# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:29:10 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: N-methyl-N-[2-(pyridin-2-yl)ethyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCc1ccccn1)C(=O)c2ccccc2
#
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
 WH1  WH1  N-methyl-N-[2-(pyridin-2-yl)ethyl]benzamide  ligand  34  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WH1
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
 WH1  N1   N  N     0  -0.417  -10.2906  -14.3217  -16.9351
 WH1  C4   C  CR16  0  -0.349  -12.1779  -12.9169  -16.5694
 WH1  C5   C  CR16  0  -0.148  -12.4647  -13.5747  -15.3834
 WH1  C6   C  CR16  0  -0.331  -11.6427  -14.6167  -14.9847
 WH1  C7   C  CR16  0  -0.078  -10.5722  -14.9501  -15.8018
 WH1  C8   C  C     0   0.517   -9.2533  -10.7469  -16.0778
 WH1  C10  C  CR16  0  -0.273   -8.8213   -9.1164  -14.2519
 WH1  C13  C  CR16  0  -0.245  -11.5150   -8.9849  -13.5948
 WH1  N    N  NT    0  -0.448   -9.8021  -10.6469  -17.3080
 WH1  C    C  CH3   0  -0.538  -10.7076   -9.5894  -17.7131
 WH1  O    O  O     0  -0.484   -8.3749  -11.5521  -15.7982
 WH1  C1   C  CH2   0  -0.314   -9.5028  -11.6456  -18.3184
 WH1  C11  C  CR16  0  -0.246   -9.2396   -8.3227  -13.1942
 WH1  C12  C  CR16  0  -0.255  -10.5866   -8.2594  -12.8604
 WH1  C14  C  CR16  0  -0.250  -11.1005   -9.7592  -14.6693
 WH1  C3   C  CR6   0   0.262  -11.0746  -13.3158  -17.3179
 WH1  C9   C  CR6   0  -0.061   -9.7516   -9.8255  -15.0072
 WH1  H7   H  HCR6  0   0.262  -12.8063  -12.1068  -16.9171
 WH1  H8   H  HCR6  0   0.272  -13.3151  -13.2773  -14.7837
 WH1  H9   H  HCR6  0   0.267  -11.8238  -15.1619  -14.0688
 WH1  H10  H  HCR6  0   0.259   -9.9126  -15.7662  -15.5260
 WH1  H14  H  HCR6  0   0.261  -12.5640   -8.9498  -13.3318
 WH1  H2   H  HCH3  0   0.269  -10.5742   -8.6999  -17.1042
 WH1  H    H  HCH3  0   0.259  -10.4901   -9.3176  -18.7461
 WH1  H1   H  HCH3  0   0.238  -11.7568   -9.8878  -17.6585
 WH1  H3   H  HCH2  0   0.257   -9.2416  -11.1369  -19.2490
 WH1  H4   H  HCH2  0   0.265   -8.6342  -12.2183  -18.0047
 WH1  H12  H  HCR6  0   0.261   -8.5127   -7.7589  -12.6244
 WH1  H13  H  HCR6  0   0.262  -10.9109   -7.6503  -12.0267
 WH1  H15  H  HCR6  0   0.259  -11.8333  -10.3231  -15.2326
 WH1  C2   C  CH2   0  -0.510  -10.6817  -12.5900  -18.5704
 WH1  H11  H  HCR6  0   0.261   -7.7687   -9.1741  -14.4981
 WH1  H6   H  HCH2  0   0.253  -11.5312  -12.0354  -18.9731
 WH1  H5   H  HCH2  0   0.264  -10.3791  -13.3076  -19.3356

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
 WH1  C    N    single    1.450  0.020  1.450
 WH1  C1   N    single    1.452  0.020  1.452
 WH1  C2   C1   single    1.531  0.020  1.531
 WH1  C3   C2   single    1.500  0.020  1.500
 WH1  C3   C4   aromatic  1.392  0.020  1.392
 WH1  C4   C5   aromatic  1.386  0.020  1.386
 WH1  C5   C6   aromatic  1.386  0.020  1.386
 WH1  C6   C7   aromatic  1.387  0.020  1.387
 WH1  C7   N1   aromatic  1.326  0.020  1.326
 WH1  N1   C3   aromatic  1.332  0.020  1.332
 WH1  N    C8   single    1.351  0.020  1.351
 WH1  C8   O    double    1.224  0.020  1.224
 WH1  C9   C8   single    1.498  0.020  1.498
 WH1  C9   C10  aromatic  1.392  0.020  1.392
