12  C03  C04  109.39  3.000
 KJ1  H11  C03  C04  109.35  3.000
 KJ1  H12  C03  C02  109.23  3.000
 KJ1  H11  C03  C02  109.24  3.000
 KJ1  C04  C03  C02  113.37  3.000
 KJ1  H14  C04  H13  106.06  3.000
 KJ1  H14  C04  C05  109.32  3.000
 KJ1  H13  C04  C05  109.30  3.000
 KJ1  H14  C04  C03  109.35  3.000
 KJ1  H13  C04  C03  109.40  3.000
 KJ1  C05  C04  C03  113.16  3.000
 KJ1  H16  C05  H15  106.06  3.000
 KJ1  H16  C05  C06  109.32  3.000
 KJ1  H15  C05  C06  109.37  3.000
 KJ1  H16  C05  C04  109.27  3.000
 KJ1  H15  C05  C04  109.32  3.000
 KJ1  C06  C05  C04  113.25  3.000
 KJ1  H18  C06  H17  106.11  3.000
 KJ1  H18  C06  C07  109.57  3.000
 KJ1  H17  C06  C07  109.29  3.000
 KJ1  H18  C06  C05  109.41  3.000
 KJ1  H17  C06  C05  109.41  3.000
 KJ1  C07  C06  C05  112.83  3.000
 KJ1  H20  C07  H19  106.48  3.000
 KJ1  H20  C07  C08  109.59  3.000
 KJ1  H19  C07  C08  109.59  3.000
 KJ1  H20  C07  C06  109.38  3.000
 KJ1  H19  C07  C06  109.38  3.000
 KJ1  C08  C07  C06  112.26  3.000
 KJ1  H22  C08  H21  106.12  3.000
 KJ1  H22  C08  C09  110.75  3.000
 KJ1  H21  C08  C09  107.22  3.000
 KJ1  H22  C08  C07  110.06  3.000
 KJ1  H21  C08  C07  109.45  3.000
 KJ1  C09  C08  C07  112.95  3.000
 KJ1  N11  C09  O10  122.96  3.000
 KJ1  N11  C09  C08  115.14  3.000
 KJ1  O10  C09  C08  121.89  3.000
 KJ1  H23  N11  C12  117.18  3.000
 KJ1  H23  N11  C09  118.20  3.000
 KJ1  C12  N11  C09  124.50  3.000
 KJ1  H25  C12  H24  106.83  3.000
 KJ1  H25  C12  N11  110.29  3.000
 KJ1  H24  C12  N11  108.49  3.000
 KJ1  H25  C12  C13  109.72  3.000
 KJ1  H24  C12  C13  109.83  3.000
 KJ1  N11  C12  C13  111.56  3.000
 KJ1  H27  C14  H26  106.09  3.000
 KJ1  H27  C14  C15  109.18  3.000
 KJ1  H26  C14  C15  109.33  3.000
 KJ1  H27  C14  C13  109.34  3.000
 KJ1  H26  C14  C13  109.41  3.000
 KJ1  C15  C14  C13  113.25  3.000
 KJ1  H34  C16  H28  106.02  3.000
 KJ1  H34  C16  C17  109.39  3.000
 KJ1  H28  C16  C17  109.40  3.000
 KJ1  H34  C16  C15  109.20  3.000
 KJ1  H28  C16  C15  109.38  3.000
 KJ1  C17  C16  C15  113.19  3.000
 KJ1  H30  C18  H29  105.86  3.000
 KJ1  H30  C18  C19  110.27  3.000
 KJ1  H29  C18  C19  107.22  3.000
 KJ1  H30  C18  C17  110.04  3.000
 KJ1  H29  C18  C17  109.55  3.000
 KJ1  C19  C18  C17  113.57  3.000
 KJ1  O21  C19  N20  122.61  3.000
 KJ1  O21  C19  C18  122.33  3.000
 KJ1  N20  C19  C18  115.04  3.000
 KJ1  H32  N20  H31  117.42  3.000
 KJ1  H32  N20  C19  121.94  3.000
 KJ1  H31  N20  C19  120.62  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
 KJ1  CONST_01  C12  N11  C09  C08   180.00   0.0  0
 KJ1  CONST_02  C12  N11  C09  O10     0.00   0.0  0
 KJ1  CONST_03  H23  N11  C09  C08     0.00   0.0  0
 KJ1  CONST_04  H31  N20  C19  C18   180.00   0.0  0
 KJ1  CONST_05  H32  N20  C19  C18     0.00   0.0  0
 KJ1  Var_01    C09  N11  C12  C13   144.41  30.0  1
 KJ1  Var_02    C16  C15  C14  C13  -179.10  30.0  3
 KJ1  Var_03    C12  C13  C14  C15   179.25  30.0  1
 KJ1  Var_04    C18  C17  C16  C15  -178.83  30.0  3
 KJ1  Var_05    C14  C15  C16  C17   179.42  30.0  3
 KJ1  Var_06    N20  C19  C18  C17  -146.49  30.0  2
 KJ1  Var_07    C04  C03  C02  C01  -179.35  30.0  3
 KJ1  Var_08    C05  C04  C03  C02  -179.63  30.0  3
 KJ1  Var_09    C06  C05  C04  C03  -179.80  30.0  3
 KJ1  Var_10    C07  C06  C05  C04  -179.40  30.0  3
 KJ1  Var_11    C08  C07  C06  C05   179.91  30.0  3
 KJ1  Var_12    C09  C08  C07  C06  -177.43  30.0  3
 KJ1  Var_13    O10  C09  C08  C07    40.23  30.0  3
 KJ1  Var_14    C14  C13  C12  N11   178.71  30.0  1
 KJ1  Var_15    C19  C18  C17  C16  -179.49  30.0  1
 KJ1  Var_16    H6   C01  C02  C03    60.11  30.0  3

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
 KJ1  plan-1  C08  0.020
 KJ1  plan-1  C09  0.020
 KJ1  plan-1  O10  0.020
 KJ1  plan-1  N11  0.020
 KJ1  plan-1  C12  0.020
 KJ1  plan-1  H23  0.020
 KJ1  plan-2  C18  0.020
 KJ1  plan-2  C19  0.020
 KJ1  plan-2  N20  0.020
 KJ1  plan-2  O21  0.020
 KJ1  plan-2  H31  0.020
 KJ1  plan-2  H32  0.020

