# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:29:48 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 2-cyano-~{N}-cyclohexyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC#N)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
 GT7  GT7  2-cyano-~{N}-cyclohexyl-ethanamide  ligand  26  12  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GT7
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
 GT7  N1   N  NH1   0  -0.643   0.3620   0.6478  -0.3330
 GT7  C4   C  CH1   0  -0.053  -0.9247   0.1656   0.1400
 GT7  C5   C  CH2   0  -0.447  -1.9360   1.3074   0.1362
 GT7  C6   C  CH2   0  -0.438  -3.2998   0.8319   0.6276
 GT7  C7   C  C     0   0.572   1.5328   0.1387   0.0587
 GT7  C8   C  CH2   0  -0.686   2.7396   0.7985  -0.6065
 GT7  C1   C  CH2   0  -0.431  -3.8079  -0.3540  -0.1859
 GT7  C2   C  CH2   0  -0.440  -2.7901  -1.4897  -0.1931
 GT7  C3   C  CH2   0  -0.425  -1.4293  -1.0130  -0.6920
 GT7  O1   O  O     0  -0.478   1.6672  -0.7558   0.8753
 GT7  C9   C  CSP   0   0.142   3.9778   0.1872  -0.1662
 GT7  N2   N  NS    0  -0.265   4.9706  -0.2848   0.1694
 GT7  H1   H  HNH1  0   0.406   0.3574   1.3536  -1.0536
 GT7  H2   H  HCH1  0   0.239  -0.7849  -0.1683   1.1721
 GT7  H3   H  HCH2  0   0.243  -1.5706   2.1278   0.7590
 GT7  H4   H  HCH2  0   0.220  -2.0331   1.7005  -0.8831
 GT7  H5   H  HCH2  0   0.216  -3.2229   0.5413   1.6806
 GT7  H6   H  HCH2  0   0.235  -4.0137   1.6572   0.5859
 GT7  H7   H  HCH2  0   0.344   2.6723   0.7182  -1.6944
 GT7  H8   H  HCH2  0   0.347   2.7684   1.8655  -0.3718
 GT7  H9   H  HCH2  0   0.231  -4.7627  -0.7022   0.2147
 GT7  H10  H  HCH2  0   0.212  -4.0015  -0.0321  -1.2147
 GT7  H11  H  HCH2  0   0.215  -2.6845  -1.8883   0.8220
 GT7  H12  H  HCH2  0   0.233  -3.1438  -2.3165  -0.8132
 GT7  H13  H  HCH2  0   0.214  -1.5087  -0.6981  -1.7381
 GT7  H14  H  HCH2  0   0.239  -0.7019  -1.8273  -0.6589

