# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:50:30 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 2-fluoro-4-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C(N)=O)c(F)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
 K3M  K3M  2-fluoro-4-methylbenzamide  ligand  19  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K3M
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
 K3M  C4  C  CR6   0  -0.265  -0.5734   0.2969  -0.1209
 K3M  C5  C  C     0   0.487  -2.0629   0.3356  -0.2413
 K3M  C6  C  CR6   0   0.563   0.1063  -0.8989   0.0717
 K3M  C7  C  CR16  0  -0.449   1.4821  -0.9677   0.1449
 K3M  N   N  NH2   0  -0.798  -2.6485   1.3824   0.3578
 K3M  C   C  CH3   0  -0.721   3.7408   0.1198   0.0418
 K3M  O   O  O     0  -0.476  -2.6818  -0.5166  -0.8604
 K3M  C1  C  CR6   0   0.113   2.2443   0.1890   0.0033
 K3M  C2  C  CR16  0  -0.302   1.5830   1.3988  -0.1952
 K3M  C3  C  CR16  0  -0.239   0.2002   1.4491  -0.2516
 K3M  F   F  F     0  -0.301  -0.5871  -2.0320   0.2360
 K3M  H1  H  HCR6  0   0.276   1.9577  -1.9253   0.3199
 K3M  H2  H  HNH2  0   0.414  -2.1404   2.0186   0.9474
 K3M  H3  H  HNH2  0   0.407  -3.6468   1.5035   0.2984
 K3M  H4  H  HCH3  0   0.258   4.1382  -0.1380  -0.9419
 K3M  H5  H  HCH3  0   0.250   4.1768   1.0749   0.3307
 K3M  H6  H  HCH3  0   0.251   4.0879  -0.6411   0.7399
 K3M  H7  H  HCR6  0   0.260   2.1544   2.3113  -0.3097
 K3M  H8  H  HCR6  0   0.275  -0.2851   2.4020  -0.4212

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
 K3M  F   C6  single    1.339  0.020  1.339
 K3M  C7  C6  aromatic  1.380  0.020  1.380
 K3M  C7  C1  aromatic  1.392  0.020  1.392
 K3M  C   C1  single    1.499  0.020  1.499
 K3M  C6  C4  aromatic  1.389  0.020  1.389
 K3M  N   C5  single    1.341  0.020  1.341
 K3M  C1  C2  aromatic  1.393  0.020  1.393
 K3M  C4  C5  single    1.495  0.020  1.495
 K3M  C4  C3  aromatic  1.394  0.020  1.394
 K3M  C2  C3  aromatic  1.385  0.020  1.385
 K3M  C5  O   double    1.222  0.020  1.222
 K3M  C7  H1  single    0.930  0.020  1.080
 K3M  N   H2  single    0.860  0.020  1.020
 K3M  N   H3  single    0.860  0.020  1.020
 K3M  C   H4  single    0.970  0.020  1.090
 K3M  C   H5  single    0.970  0.020  1.090
 K3M  C   H6  single    0.970  0.020  1.090
 K3M  C2  H7  single    0.930  0.020  1.080
 K3M  C3  H8  single    0.930  0.020  1.080

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
 K3M  C3  C4  C6  116.94  3.000
 K3M  C3  C4  C5  121.60  3.000
 K3M  C6  C4  C5  121.41  3.000
 K3M  O   C5  N   123.35  3.000
 K3M  O   C5  C4  121.84  3.000
 K3M  N   C5  C4  114.80  3.000
 K3M  F   C6  C7  117.90  3.000
 K3M  C7  C6  C4  122.57  3.000
 K3M  F   C6  C4  119.49  3.000
 K3M  H1  C7  C1  120.69  3.000
 K3M  H1  C7  C6  119.37  3.000
 K3M  C1  C7  C6  119.94  3.000
 K3M  H3  N   H2  117.35  3.000
 K3M  H3  N   C5  120.02  3.000
 K3M  H2  N   C5  122.37  3.000
 K3M  H6  C   H5  108.37  3.000
 K3M  H6  C   H4  107.24  3.000
 K3M  H5  C   H4  107.48  3.000
 K3M  H6  C   C1  111.52  3.000
 K3M  H5  C   C1  111.48  3.000
 K3M  H4  C   C1  110.56  3.000
 K3M  C2  C1  C   121.18  3.000
 K3M  C2  C1  C7  118.43  3.000
 K3M  C   C1  C7  120.38  3.000
 K3M  H7  C2  C3  119.48  3.000
 K3M  H7  C2  C1  119.77  3.000
 K3M  C3  C2  C1  120.75  3.000
 K3M  H8  C3  C2  119.07  3.000
 K3M  H8  C3  C4  119.57  3.000
 K3M  C2  C3  C4  121.35  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
 K3M  CONST_01  C1  C7  C6  C4    0.00   0.0  0
 K3M  CONST_02  C1  C2  C3  C4    0.00   0.0  0
 K3M  CONST_03  C2  C1  C7  C6    0.00   0.0  0
 K3M  CONST_04  C2  C3  C4  C6    0.00   0.0  0
 K3M  CONST_05  C3  C4  C6  C7    0.00   0.0  0
 K3M  CONST_06  C3  C2  C1  C7    0.00   0.0  0
 K3M  CONST_07  C7  C6  C4  C5  180.00   0.0  0
 K3M  CONST_08  C2  C3  C4  C5  180.00   0.0  0
 K3M  CONST_09  C   C1  C7  C6  180.00   0.0  0
 K3M  CONST_10  C3  C2  C1  C   180.00   0.0  0
 K3M  CONST_11  F   C6  C7  C1  180.00   0.0  0
 K3M  CONST_12  F   C6  C4  C3  180.00   0.0  0
 K3M  CONST_13  H1  C7  C6  C4  180.00   0.0  0
 K3M  CONST_14  H7  C2  C3  C4  180.00   0.0  0
 K3M  CONST_15  H8  C3  C4  C6  180.00   0.0  0
 K3M  CONST_16  H2  N   C5  C4    0.00   0.0  0
 K3M  CONST_17  H3  N   C5  C4  180.00   0.0  0
 K3M  Var_01    N   C5  C4  C6  141.39  30.0  2
 K3M  Var_02    H4  C   C1  C7   84.12  30.0  2

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
 K3M  plan-1  C4  0.020
 K3M  plan-1  C5  0.020
 K3M  plan-1  C6  0.020
 K3M  plan-1  C7  0.020
 K3M  plan-1  C   0.020
 K3M  plan-1  C1  0.020
 K3M  plan-1  C2  0.020
 K3M  plan-1  C3  0.020
 K3M  plan-1  F   0.020
 K3M  plan-1  H1  0.020
 K3M  plan-1  H7  0.020
 K3M  plan-1  H8  0.020
 K3M  plan-2  C4  0.020
 K3M  plan-2  C5  0.020
 K3M  plan-2  N   0.020
 K3M  plan-2  O   0.020
 K3M  plan-2  H2  0.020
 K3M  plan-2  H3  0.020

