# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:38:34 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: N-[(4-fluoro-3-methylphenyl)methyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCc1ccc(F)c(C)c1
#
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
 J5D  J5D  N-[(4-fluoro-3-methylphenyl)methyl]acetamide  ligand  25  13  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J5D
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
 J5D  C    C  CH3   0  -0.777   4.2213  -0.4483  -1.4379
 J5D  O    O  O     0  -0.508   4.1650   0.0268   0.9184
 J5D  C1   C  C     0   0.515   3.5490  -0.1032  -0.1317
 J5D  C2   C  CH2   0  -0.313   1.3991   0.2976   0.9741
 J5D  C3   C  CR6   0   0.050  -0.0517   0.3548   0.5853
 J5D  C4   C  CR16  0  -0.296  -0.6961   1.5719   0.4060
 J5D  C5   C  CR16  0  -0.391  -2.0276   1.6127   0.0136
 J5D  C6   C  CR6   0   0.506  -2.6918   0.4235  -0.1991
 J5D  F    F  F     0  -0.313  -3.9801   0.4635  -0.5841
 J5D  C7   C  CR6   0  -0.077  -2.0956  -0.8198  -0.0345
 J5D  C8   C  CH3   0  -0.716  -2.8605  -2.0871  -0.2695
 J5D  C9   C  CR16  0  -0.308  -0.7630  -0.8224   0.3614
 J5D  N    N  NH1   0  -0.618   2.2134   0.0228  -0.1957
 J5D  H1   H  HCH3  0   0.260   5.2736  -0.1774  -1.4041
 J5D  H2   H  HCH3  0   0.270   4.1546  -1.5242  -1.6098
 J5D  H3   H  HCH3  0   0.255   3.7536   0.0489  -2.2868
 J5D  H4   H  HCH2  0   0.253   1.7025   1.2446   1.4268
 J5D  H5   H  HCH2  0   0.253   1.5565  -0.4799   1.7260
 J5D  H6   H  HCR6  0   0.263  -0.1639   2.4995   0.5754
 J5D  H7   H  HCR6  0   0.277  -2.5388   2.5562  -0.1270
 J5D  H8   H  HCH3  0   0.252  -3.2705  -2.1290  -1.2792
 J5D  H9   H  HCH3  0   0.250  -2.2150  -2.9533  -0.1361
 J5D  H10  H  HCH3  0   0.252  -3.6970  -2.1861   0.4236
 J5D  H11  H  HCR6  0   0.258  -0.2686  -1.7769   0.5056
 J5D  H12  H  HNH1  0   0.404   1.7500  -0.0872  -1.0831

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
 J5D  O   C1   double    1.224  0.020  1.224
 J5D  C   C1   single    1.509  0.020  1.509
 J5D  C1  N    single    1.343  0.020  1.343
 J5D  N   C2   single    1.452  0.020  1.452
 J5D  C2  C3   single    1.503  0.020  1.503
 J5D  C3  C9   aromatic  1.393  0.020  1.393
 J5D  C3  C4   aromatic  1.389  0.020  1.389
 J5D  C9  C7   aromatic  1.390  0.020  1.390
 J5D  C4  C5   aromatic  1.389  0.020  1.389
 J5D  C7  C8   single    1.499  0.020  1.499
 J5D  C7  C6   aromatic  1.389  0.020  1.389
 J5D  C5  C6   aromatic  1.379  0.020  1.379
 J5D  C6  F    single    1.345  0.020  1.345
 J5D  C   H1   single    0.970  0.020  1.090
 J5D  C   H2   single    0.970  0.020  1.090
 J5D  C   H3   single    0.970  0.020  1.090
 J5D  C2  H4   single    0.970  0.020  1.090
 J5D  C2  H5   single    0.970  0.020  1.090
 J5D  C4  H6   single    0.930  0.020  1.080
 J5D  C5  H7   single    0.930  0.020  1.080
 J5D  C8  H8   single    0.970  0.020  1.090
 J5D  C8  H9   single    0.970  0.020  1.090
 J5D  C8  H10  single    0.970  0.020  1.090
 J5D  C9  H11  single    0.930  0.020  1.080
 J5D  N   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