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
 GT7  N2  C9   triple  1.149  0.020  1.149
 GT7  C9  C8   single  1.449  0.020  1.449
 GT7  O1  C7   double  1.219  0.020  1.219
 GT7  C8  C7   single  1.528  0.020  1.528
 GT7  C7  N1   single  1.335  0.020  1.335
 GT7  N1  C4   single  1.453  0.020  1.453
 GT7  C3  C4   single  1.528  0.020  1.528
 GT7  C3  C2   single  1.526  0.020  1.526
 GT7  C4  C5   single  1.525  0.020  1.525
 GT7  C2  C1   single  1.525  0.020  1.525
 GT7  C5  C6   single  1.526  0.020  1.526
 GT7  C1  C6   single  1.525  0.020  1.525
 GT7  N1  H1   single  0.860  0.020  1.020
 GT7  C4  H2   single  0.970  0.020  1.090
 GT7  C5  H3   single  0.970  0.020  1.090
 GT7  C5  H4   single  0.970  0.020  1.090
 GT7  C6  H5   single  0.970  0.020  1.090
 GT7  C6  H6   single  0.970  0.020  1.090
 GT7  C8  H7   single  0.970  0.020  1.090
 GT7  C8  H8   single  0.970  0.020  1.090
 GT7  C1  H9   single  0.970  0.020  1.090
 GT7  C1  H10  single  0.970  0.020  1.090
 GT7  C2  H11  single  0.970  0.020  1.090
 GT7  C2  H12  single  0.970  0.020  1.090
 GT7  C3  H13  single  0.970  0.020  1.090
 GT7  C3  H14  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
 GT7  H1   N1  C7   118.71  3.000
 GT7  H1   N1  C4   117.43  3.000
 GT7  C7   N1  C4   123.66  3.000
 GT7  H2   C4  C3   108.69  3.000
 GT7  H2   C4  C5   108.40  3.000
 GT7  C3   C4  C5   110.92  3.000
 GT7  H2   C4  N1   107.17  3.000
 GT7  C5   C4  N1   109.75  3.000
 GT7  C3   C4  N1   111.78  3.000
 GT7  H4   C5  H3   106.87  3.000
 GT7  H4   C5  C6   109.39  3.000
 GT7  H3   C5  C6   110.44  3.000
 GT7  H4   C5  C4   109.22  3.000
 GT7  H3   C5  C4   109.80  3.000
 GT7  C6   C5  C4   111.02  3.000
 GT7  H6   C6  H5   106.46  3.000
 GT7  H6   C6  C1   110.45  3.000
 GT7  H5   C6  C1   109.26  3.000
 GT7  H6   C6  C5   109.67  3.000
 GT7  H5   C6  C5   109.25  3.000
 GT7  C1   C6  C5   111.61  3.000
 GT7  O1   C7  C8   121.44  3.000
 GT7  C8   C7  N1   113.59  3.000
 GT7  O1   C7  N1   124.96  3.000
 GT7  H8   C8  H7   106.68  3.000
 GT7  H8   C8  C9   108.90  3.000
 GT7  H7   C8  C9   108.91  3.000
 GT7  H8   C8  C7   110.42  3.000
 GT7  H7   C8  C7   110.67  3.000
 GT7  C9   C8  C7   111.12  3.000
 GT7  H10  C1  H9   106.48  3.000
 GT7  H10  C1  C2   109.42  3.000
 GT7  H9   C1  C2   110.35  3.000
 GT7  H10  C1  C6   109.35  3.000
 GT7  H9   C1  C6   110.08  3.000
 GT7  C2   C1  C6   111.05  3.000
 GT7  H12  C2  H11  106.36  3.000
 GT7  H12  C2  C3   109.86  3.000
 GT7  H11  C2  C3   109.31  3.000
 GT7  H12  C2  C1   110.50  3.000
 GT7  H11  C2  C1   109.32  3.000
 GT7  C3   C2  C1   111.35  3.000
 GT7  H14  C3  H13  106.94  3.000
 GT7  H14  C3  C2   110.56  3.000
 GT7  H13  C3  C2   109.72  3.000
 GT7  H14  C3  C4   109.78  3.000
 GT7  H13  C3  C4   108.79  3.000
 GT7  C2   C3  C4   110.94  3.000
 GT7  N2   C9  C8   180.00  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
 GT7  CONST_01  O1  C7  N1  C4     0.00   0.0  0
 GT7  CONST_02  C8  C7  N1  C4   180.00   0.0  0
 GT7  CONST_03  H1  N1  C7  C8     0.00   0.0  0
 GT7  Var_01    C1  C2  C3  C4    55.98  30.0  1
 GT7  Var_02    C1  C6  C5  C4   -55.47  30.0  1
 GT7  Var_03    C2  C1  C6  C5    54.94  30.0  1
 GT7  Var_04    C3  C2  C1  C6   -55.17  30.0  1
 GT7  Var_05    C9  C8  C7  N1  -178.76  30.0  2

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
 GT7  chir_01  C4  N1  C3  C5  positiv

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
 GT7  plan-1  N1  0.020
 GT7  plan-1  C4  0.020
 GT7  plan-1  C7  0.020
 GT7  plan-1  C8  0.020
 GT7  plan-1  O1  0.020
 GT7  plan-1  H1  0.020

