# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:31:57 2022
#   Inital geometry file: a 97 line input string
#   Ligand name: 6-[(cyclohexylcarbamoyl)amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCNC(=O)NC1CCCCC1
#
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
 NC6  NC6  '6-[(cyclohexylcarbamoyl)amino]hexanoic acid'  ligand  41  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NC6
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
 NC6  C1    C  CH1    0  -0.047  -4.1298   0.1840   0.2175
 NC6  N2    N  NH1    0  -0.687  -2.7557   0.5797  -0.0155
 NC6  C3    C  C      0   0.731  -1.7037  -0.1909   0.3741
 NC6  N4    N  NH1    0  -0.688  -0.4857   0.2339  -0.0584
 NC6  C5    C  CH2    0  -0.235   0.7113  -0.5548   0.1379
 NC6  C6    C  CH2    0  -0.453   1.9594   0.2963  -0.0328
 NC6  C7    C  CH2    0  -0.415   3.2351  -0.5147   0.1528
 NC6  C8    C  CH2    0  -0.402   4.5005   0.3196  -0.0030
 NC6  C9    C  CH2    0  -0.581   5.7681  -0.4963   0.1883
 NC6  O10   O  O      0  -0.554  -1.8362  -1.1706   1.1034
 NC6  C11   C  C      0   0.410   7.0952   0.2732   0.0624
 NC6  O12   O  OC    -1  -0.635   8.1351  -0.4055   0.2049
 NC6  O13   O  O      0  -0.609   7.0417   1.4980  -0.1644
 NC6  C14   C  CH2    0  -0.440  -5.0220   1.4195   0.2865
 NC6  C15   C  CH2    0  -0.436  -6.4770   1.0390   0.5442
 NC6  C16   C  CH2    0  -0.430  -6.9925   0.0462  -0.4926
 NC6  C17   C  CH2    0  -0.438  -6.0949  -1.1840  -0.5706
 NC6  C18   C  CH2    0  -0.426  -4.6441  -0.7958  -0.8379
 NC6  H1    H  HCH1   0   0.228  -4.1611  -0.3129   1.1911
 NC6  HN2   H  HNH1   0   0.380  -2.6046   1.2816  -0.7240
 NC6  HN4   H  HNH1   0   0.383  -0.4511   0.9219  -0.7938
 NC6  H51   H  HCH2   0   0.213   0.7477  -1.4016  -0.5590
 NC6  H52   H  HCH2   0   0.230   0.6936  -0.9765   1.1431
 NC6  H61   H  HCH2   0   0.221   1.9363   1.1206   0.6868
 NC6  H62   H  HCH2   0   0.218   1.9620   0.7528  -1.0289
 NC6  H71   H  HCH2   0   0.208   3.2493  -1.3393  -0.5689
 NC6  H72   H  HCH2   0   0.208   3.2260  -0.9822   1.1439
 NC6  H81   H  HCH2   0   0.202   4.4793   1.1437   0.7162
 NC6  H82   H  HCH2   0   0.202   4.5052   0.7862  -0.9928
 NC6  H91   H  HCH2   0   0.216   5.7848  -1.3250  -0.5296
 NC6  H92   H  HCH2   0   0.216   5.7490  -0.9796   1.1728
 NC6  H141  H  HCH2   0   0.236  -4.6598   2.0921   1.0677
 NC6  H142  H  HCH2   0   0.213  -4.9535   1.9709  -0.6595
 NC6  H151  H  HCH2   0   0.213  -6.5642   0.5997   1.5437
 NC6  H152  H  HCH2   0   0.231  -7.0982   1.9377   0.5491
 NC6  H161  H  HCH2   0   0.228  -8.0181  -0.2469  -0.2558
 NC6  H162  H  HCH2   0   0.210  -7.0257   0.5327  -1.4736
 NC6  H171  H  HCH2   0   0.212  -6.1520  -1.7372   0.3736
 NC6  H172  H  HCH2   0   0.229  -6.4492  -1.8665  -1.3465
 NC6  H181  H  HCH2   0   0.208  -4.5628  -0.3296  -1.8266
 NC6  H182  H  HCH2   0   0.232  -4.0073  -1.6837  -0.8527

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
 NC6  C1   N2    single  1.449  0.020  1.449
 NC6  C1   C14   single  1.526  0.020  1.526
