# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:09:19 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2,6-dimethylphenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C)c1CN
#
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
 8YU  8YU  (2,6-dimethylphenyl)methanamine  ligand  23  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 PERFECT
;

data_comp_8YU
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
 8YU  C2   C  CH2   0  -0.391   1.8477   0.0156  -0.4560
 8YU  N1   N  NH2   0  -0.786   2.5406   0.2503   0.8083
 8YU  C4   C  CR6   0   0.079  -0.3097  -1.2488  -0.1132
 8YU  C5   C  CR16  0  -0.320  -1.6842  -1.2588   0.1178
 8YU  C6   C  CR16  0  -0.241  -2.3941  -0.0748   0.2293
 8YU  C7   C  CR16  0  -0.322  -1.7302   1.1370   0.1166
 8YU  C8   C  CR6   0   0.090  -0.3579   1.1786  -0.1129
 8YU  C81  C  CH3   0  -0.746   0.3372   2.5053  -0.2315
 8YU  C3   C  CR6   0   0.030   0.3556  -0.0219  -0.2388
 8YU  H26  H  HCH2  0   0.238   2.1002   0.8345  -1.1326
 8YU  H27  H  HCH2  0   0.225   2.1727  -0.8992  -0.9650
 8YU  H35  H  HNH2  0   0.340   2.3644  -0.5242   1.4371
 8YU  H40  H  HCH3  0   0.247   0.7847  -2.7320  -1.2434
 8YU  H41  H  HCH3  0   0.240   1.2944  -2.6001   0.4289
 8YU  H42  H  HCH3  0   0.251  -0.2262  -3.3915   0.0347
 8YU  H43  H  HCR6  0   0.241  -2.2003  -2.2065   0.2171
 8YU  H44  H  HCR6  0   0.248  -3.4617  -0.0959   0.4082
 8YU  H45  H  HCR6  0   0.241  -2.2828   2.0644   0.2120
 8YU  H46  H  HCH3  0   0.246   1.2136   2.5490   0.4150
 8YU  H47  H  HCH3  0   0.243   0.6831   2.6865  -1.2520
 8YU  H48  H  HCH3  0   0.245  -0.3301   3.3235   0.0369
 8YU  H2   H  HNH2  0   0.349   3.5398   0.2434   0.6425
 8YU  C41  C  CH3   0  -0.747   0.4242  -2.5580  -0.2275

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
 8YU  N1   C2   single    1.461  0.020  1.461
 8YU  C2   C3   single    1.508  0.020  1.508
 8YU  C81  C8   single    1.503  0.020  1.503
 8YU  C3   C8   aromatic  1.402  0.020  1.402
 8YU  C3   C4   aromatic  1.401  0.020  1.401
 8YU  C8   C7   aromatic  1.392  0.020  1.392
 8YU  C41  C4   single    1.505  0.020  1.505
 8YU  C4   C5   aromatic  1.394  0.020  1.394
 8YU  C7   C6   aromatic  1.386  0.020  1.386
 8YU  C5   C6   aromatic  1.385  0.020  1.385
 8YU  C2   H26  single    0.970  0.020  1.090
 8YU  C2   H27  single    0.970  0.020  1.090
 8YU  N1   H35  single    0.890  0.020  1.040
 8YU  C41  H40  single    0.970  0.020  1.090
 8YU  C41  H41  single    0.970  0.020  1.090
 8YU  C41  H42  single    0.970  0.020  1.090
 8YU  C5   H43  single    0.930  0.020  1.080
 8YU  C6   H44  single    0.930  0.020  1.080
 8YU  C7   H45  single    0.930  0.020  1.080
 8YU  C81  H46  single    0.970  0.020  1.090
 8YU  C81  H47  single    0.970  0.020  1.090
 8YU  C81  H48  single    0.970  0.020  1.090
