# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:11:16 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: [3-chloranyl-4-(2-methoxy-5-methyl-phenyl)phenyl]methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C)cc1c2ccc(CN)cc2Cl
#
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
 AFK  AFK  '[3-chloranyl-4-(2-methoxy-5-methyl-phenyl)phenyl]methanamine'  ligand  34  18  .  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_AFK
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
 AFK  C1   C   CR6   0   0.355  -1.9102  -0.6830   0.6030
 AFK  C2   C   CR16  0  -0.370  -3.2936  -0.5553   0.5708
 AFK  C3   C   CR16  0  -0.297  -3.8746   0.6232   0.1133
 AFK  C4   C   CR6   0   0.085  -3.1055   1.6949  -0.3162
 AFK  C5   C   CH3   0  -0.723  -3.7258   2.9803  -0.7839
 AFK  C6   C   CR16  0  -0.314  -1.7192   1.5425  -0.2895
 AFK  C14  C   CR6   0  -0.092   1.0632  -0.6214  -0.6501
 AFK  CL   CL  CL    0  -0.134   0.1982  -1.6572  -1.7395
 AFK  C13  C   CR16  0  -0.247   2.4471  -0.6818  -0.6496
 AFK  C11  C   CR6   0   0.064   3.1887   0.1537   0.1793
 AFK  C12  C   CH2   0  -0.333   4.6929   0.0455   0.1978
 AFK  N    N   NH2   0  -0.794   5.3282   1.3040   0.5384
 AFK  C10  C   CR16  0  -0.268   2.5081   1.0581   0.9873
 AFK  C9   C   CR16  0  -0.298   1.1230   1.1096   0.9737
 AFK  C8   C   CR6   0   0.157   0.3641   0.2696   0.1612
 AFK  C7   C   CR6   0  -0.047  -1.1104   0.3760   0.1489
 AFK  O    O   O2    0  -0.460  -1.2574  -1.7658   1.0614
 AFK  C    C   CH3   0  -0.436  -2.0077  -2.9108   1.4071
 AFK  H1   H   HCR6  0   0.275  -3.9372  -1.3584   0.9044
 AFK  H2   H   HCR6  0   0.251  -4.9557   0.6966   0.0982
 AFK  H3   H   HCH3  0   0.244  -3.6501   3.7574  -0.0208
 AFK  H4   H   HCH3  0   0.241  -3.2294   3.3594  -1.6776
 AFK  H5   H   HCH3  0   0.242  -4.7825   2.8537  -1.0165
 AFK  H6   H   HCR6  0   0.244  -1.0902   2.3541  -0.6390
 AFK  H7   H   HCR6  0   0.268   2.9519  -1.3793  -1.3072
 AFK  H8   H   HCH2  0   0.247   4.9732  -0.6896   0.9582
 AFK  H9   H   HCH2  0   0.218   5.0230  -0.3777  -0.7603
 AFK  H10  H   HNH2  0   0.357   6.3211   1.1547   0.6602
 AFK  H11  H   HNH2  0   0.346   5.2345   1.9511  -0.2342
 AFK  H13  H   HCR6  0   0.253   3.0664   1.7274   1.6279
 AFK  H14  H   HCR6  0   0.255   0.6087   1.8170   1.6128
 AFK  H15  H   HCH3  0   0.258  -1.2907  -3.6732   1.7017
 AFK  H16  H   HCH3  0   0.226  -2.6823  -2.7214   2.2464
 AFK  H17  H   HCH3  0   0.226  -2.5932  -3.2851   0.5629

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
 AFK  C    O    single    1.412  0.020  1.412
 AFK  O    C1   single    1.345  0.020  1.345
 AFK  N    C12  single    1.450  0.020  1.450
 AFK  C1   C2   aromatic  1.390  0.020  1.390
 AFK  C1   C7   aromatic  1.403  0.020  1.403
 AFK  CL   C14  single    1.734  0.020  1.734
 AFK  C13  C14  aromatic  1.385  0.020  1.385
 AFK  C13  C11  aromatic  1.391  0.020  1.391
 AFK  C12  C11  single    1.508  0.020  1.508