 J5D  H3   C   H2  107.52  3.000
 J5D  H3   C   H1  109.03  3.000
 J5D  H2   C   H1  108.04  3.000
 J5D  H3   C   C1  112.26  3.000
 J5D  H2   C   C1  109.54  3.000
 J5D  H1   C   C1  110.32  3.000
 J5D  N    C1  O   122.09  3.000
 J5D  N    C1  C   115.03  3.000
 J5D  O    C1  C   122.86  3.000
 J5D  H5   C2  H4  106.95  3.000
 J5D  H5   C2  N   109.81  3.000
 J5D  H4   C2  N   110.01  3.000
 J5D  H5   C2  C3  110.12  3.000
 J5D  H4   C2  C3  110.01  3.000
 J5D  N    C2  C3  109.89  3.000
 J5D  C9   C3  C4  118.87  3.000
 J5D  C4   C3  C2  120.97  3.000
 J5D  C9   C3  C2  120.14  3.000
 J5D  H6   C4  C5  119.36  3.000
 J5D  H6   C4  C3  120.17  3.000
 J5D  C5   C4  C3  120.47  3.000
 J5D  H7   C5  C6  120.29  3.000
 J5D  H7   C5  C4  121.01  3.000
 J5D  C6   C5  C4  118.69  3.000
 J5D  C7   C6  F   118.15  3.000
 J5D  F    C6  C5  118.67  3.000
 J5D  C7   C6  C5  123.17  3.000
 J5D  C9   C7  C8  122.16  3.000
 J5D  C8   C7  C6  121.29  3.000
 J5D  C9   C7  C6  116.55  3.000
 J5D  H10  C8  H9  107.73  3.000
 J5D  H10  C8  H8  107.25  3.000
 J5D  H9   C8  H8  107.81  3.000
 J5D  H10  C8  C7  111.62  3.000
 J5D  H9   C8  C7  110.55  3.000
 J5D  H8   C8  C7  111.69  3.000
 J5D  H11  C9  C7  118.45  3.000
 J5D  H11  C9  C3  119.31  3.000
 J5D  C7   C9  C3  122.24  3.000
 J5D  H12  N   C2  118.21  3.000
 J5D  H12  N   C1  119.30  3.000
 J5D  C2   N   C1  122.49  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
 J5D  CONST_01  C6   C7  C9  C3     0.00   0.0  0
 J5D  CONST_02  C6   C5  C4  C3     0.00   0.0  0
 J5D  CONST_03  C7   C9  C3  C4     0.00   0.0  0
 J5D  CONST_04  C7   C6  C5  C4     0.00   0.0  0
 J5D  CONST_05  C9   C3  C4  C5     0.00   0.0  0
 J5D  CONST_06  C9   C7  C6  C5     0.00   0.0  0
 J5D  CONST_07  C7   C9  C3  C2   180.00   0.0  0
 J5D  CONST_08  C5   C4  C3  C2   180.00   0.0  0
 J5D  CONST_09  C8   C7  C9  C3   180.00   0.0  0
 J5D  CONST_10  F    C6  C5  C4   180.00   0.0  0
 J5D  CONST_11  C8   C7  C6  C5   180.00   0.0  0
 J5D  CONST_12  C9   C7  C6  F    180.00   0.0  0
 J5D  CONST_13  H7   C5  C4  C3   180.00   0.0  0
 J5D  CONST_14  H11  C9  C3  C4   180.00   0.0  0
 J5D  CONST_15  H6   C4  C5  C6   180.00   0.0  0
 J5D  CONST_16  C2   N   C1  C    180.00   0.0  0
 J5D  CONST_17  C2   N   C1  O      0.00   0.0  0
 J5D  CONST_18  H12  N   C1  C      0.00   0.0  0
 J5D  Var_01    N    C2  C3  C4  -100.51  30.0  2
 J5D  Var_02    H8   C8  C7  C6    57.33  30.0  2
 J5D  Var_03    C3   C2  N   C1  -178.91  30.0  3
 J5D  Var_04    H1   C   C1  O    -22.36  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
 J5D  plan-1  C2   0.020
 J5D  plan-1  C3   0.020
 J5D  plan-1  C4   0.020
 J5D  plan-1  C5   0.020
 J5D  plan-1  C6   0.020
 J5D  plan-1  F    0.020
 J5D  plan-1  C7   0.020
 J5D  plan-1  C8   0.020
 J5D  plan-1  C9   0.020
 J5D  plan-1  H6   0.020
 J5D  plan-1  H7   0.020
 J5D  plan-1  H11  0.020
 J5D  plan-2  C    0.020
 J5D  plan-2  O    0.020
 J5D  plan-2  C1   0.020
 J5D  plan-2  C2   0.020
 J5D  plan-2  N    0.020
 J5D  plan-2  H12  0.020