 NC6  C1   C18   single  1.529  0.020  1.529
 NC6  C1   H1    single  0.970  0.020  1.090
 NC6  N2   C3    single  1.361  0.020  1.361
 NC6  N2   HN2   single  0.860  0.020  1.020
 NC6  C3   N4    single  1.361  0.020  1.361
 NC6  C3   O10   double  1.228  0.020  1.228
 NC6  N4   C5    single  1.447  0.020  1.447
 NC6  N4   HN4   single  0.890  0.020  1.040
 NC6  C5   C6    single  1.520  0.020  1.520
 NC6  C5   H51   single  0.970  0.020  1.090
 NC6  C5   H52   single  0.970  0.020  1.090
 NC6  C6   C7    single  1.523  0.020  1.523
 NC6  C6   H61   single  0.970  0.020  1.090
 NC6  C6   H62   single  0.970  0.020  1.090
 NC6  C7   C8    single  1.524  0.020  1.524
 NC6  C7   H71   single  0.970  0.020  1.090
 NC6  C7   H72   single  0.970  0.020  1.090
 NC6  C8   C9    single  1.520  0.020  1.520
 NC6  C8   H81   single  0.970  0.020  1.090
 NC6  C8   H82   single  0.970  0.020  1.090
 NC6  C9   C11   single  1.539  0.020  1.539
 NC6  C9   H91   single  0.970  0.020  1.090
 NC6  C9   H92   single  0.970  0.020  1.090
 NC6  C11  O12   deloc   1.250  0.020  1.250
 NC6  C11  O13   deloc   1.247  0.020  1.247
 NC6  C14  C15   single  1.526  0.020  1.526
 NC6  C14  H141  single  0.970  0.020  1.090
 NC6  C14  H142  single  0.970  0.020  1.090
 NC6  C15  C16   single  1.525  0.020  1.525
 NC6  C15  H151  single  0.970  0.020  1.090
 NC6  C15  H152  single  0.970  0.020  1.090
 NC6  C16  C17   single  1.525  0.020  1.525
 NC6  C16  H161  single  0.970  0.020  1.090
 NC6  C16  H162  single  0.970  0.020  1.090
 NC6  C17  C18   single  1.525  0.020  1.525
 NC6  C17  H171  single  0.970  0.020  1.090
 NC6  C17  H172  single  0.970  0.020  1.090
 NC6  C18  H181  single  0.970  0.020  1.090
 NC6  C18  H182  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
 NC6  H1    C1   C18   108.28  3.000
 NC6  H1    C1   C14   108.12  3.000
 NC6  C18   C1   C14   110.70  3.000
 NC6  H1    C1   N2    107.13  3.000
 NC6  C18   C1   N2    112.52  3.000
 NC6  C14   C1   N2    109.92  3.000
 NC6  HN2   N2   C3    118.64  3.000
 NC6  HN2   N2   C1    116.43  3.000
 NC6  C3    N2   C1    122.16  3.000
 NC6  O10   C3   N4    122.29  3.000
 NC6  O10   C3   N2    122.56  3.000
 NC6  N4    C3   N2    115.10  3.000
 NC6  HN4   N4   C5    116.29  3.000
 NC6  HN4   N4   C3    118.42  3.000
 NC6  C5    N4   C3    121.83  3.000
 NC6  H52   C5   H51   106.72  3.000
 NC6  H52   C5   C6    109.47  3.000
 NC6  H51   C5   C6    109.48  3.000
 NC6  H52   C5   N4    108.82  3.000
 NC6  H51   C5   N4    111.22  3.000
 NC6  C6    C5   N4    111.03  3.000
 NC6  H62   C6   H61   106.50  3.000
 NC6  H62   C6   C7    109.30  3.000
 NC6  H61   C6   C7    109.79  3.000
 NC6  H62   C6   C5    109.71  3.000
 NC6  H61   C6   C5    109.30  3.000
 NC6  C7    C6   C5    112.08  3.000
 NC6  H72   C7   H71   105.95  3.000
 NC6  H72   C7   C8    109.44  3.000
 NC6  H71   C7   C8    109.51  3.000
 NC6  H72   C7   C6    109.29  3.000
 NC6  H71   C7   C6    109.35  3.000
 NC6  C8    C7   C6    113.06  3.000