 AFK  C2   C3   aromatic  1.391  0.020  1.391
 AFK  C14  C8   aromatic  1.393  0.020  1.393
 AFK  C11  C10  aromatic  1.391  0.020  1.391
 AFK  C8   C9   aromatic  1.393  0.020  1.393
 AFK  C8   C7   single    1.478  0.020  1.478
 AFK  C10  C9   aromatic  1.386  0.020  1.386
 AFK  C7   C6   aromatic  1.387  0.020  1.387
 AFK  C3   C4   aromatic  1.387  0.020  1.387
 AFK  C6   C4   aromatic  1.395  0.020  1.395
 AFK  C4   C5   single    1.502  0.020  1.502
 AFK  C2   H1   single    0.930  0.020  1.080
 AFK  C3   H2   single    0.930  0.020  1.080
 AFK  C5   H3   single    0.970  0.020  1.090
 AFK  C5   H4   single    0.970  0.020  1.090
 AFK  C5   H5   single    0.970  0.020  1.090
 AFK  C6   H6   single    0.930  0.020  1.080
 AFK  C13  H7   single    0.930  0.020  1.080
 AFK  C12  H8   single    0.970  0.020  1.090
 AFK  C12  H9   single    0.970  0.020  1.090
 AFK  N    H10  single    0.890  0.020  1.040
 AFK  N    H11  single    0.890  0.020  1.040
 AFK  C10  H13  single    0.930  0.020  1.080
 AFK  C9   H14  single    0.930  0.020  1.080
 AFK  C    H15  single    0.970  0.020  1.090
 AFK  C    H16  single    0.970  0.020  1.090
 AFK  C    H17  single    0.970  0.020  1.090

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
 AFK  O    C1   C7   116.19  3.000
 AFK  C7   C1   C2   119.38  3.000
 AFK  O    C1   C2   124.42  3.000
 AFK  H1   C2   C3   118.80  3.000
 AFK  H1   C2   C1   121.11  3.000
 AFK  C3   C2   C1   120.08  3.000
 AFK  H2   C3   C4   119.77  3.000
 AFK  H2   C3   C2   118.59  3.000
 AFK  C4   C3   C2   121.64  3.000
 AFK  C6   C4   C5   120.66  3.000
 AFK  C5   C4   C3   121.91  3.000
 AFK  C6   C4   C3   117.43  3.000
 AFK  H5   C5   H4   107.88  3.000
 AFK  H5   C5   H3   107.41  3.000
 AFK  H4   C5   H3   107.09  3.000
 AFK  H5   C5   C4   111.57  3.000
 AFK  H4   C5   C4   111.40  3.000
 AFK  H3   C5   C4   111.27  3.000
 AFK  H6   C6   C7   118.47  3.000
 AFK  H6   C6   C4   119.23  3.000
 AFK  C7   C6   C4   122.29  3.000
 AFK  C8   C14  C13  121.93  3.000
 AFK  C8   C14  CL   119.84  3.000
 AFK  C13  C14  CL   118.20  3.000
 AFK  H7   C13  C11  120.00  3.000
 AFK  H7   C13  C14  119.56  3.000
 AFK  C11  C13  C14  120.44  3.000
 AFK  C10  C11  C12  121.85  3.000
 AFK  C10  C11  C13  118.41  3.000
 AFK  C12  C11  C13  119.73  3.000
 AFK  H9   C12  H8   105.69  3.000
 AFK  H9   C12  N    114.05  3.000
 AFK  H8   C12  N    107.91  3.000
 AFK  H9   C12  C11  108.47  3.000
 AFK  H8   C12  C11  108.19  3.000
 AFK  N    C12  C11  112.18  3.000
 AFK  H11  N    H10  106.10  3.000
 AFK  H11  N    C12  109.57  3.000
 AFK  H10  N    C12  109.28  3.000
 AFK  H13  C10  C9   119.91  3.000
 AFK  H13  C10  C11  119.60  3.000
 AFK  C9   C10  C11  120.50  3.000
 AFK  H14  C9   C8   118.63  3.000
 AFK  H14  C9   C10  119.53  3.000
 AFK  C8   C9   C10  121.84  3.000
 AFK  C7   C8   C9   120.31  3.000
 AFK  C7   C8   C14  122.79  3.000
 AFK  C9   C8   C14  116.86  3.000
