# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 16:27:32 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 2-(phenylmethyl)imidazolidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CNC(Cc2ccccc2)N1
#
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
 M6H  M6H  2-(phenylmethyl)imidazolidine  ligand  26  12  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_M6H
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
 M6H  CAA  C  CR16  0  -0.275   3.5554   0.5409  -0.2312
 M6H  CAB  C  CR16  0  -0.245   2.6796   1.3433   0.4893
 M6H  CAC  C  CR16  0  -0.242   3.1532  -0.7303  -0.6203
 M6H  CAD  C  CR16  0  -0.299   1.4117   0.8785   0.8131
 M6H  CAE  C  CR16  0  -0.311   1.8859  -1.1914  -0.2891
 M6H  CAF  C  CH2   0  -0.283  -2.9057   1.1820  -0.6612
 M6H  CAG  C  CH2   0  -0.337  -3.4888   0.1020   0.2398
 M6H  CAK  C  CR15  0   0.067  -1.3665  -0.5944  -0.4033
 M6H  CAL  C  CR6   0   0.132   0.9966  -0.3963   0.4328
 M6H  NAI  N  NR15  0  -0.620  -1.4900   0.8543  -0.6135
 M6H  NAJ  N  NR15  0  -0.608  -2.7046  -1.0860  -0.0812
 M6H  H1   H  HCR6  0   0.251   4.5442   0.9012  -0.4845
 M6H  H2   H  HCR6  0   0.249   2.9836   2.3345   0.8012
 M6H  H3   H  HCR6  0   0.251   3.8277  -1.3654  -1.1807
 M6H  H4   H  HCR6  0   0.240   0.7352   1.5107   1.3742
 M6H  H5   H  HCR6  0   0.243   1.5844  -2.1870  -0.5949
 M6H  H7   H  HCH2  0   0.219  -3.0968   2.1925  -0.2920
 M6H  H8   H  HCH2  0   0.225  -3.3562   0.3685   1.2920
 M6H  H9   H  HCH2  0   0.242  -4.5505  -0.0753   0.0733
 M6H  H12  H  HCR5  0   0.229  -1.0080  -1.1088  -1.3031
 M6H  H13  H  HNR5  0   0.352  -0.9947   1.1570  -1.4388
 M6H  H15  H  HNR5  0   0.353  -3.0999  -1.5075  -0.9122
 M6H  CAH  C  CH2   0  -0.495  -0.3875  -0.8899   0.7379
 M6H  H6   H  HCH2  0   0.198  -3.3425   1.1068  -1.6664
 M6H  H10  H  HCH2  0   0.232  -0.7676  -0.4235   1.6504
 M6H  H11  H  HCH2  0   0.233  -0.3702  -1.9696   0.9049

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
 M6H  NAI  CAF  single    1.454  0.020  1.454
 M6H  NAI  CAK  single    1.469  0.020  1.469
 M6H  CAD  CAB  aromatic  1.389  0.020  1.389
 M6H  CAD  CAL  aromatic  1.394  0.020  1.394
 M6H  CAH  CAK  single    1.532  0.020  1.532
 M6H  CAH  CAL  single    1.501  0.020  1.501
 M6H  CAB  CAA  aromatic  1.389  0.020  1.389
 M6H  CAF  CAG  single    1.523  0.020  1.523
 M6H  CAK  NAJ  single    1.461  0.020  1.461
 M6H  CAL  CAE  aromatic  1.394  0.020  1.394
 M6H  CAA  CAC  aromatic  1.389  0.020  1.389
 M6H  CAE  CAC  aromatic  1.389  0.020  1.389
 M6H  CAG  NAJ  single    1.459  0.020  1.459
 M6H  CAA  H1   single    0.930  0.020  1.080
 M6H  CAB  H2   single    0.930  0.020  1.080
 M6H  CAC  H3   single    0.930  0.020  1.080
 M6H  CAD  H4   single    0.930  0.020  1.080
 M6H  CAE  H5   single    0.930  0.020  1.080
 M6H  CAF  H6   single    0.970  0.020  1.090
 M6H  CAF  H7   single    0.970  0.020  1.090
 M6H  CAG  H8   single    0.970  0.020  1.090
 M6H  CAG  H9   single    0.970  0.020  1.090
 M6H  CAH  H10  single    0.970  0.020  1.090
 M6H  CAH  H11  single    0.970  0.020  1.090
 M6H  CAK  H12  single    0.970  0.020  1.090
 M6H  NAI  H13  single    0.890  0.020  1.040