 8YU  N1   H2   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
 8YU  H27  C2   H26  105.64  3.000
 8YU  H27  C2   C3   109.84  3.000
 8YU  H26  C2   C3   109.68  3.000
 8YU  H27  C2   N1   113.29  3.000
 8YU  H26  C2   N1   107.83  3.000
 8YU  C3   C2   N1   110.40  3.000
 8YU  H2   N1   H35  105.55  3.000
 8YU  H2   N1   C2   108.97  3.000
 8YU  H35  N1   C2   109.38  3.000
 8YU  C3   C4   C5   119.30  3.000
 8YU  C5   C4   C41  119.15  3.000
 8YU  C3   C4   C41  121.55  3.000
 8YU  H43  C5   C6   119.75  3.000
 8YU  H43  C5   C4   119.41  3.000
 8YU  C6   C5   C4   120.84  3.000
 8YU  H44  C6   C7   120.18  3.000
 8YU  H44  C6   C5   120.13  3.000
 8YU  C7   C6   C5   119.68  3.000
 8YU  H45  C7   C8   119.45  3.000
 8YU  H45  C7   C6   119.78  3.000
 8YU  C8   C7   C6   120.77  3.000
 8YU  C3   C8   C81  120.90  3.000
 8YU  C3   C8   C7   119.40  3.000
 8YU  C81  C8   C7   119.70  3.000
 8YU  H48  C81  H47  107.43  3.000
 8YU  H48  C81  H46  108.44  3.000
 8YU  H47  C81  H46  107.03  3.000
 8YU  H48  C81  C8   111.12  3.000
 8YU  H47  C81  C8   111.51  3.000
 8YU  H46  C81  C8   111.13  3.000
 8YU  C8   C3   C4   120.00  3.000
 8YU  C4   C3   C2   120.29  3.000
 8YU  C8   C3   C2   119.67  3.000
 8YU  H42  C41  H41  107.57  3.000
 8YU  H42  C41  H40  107.41  3.000
 8YU  H41  C41  H40  106.88  3.000
 8YU  H42  C41  C4   110.86  3.000
 8YU  H41  C41  C4   112.13  3.000
 8YU  H40  C41  C4   111.73  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
 8YU  CONST_01  C7   C8   C3  C4     0.00   0.0  0
 8YU  CONST_02  C7   C6   C5  C4     0.00   0.0  0
 8YU  CONST_03  C8   C3   C4  C5     0.00   0.0  0
 8YU  CONST_04  C8   C7   C6  C5     0.00   0.0  0
 8YU  CONST_05  C3   C8   C7  C6     0.00   0.0  0
 8YU  CONST_06  C3   C4   C5  C6     0.00   0.0  0
 8YU  CONST_07  C7   C8   C3  C2   180.00   0.0  0
 8YU  CONST_08  C5   C4   C3  C2   180.00   0.0  0
 8YU  CONST_09  C8   C3   C4  C41  180.00   0.0  0
 8YU  CONST_10  C6   C5   C4  C41  180.00   0.0  0
 8YU  CONST_11  C81  C8   C3  C4   180.00   0.0  0
 8YU  CONST_12  C81  C8   C7  C6   180.00   0.0  0
 8YU  CONST_13  H44  C6   C5  C4   180.00   0.0  0
 8YU  CONST_14  H45  C7   C6  C5   180.00   0.0  0
 8YU  CONST_15  H43  C5   C6  C7   180.00   0.0  0
 8YU  Var_01    C8   C3   C2  N1    79.64  30.0  2
 8YU  Var_02    H40  C41  C4  C5   111.57  30.0  2
 8YU  Var_03    H46  C81  C8  C7   129.69  30.0  2
 8YU  Var_04    H35  N1   C2  C3    63.37  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
 8YU  plan-1  C2   0.020
 8YU  plan-1  C4   0.020
 8YU  plan-1  C5   0.020
 8YU  plan-1  C6   0.020
 8YU  plan-1  C7   0.020
 8YU  plan-1  C8   0.020
 8YU  plan-1  C81  0.020
 8YU  plan-1  C3   0.020
 8YU  plan-1  H43  0.020
 8YU  plan-1  H44  0.020
 8YU  plan-1  H45  0.020
 8YU  plan-1  C41  0.020