 AFK  C8   C7   C6   120.07  3.000
 AFK  C6   C7   C1   119.15  3.000
 AFK  C8   C7   C1   120.77  3.000
 AFK  C    O    C1   118.58  3.000
 AFK  H17  C    H16  108.76  3.000
 AFK  H17  C    H15  108.80  3.000
 AFK  H16  C    H15  108.68  3.000
 AFK  H17  C    O    111.91  3.000
 AFK  H16  C    O    112.05  3.000
 AFK  H15  C    O    106.53  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
 AFK  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 AFK  CONST_04  C4   C6   C7   C1     0.00   0.0  0
 AFK  CONST_05  C8   C7   C1   C2   180.00   0.0  0
 AFK  CONST_06  C6   C7   C1   C2     0.00   0.0  0
 AFK  CONST_07  C6   C4   C3   C2     0.00   0.0  0
 AFK  CONST_08  C7   C1   C2   C3     0.00   0.0  0
 AFK  CONST_09  C7   C6   C4   C3     0.00   0.0  0
 AFK  CONST_10  C8   C7   C6   C4   180.00   0.0  0
 AFK  CONST_13  C10  C11  C13  C14    0.00   0.0  0
 AFK  CONST_14  C10  C9   C8   C14    0.00   0.0  0
 AFK  CONST_15  C9   C8   C14  C13    0.00   0.0  0
 AFK  CONST_16  C7   C8   C14  C13  180.00   0.0  0
 AFK  CONST_17  C9   C10  C11  C13    0.00   0.0  0
 AFK  CONST_18  C8   C14  C13  C11    0.00   0.0  0
 AFK  CONST_19  C8   C9   C10  C11    0.00   0.0  0
 AFK  CONST_20  C7   C8   C9   C10  180.00   0.0  0
 AFK  CONST_21  C5   C4   C3   C2   180.00   0.0  0
 AFK  CONST_22  O    C1   C2   C3   180.00   0.0  0
 AFK  CONST_23  C7   C6   C4   C5   180.00   0.0  0
 AFK  CONST_24  O    C1   C7   C6   180.00   0.0  0
 AFK  CONST_25  C12  C11  C13  C14  180.00   0.0  0
 AFK  CONST_26  C11  C13  C14  CL   180.00   0.0  0
 AFK  CONST_27  C9   C8   C14  CL   180.00   0.0  0
 AFK  CONST_28  C7   C8   C14  CL     0.00   0.0  0
 AFK  CONST_29  C9   C10  C11  C12  180.00   0.0  0
 AFK  CONST_30  O    C1   C7   C8     0.00   0.0  0
 AFK  CONST_31  H2   C3   C2   C1   180.00   0.0  0
 AFK  CONST_32  H6   C6   C7   C1   180.00   0.0  0
 AFK  CONST_33  H1   C2   C3   C4   180.00   0.0  0
 AFK  CONST_34  H14  C9   C8   C14  180.00   0.0  0
 AFK  CONST_35  H13  C10  C11  C13  180.00   0.0  0
 AFK  CONST_36  H7   C13  C11  C10  180.00   0.0  0
 AFK  Var_01    N    C12  C11  C13  151.61  30.0  2
 AFK  Var_02    H3   C5   C4   C3   103.16  30.0  2
 AFK  Var_03    H15  C    O    C1   177.28  30.0  3
 AFK  Var_04    H10  N    C12  C11  172.45  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
 AFK  plan-1  C1   0.020
 AFK  plan-1  C2   0.020
 AFK  plan-1  C3   0.020
 AFK  plan-1  C4   0.020
 AFK  plan-1  C5   0.020
 AFK  plan-1  C6   0.020
 AFK  plan-1  C8   0.020
 AFK  plan-1  C7   0.020
 AFK  plan-1  O    0.020
 AFK  plan-1  H1   0.020
 AFK  plan-1  H2   0.020
 AFK  plan-1  H6   0.020
 AFK  plan-2  C14  0.020
 AFK  plan-2  CL   0.020
 AFK  plan-2  C13  0.020
 AFK  plan-2  C11  0.020
 AFK  plan-2  C12  0.020
 AFK  plan-2  C10  0.020
 AFK  plan-2  C9   0.020
 AFK  plan-2  C8   0.020
 AFK  plan-2  C7   0.020
 AFK  plan-2  H7   0.020
 AFK  plan-2  H13  0.020
 AFK  plan-2  H14  0.020

