# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 15:56:46 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 1-(2,4-difluorophenyl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc(F)cc1F
#
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
 M5Y  M5Y  1-(2,4-difluorophenyl)methanamine  ligand  17  10  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M5Y
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
 M5Y  C29  C  CH2   0  -0.349   2.3054   0.6460  -0.4272
 M5Y  C30  C  CR6   0  -0.099   0.8229   0.4468  -0.2776
 M5Y  C31  C  CR16  0  -0.269  -0.0610   1.5202  -0.2686
 M5Y  C32  C  CR16  0  -0.412  -1.4293   1.3531  -0.0969
 M5Y  C33  C  CR6   0   0.529  -1.9106   0.0715   0.0730
 M5Y  C35  C  CR16  0  -0.555  -1.0815  -1.0348   0.0743
 M5Y  C36  C  CR6   0   0.547   0.2707  -0.8144  -0.0979
 M5Y  F34  F  F     0  -0.311  -3.2269  -0.1188   0.2406
 M5Y  F37  F  F     0  -0.304   1.0800  -1.8819  -0.1096
 M5Y  N28  N  NH2   0  -0.790   2.9888   0.3597   0.8261
 M5Y  H24  H  HCH2  0   0.241   2.6967  -0.0293  -1.1910
 M5Y  H25  H  HCH2  0   0.222   2.4748   1.6625  -0.8041
 M5Y  H26  H  HCR6  0   0.273   0.3315   2.5205  -0.4035
 M5Y  H27  H  HCR6  0   0.283  -2.1008   2.2009  -0.0941
 M5Y  H28  H  HCR6  0   0.299  -1.4736  -2.0351   0.2041
 M5Y  H31  H  HNH2  0   0.352   3.9882   0.4336   0.6825
 M5Y  H2   H  HNH2  0   0.343   2.7540   1.0724   1.5060

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
 M5Y  C29  C30  single    1.503  0.020  1.503
 M5Y  C29  N28  single    1.456  0.020  1.456
 M5Y  C30  C31  aromatic  1.391  0.020  1.391
 M5Y  C30  C36  aromatic  1.388  0.020  1.388
 M5Y  C31  C32  aromatic  1.389  0.020  1.389
 M5Y  C32  C33  aromatic  1.379  0.020  1.379
 M5Y  C33  F34  single    1.341  0.020  1.341
 M5Y  C33  C35  aromatic  1.383  0.020  1.383
 M5Y  C35  C36  aromatic  1.381  0.020  1.381
 M5Y  C36  F37  single    1.340  0.020  1.340
 M5Y  C29  H24  single    0.970  0.020  1.090
 M5Y  C29  H25  single    0.970  0.020  1.090
 M5Y  C31  H26  single    0.930  0.020  1.080
 M5Y  C32  H27  single    0.930  0.020  1.080
 M5Y  C35  H28  single    0.930  0.020  1.080
 M5Y  N28  H31  single    0.890  0.020  1.040
 M5Y  N28  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
 M5Y  H25  C29  H24  106.10  3.000
 M5Y  H25  C29  N28  113.91  3.000
 M5Y  H24  C29  N28  108.19  3.000
 M5Y  H25  C29  C30  108.01  3.000
 M5Y  H24  C29  C30  109.94  3.000
 M5Y  N28  C29  C30  110.56  3.000
 M5Y  C36  C30  C31  116.58  3.000
 M5Y  C36  C30  C29  121.70  3.000
 M5Y  C31  C30  C29  121.68  3.000
 M5Y  H26  C31  C32  118.91  3.000
 M5Y  H26  C31  C30  118.80  3.000
 M5Y  C32  C31  C30  122.29  3.000
 M5Y  H27  C32  C33  120.75  3.000
 M5Y  H27  C32  C31  121.17  3.000
 M5Y  C33  C32  C31  118.07  3.000
 M5Y  F34  C33  C35  118.37  3.000
 M5Y  C35  C33  C32  122.30  3.000
 M5Y  F34  C33  C32  119.33  3.000
 M5Y  H28  C35  C36  121.16  3.000
 M5Y  H28  C35  C33  121.50  3.000
 M5Y  C36  C35  C33  117.35  3.000
 M5Y  F37  C36  C35  117.74  3.000
 M5Y  F37  C36  C30  118.84  3.000
 M5Y  C35  C36  C30  123.41  3.000
 M5Y  H2   N28  H31  105.83  3.000
 M5Y  H2   N28  C29  109.32  3.000
 M5Y  H31  N28  C29  109.08  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
 M5Y  CONST_01  C33  C32  C31  C30    0.00   0.0  0
 M5Y  CONST_02  C33  C35  C36  C30    0.00   0.0  0
 M5Y  CONST_03  C35  C36  C30  C31    0.00   0.0  0
 M5Y  CONST_04  C35  C33  C32  C31    0.00   0.0  0
 M5Y  CONST_05  C36  C30  C31  C32    0.00   0.0  0
 M5Y  CONST_06  C36  C35  C33  C32    0.00   0.0  0
 M5Y  CONST_07  C32  C31  C30  C29  180.00   0.0  0
 M5Y  CONST_08  C35  C36  C30  C29  180.00   0.0  0
 M5Y  CONST_09  F37  C36  C30  C31  180.00   0.0  0
 M5Y  CONST_10  F34  C33  C32  C31  180.00   0.0  0
 M5Y  CONST_11  F37  C36  C35  C33  180.00   0.0  0
 M5Y  CONST_12  F34  C33  C35  C36  180.00   0.0  0
 M5Y  CONST_13  H27  C32  C31  C30  180.00   0.0  0
 M5Y  CONST_14  H28  C35  C36  C30  180.00   0.0  0
 M5Y  CONST_15  H26  C31  C32  C33  180.00   0.0  0
 M5Y  Var_01    N28  C29  C30  C31  109.05  30.0  2
 M5Y  Var_02    H31  N28  C29  C30  175.83  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
 M5Y  plan-1  C29  0.020
 M5Y  plan-1  C30  0.020
 M5Y  plan-1  C31  0.020
 M5Y  plan-1  C32  0.020
 M5Y  plan-1  C33  0.020
 M5Y  plan-1  C35  0.020
 M5Y  plan-1  C36  0.020
 M5Y  plan-1  F34  0.020
 M5Y  plan-1  F37  0.020
 M5Y  plan-1  H26  0.020
 M5Y  plan-1  H27  0.020
 M5Y  plan-1  H28  0.020