 M6H  NAJ  H15  single    0.890  0.020  1.040

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
 M6H  H1   CAA  CAC  120.23  3.000
 M6H  H1   CAA  CAB  120.34  3.000
 M6H  CAC  CAA  CAB  119.43  3.000
 M6H  H2   CAB  CAD  119.70  3.000
 M6H  H2   CAB  CAA  120.08  3.000
 M6H  CAD  CAB  CAA  120.22  3.000
 M6H  H3   CAC  CAE  119.82  3.000
 M6H  H3   CAC  CAA  120.10  3.000
 M6H  CAE  CAC  CAA  120.08  3.000
 M6H  H4   CAD  CAL  119.31  3.000
 M6H  H4   CAD  CAB  119.73  3.000
 M6H  CAL  CAD  CAB  120.96  3.000
 M6H  H5   CAE  CAL  119.49  3.000
 M6H  H5   CAE  CAC  119.43  3.000
 M6H  CAL  CAE  CAC  121.08  3.000
 M6H  H7   CAF  H6   107.63  3.000
 M6H  H7   CAF  NAI  111.57  3.000
 M6H  H6   CAF  NAI  113.69  3.000
 M6H  H7   CAF  CAG  112.90  3.000
 M6H  H6   CAF  CAG  109.92  3.000
 M6H  NAI  CAF  CAG  101.16  3.000
 M6H  H9   CAG  H8   107.75  3.000
 M6H  H9   CAG  NAJ  110.96  3.000
 M6H  H8   CAG  NAJ  110.18  3.000
 M6H  H9   CAG  CAF  113.47  3.000
 M6H  H8   CAG  CAF  110.49  3.000
 M6H  NAJ  CAG  CAF  103.98  3.000
 M6H  H12  CAK  NAJ  108.80  3.000
 M6H  H12  CAK  NAI  111.88  3.000
 M6H  NAJ  CAK  NAI  106.64  3.000
 M6H  H12  CAK  CAH  108.16  3.000
 M6H  NAJ  CAK  CAH  110.85  3.000
 M6H  NAI  CAK  CAH  110.52  3.000
 M6H  CAH  CAL  CAE  120.40  3.000
 M6H  CAE  CAL  CAD  118.22  3.000
 M6H  CAH  CAL  CAD  121.33  3.000
 M6H  H13  NAI  CAK  111.81  3.000
 M6H  H13  NAI  CAF  112.56  3.000
 M6H  CAK  NAI  CAF  107.99  3.000
 M6H  H15  NAJ  CAK  108.47  3.000
 M6H  H15  NAJ  CAG  108.04  3.000
 M6H  CAK  NAJ  CAG  105.46  3.000
 M6H  H11  CAH  H10  107.44  3.000
 M6H  H11  CAH  CAL  109.96  3.000
 M6H  H10  CAH  CAL  110.49  3.000
 M6H  H11  CAH  CAK  108.33  3.000
 M6H  H10  CAH  CAK  108.50  3.000
 M6H  CAL  CAH  CAK  111.98  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
 M6H  CONST_01  CAL  CAD  CAB  CAA    0.00   0.0  0
 M6H  CONST_02  CAL  CAE  CAC  CAA    0.00   0.0  0
 M6H  CONST_03  CAE  CAL  CAD  CAB    0.00   0.0  0
 M6H  CONST_04  CAE  CAC  CAA  CAB    0.00   0.0  0
 M6H  CONST_05  CAD  CAB  CAA  CAC    0.00   0.0  0
 M6H  CONST_06  CAD  CAL  CAE  CAC    0.00   0.0  0
 M6H  CONST_07  CAH  CAL  CAD  CAB  180.00   0.0  0
 M6H  CONST_08  CAH  CAL  CAE  CAC  180.00   0.0  0
 M6H  CONST_09  H4   CAD  CAB  CAA  180.00   0.0  0
 M6H  CONST_10  H5   CAE  CAC  CAA  180.00   0.0  0
 M6H  CONST_11  H3   CAC  CAA  CAB  180.00   0.0  0
 M6H  CONST_12  H2   CAB  CAA  CAC  180.00   0.0  0
 M6H  CONST_13  H1   CAA  CAB  CAD  180.00   0.0  0
 M6H  Var_01    CAK  NAJ  CAG  CAF   33.03  30.0  1
 M6H  Var_02    CAK  NAI  CAF  CAG   29.55  30.0  1
 M6H  Var_03    NAJ  CAG  CAF  NAI  -38.38  30.0  1
 M6H  Var_04    CAK  CAH  CAL  CAD   91.62  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
 M6H  chir_01  CAK  NAI  CAH  NAJ  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
 M6H  plan-1  CAA  0.020
 M6H  plan-1  CAB  0.020
 M6H  plan-1  CAC  0.020
 M6H  plan-1  CAD  0.020
 M6H  plan-1  CAE  0.020
 M6H  plan-1  CAL  0.020
 M6H  plan-1  H1   0.020
 M6H  plan-1  H2   0.020
 M6H  plan-1  H3   0.020
 M6H  plan-1  H4   0.020
 M6H  plan-1  H5   0.020
 M6H  plan-1  CAH  0.020

