# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:18:29 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: hexanediamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)CCCCC(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
 9EE  9EE  'hexanediamide            '  ligand  22  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9EE
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
 9EE  NAG  N  NH2   0  -0.806  -4.2655   0.7080  -0.0371
 9EE  CAB  C  C     0   0.523  -3.2120  -0.1220   0.0425
 9EE  OAH  O  O     0  -0.496  -3.3346  -1.3363   0.1173
 9EE  CAA  C  CH2   0  -0.581  -1.8636   0.5700   0.0319
 9EE  CAC  C  CH2   0  -0.414  -0.6762  -0.3779   0.0127
 9EE  CAD  C  CH2   0  -0.414   0.6457   0.3811   0.0031
 9EE  CAE  C  CH2   0  -0.581   1.8326  -0.5676  -0.0166
 9EE  CAF  C  C     0   0.523   3.1817   0.1233  -0.0257
 9EE  OAI  O  O     0  -0.496   3.3051   1.3398  -0.0411
 9EE  NAJ  N  NH2   0  -0.806   4.2351  -0.7105  -0.0175
 9EE  H1   H  HNH2  0   0.396  -5.2053   0.3485  -0.0059
 9EE  H2   H  HNH2  0   0.404  -4.1527   1.7061  -0.0752
 9EE  H3   H  HCH2  0   0.262  -1.8218   1.2414  -0.8317
 9EE  H4   H  HCH2  0   0.266  -1.8075   1.2222   0.9101
 9EE  H5   H  HCH2  0   0.223  -0.7125  -1.0372   0.8841
 9EE  H6   H  HCH2  0   0.223  -0.7320  -1.0261  -0.8666
 9EE  H7   H  HCH2  0   0.223   0.6828   1.0410  -0.8680
 9EE  H8   H  HCH2  0   0.223   0.7021   1.0285   0.8825
 9EE  H9   H  HCH2  0   0.263   1.7916  -1.2369   0.8488
 9EE  H10  H  HCH2  0   0.264   1.7760  -1.2218  -0.8930
 9EE  H11  H  HNH2  0   0.396   5.1750  -0.3500  -0.0256
 9EE  H12  H  HNH2  0   0.404   4.1220  -1.7093  -0.0039

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
 9EE  NAJ  CAF  single  1.344  0.020  1.344
 9EE  CAF  OAI  double  1.223  0.020  1.223
 9EE  CAF  CAE  single  1.516  0.020  1.516
 9EE  CAD  CAE  single  1.520  0.020  1.520
 9EE  CAD  CAC  single  1.524  0.020  1.524
 9EE  CAA  CAC  single  1.519  0.020  1.519
 9EE  CAA  CAB  single  1.516  0.020  1.516
 9EE  CAB  NAG  single  1.344  0.020  1.344
 9EE  CAB  OAH  double  1.223  0.020  1.223
 9EE  NAG  H1   single  0.860  0.020  1.020
 9EE  NAG  H2   single  0.860  0.020  1.020
 9EE  CAA  H3   single  0.970  0.020  1.090
 9EE  CAA  H4   single  0.970  0.020  1.090
 9EE  CAC  H5   single  0.970  0.020  1.090
 9EE  CAC  H6   single  0.970  0.020  1.090
 9EE  CAD  H7   single  0.970  0.020  1.090
 9EE  CAD  H8   single  0.970  0.020  1.090
 9EE  CAE  H9   single  0.970  0.020  1.090
 9EE  CAE  H10  single  0.970  0.020  1.090
 9EE  NAJ  H11  single  0.860  0.020  1.020
 9EE  NAJ  H12  single  0.860  0.020  1.020

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
 9EE  H2   NAG  H1   117.42  3.000
 9EE  H2   NAG  CAB  121.85  3.000
 9EE  H1   NAG  CAB  120.63  3.000
 9EE  CAA  CAB  OAH  122.89  3.000
 9EE  OAH  CAB  NAG  122.58  3.000
 9EE  CAA  CAB  NAG  114.53  3.000
 9EE  H4   CAA  H3   105.39  3.000
 9EE  H4   CAA  CAC  109.97  3.000
 9EE  H3   CAA  CAC  110.05  3.000
 9EE  H4   CAA  CAB  108.17  3.000
 9EE  H3   CAA  CAB  108.63  3.000
 9EE  CAC  CAA  CAB  114.23  3.000
 9EE  H6   CAC  H5   106.36  3.000
 9EE  H6   CAC  CAD  109.53  3.000
 9EE  H5   CAC  CAD  109.51  3.000
 9EE  H6   CAC  CAA  109.88  3.000
 9EE  H5   CAC  CAA  109.89  3.000
 9EE  CAD  CAC  CAA  111.54  3.000
 9EE  H8   CAD  H7   106.36  3.000
 9EE  H8   CAD  CAE  109.87  3.000
 9EE  H7   CAD  CAE  109.87  3.000
 9EE  H8   CAD  CAC  109.54  3.000
 9EE  H7   CAD  CAC  109.57  3.000
 9EE  CAE  CAD  CAC  111.50  3.000
 9EE  H10  CAE  H9   105.40  3.000
 9EE  H10  CAE  CAF  108.27  3.000
 9EE  H9   CAE  CAF  108.46  3.000
 9EE  H10  CAE  CAD  110.06  3.000
 9EE  H9   CAE  CAD  110.01  3.000
 9EE  CAF  CAE  CAD  114.25  3.000
 9EE  NAJ  CAF  OAI  122.57  3.000
 9EE  OAI  CAF  CAE  122.91  3.000
 9EE  NAJ  CAF  CAE  114.52  3.000
 9EE  H12  NAJ  H11  117.45  3.000
 9EE  H12  NAJ  CAF  121.90  3.000
 9EE  H11  NAJ  CAF  120.65  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
 9EE  CONST_01  H1   NAG  CAB  OAH     0.00   0.0  0
 9EE  CONST_02  H2   NAG  CAB  OAH   180.00   0.0  0
 9EE  CONST_03  H11  NAJ  CAF  CAE   180.00   0.0  0
 9EE  CONST_04  H12  NAJ  CAF  CAE     0.00   0.0  0
 9EE  Var_01    CAC  CAA  CAB  NAG  -175.47  30.0  1
 9EE  Var_02    CAD  CAC  CAA  CAB  -179.99  30.0  3
 9EE  Var_03    CAE  CAD  CAC  CAA  -179.98  30.0  1
 9EE  Var_04    CAF  CAE  CAD  CAC  -179.95  30.0  3
 9EE  Var_05    NAJ  CAF  CAE  CAD   178.80  30.0  2

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
 9EE  plan-1  NAG  0.020
 9EE  plan-1  CAB  0.020
 9EE  plan-1  OAH  0.020
 9EE  plan-1  CAA  0.020
 9EE  plan-1  H1   0.020
 9EE  plan-1  H2   0.020
 9EE  plan-2  CAE  0.020
 9EE  plan-2  CAF  0.020
 9EE  plan-2  OAI  0.020
 9EE  plan-2  NAJ  0.020
 9EE  plan-2  H11  0.020
 9EE  plan-2  H12  0.020