 NC6  H82   C8   H81   105.87  3.000
 NC6  H82   C8   C9    109.83  3.000
 NC6  H81   C8   C9    109.75  3.000
 NC6  H82   C8   C7    109.24  3.000
 NC6  H81   C8   C7    109.22  3.000
 NC6  C9    C8   C7    112.70  3.000
 NC6  H92   C9   H91   104.77  3.000
 NC6  H92   C9   C11   107.98  3.000
 NC6  H91   C9   C11   108.13  3.000
 NC6  H92   C9   C8    109.57  3.000
 NC6  H91   C9   C8    109.64  3.000
 NC6  C11   C9   C8    116.14  3.000
 NC6  O13   C11  O12   126.15  3.000
 NC6  O13   C11  C9    117.97  3.000
 NC6  O12   C11  C9    115.88  3.000
 NC6  H142  C14  H141  106.64  3.000
 NC6  H142  C14  C15   109.30  3.000
 NC6  H141  C14  C15   110.42  3.000
 NC6  H142  C14  C1    109.36  3.000
 NC6  H141  C14  C1    109.70  3.000
 NC6  C15   C14  C1    111.31  3.000
 NC6  H152  C15  H151  106.29  3.000
 NC6  H152  C15  C16   110.26  3.000
 NC6  H151  C15  C16   109.41  3.000
 NC6  H152  C15  C14   109.75  3.000
 NC6  H151  C15  C14   109.27  3.000
 NC6  C16   C15  C14   111.70  3.000
 NC6  H162  C16  H161  106.54  3.000
 NC6  H162  C16  C17   109.29  3.000
 NC6  H161  C16  C17   110.32  3.000
 NC6  H162  C16  C15   109.26  3.000
 NC6  H161  C16  C15   110.16  3.000
 NC6  C17   C16  C15   111.16  3.000
 NC6  H172  C17  H171  106.24  3.000
 NC6  H172  C17  C18   110.06  3.000
 NC6  H171  C17  C18   109.21  3.000
 NC6  H172  C17  C16   110.45  3.000
 NC6  H171  C17  C16   109.43  3.000
 NC6  C18   C17  C16   111.31  3.000
 NC6  H182  C18  H181  106.87  3.000
 NC6  H182  C18  C17   110.47  3.000
 NC6  H181  C18  C17   109.68  3.000
 NC6  H182  C18  C1    109.51  3.000
 NC6  H181  C18  C1    108.97  3.000
 NC6  C17   C18  C1    111.22  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
 NC6  CONST_01  O10  C3   N2   C1      0.00   0.0  0
 NC6  CONST_02  N4   C3   N2   C1    180.00   0.0  0
 NC6  CONST_03  O10  C3   N4   C5      0.00   0.0  0
 NC6  CONST_04  C5   N4   C3   N2    180.00   0.0  0
 NC6  CONST_05  HN2  N2   C3   O10   180.00   0.0  0
 NC6  CONST_06  HN4  N4   C3   O10   180.00   0.0  0
 NC6  Var_01    C16  C15  C14  C1    -55.15  30.0  1
 NC6  Var_02    C16  C17  C18  C1     55.98  30.0  1
 NC6  Var_03    C17  C16  C15  C14    54.57  30.0  1
 NC6  Var_04    C18  C17  C16  C15   -54.93  30.0  1
 NC6  Var_05    C6   C5   N4   C3   -162.46  30.0  3
 NC6  Var_06    C7   C6   C5   N4   -179.33  30.0  3
 NC6  Var_07    C8   C7   C6   C5   -179.55  30.0  3
 NC6  Var_08    C9   C8   C7   C6    179.81  30.0  3
 NC6  Var_09    C11  C9   C8   C7   -179.38  30.0  3
 NC6  Var_10    O12  C11  C9   C8   -179.19  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
 NC6  chir_01  C1  N2  C14  C18  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
 NC6  plan-1  C1   0.020
 NC6  plan-1  N2   0.020
 NC6  plan-1  C3   0.020
 NC6  plan-1  N4   0.020
 NC6  plan-1  C5   0.020
 NC6  plan-1  O10  0.020
 NC6  plan-1  HN2  0.020
 NC6  plan-1  HN4  0.020
 NC6  plan-2  C9   0.020
 NC6  plan-2  C11  0.020
 NC6  plan-2  O12  0.020
 NC6  plan-2  O13  0.020