 WH1  C10  C11  aromatic  1.387  0.020  1.387
 WH1  C11  C12  aromatic  1.389  0.020  1.389
 WH1  C12  C13  aromatic  1.388  0.020  1.388
 WH1  C13  C14  aromatic  1.388  0.020  1.388
 WH1  C14  C9   aromatic  1.392  0.020  1.392
 WH1  C4   H7   single    0.930  0.020  1.080
 WH1  C5   H8   single    0.930  0.020  1.080
 WH1  C6   H9   single    0.930  0.020  1.080
 WH1  C7   H10  single    0.930  0.020  1.080
 WH1  C10  H11  single    0.930  0.020  1.080
 WH1  C13  H14  single    0.930  0.020  1.080
 WH1  C    H2   single    0.970  0.020  1.090
 WH1  C    H    single    0.970  0.020  1.090
 WH1  C    H1   single    0.970  0.020  1.090
 WH1  C1   H3   single    0.970  0.020  1.090
 WH1  C1   H4   single    0.970  0.020  1.090
 WH1  C11  H12  single    0.930  0.020  1.080
 WH1  C12  H13  single    0.930  0.020  1.080
 WH1  C14  H15  single    0.930  0.020  1.080
 WH1  C2   H6   single    0.970  0.020  1.090
 WH1  C2   H5   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
 WH1  C3   N1   C7   118.60  3.000
 WH1  H7   C4   C3   120.12  3.000
 WH1  H7   C4   C5   120.65  3.000
 WH1  C3   C4   C5   119.23  3.000
 WH1  H8   C5   C6   120.89  3.000
 WH1  H8   C5   C4   120.41  3.000
 WH1  C6   C5   C4   118.70  3.000
 WH1  H9   C6   C7   120.46  3.000
 WH1  H9   C6   C5   121.57  3.000
 WH1  C7   C6   C5   117.97  3.000
 WH1  H10  C7   C6   120.01  3.000
 WH1  H10  C7   N1   116.40  3.000
 WH1  C6   C7   N1   123.59  3.000
 WH1  C9   C8   O    118.70  3.000
 WH1  C9   C8   N    118.05  3.000
 WH1  O    C8   N    123.25  3.000
 WH1  H11  C10  C9   119.94  3.000
 WH1  H11  C10  C11  119.81  3.000
 WH1  C9   C10  C11  120.24  3.000
 WH1  H14  C13  C14  119.73  3.000
 WH1  H14  C13  C12  120.18  3.000
 WH1  C14  C13  C12  120.09  3.000
 WH1  C1   N    C    115.85  3.000
 WH1  C1   N    C8   119.94  3.000
 WH1  C    N    C8   124.20  3.000
 WH1  H1   C    H    107.89  3.000
 WH1  H1   C    H2   108.28  3.000
 WH1  H    C    H2   107.61  3.000
 WH1  H1   C    N    112.75  3.000
 WH1  H    C    N    108.78  3.000
 WH1  H2   C    N    111.34  3.000
 WH1  H4   C1   H3   107.48  3.000
 WH1  H4   C1   C2   109.75  3.000
 WH1  H3   C1   C2   109.33  3.000
 WH1  H4   C1   N    109.05  3.000
 WH1  H3   C1   N    108.77  3.000
 WH1  C2   C1   N    112.33  3.000
 WH1  H12  C11  C12  120.07  3.000
 WH1  H12  C11  C10  119.81  3.000
 WH1  C12  C11  C10  120.11  3.000
 WH1  H13  C12  C11  120.08  3.000
 WH1  H13  C12  C13  120.08  3.000
 WH1  C11  C12  C13  119.84  3.000
 WH1  H15  C14  C9   120.31  3.000
 WH1  H15  C14  C13  119.42  3.000
 WH1  C9   C14  C13  120.26  3.000
 WH1  C2   C3   C4   121.21  3.000
 WH1  C4   C3   N1   121.91  3.000
 WH1  C2   C3   N1   116.83  3.000
 WH1  C14  C9   C10  119.44  3.000
 WH1  C14  C9   C8   121.68  3.000
 WH1  C10  C9   C8   118.60  3.000
 WH1  H5   C2   H6   106.92  3.000
 WH1  H5   C2   C3   109.86  3.000
 WH1  H6   C2   C3   110.49  3.000
 WH1  H5   C2   C1   107.90  3.000
 WH1  H6   C2   C1   110.28  3.000
 WH1  C3   C2   C1   111.26  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
 WH1  CONST_01  C5   C6   C7   N1      0.00   0.0  0
 WH1  CONST_02  C5   C4   C3   N1      0.00   0.0  0
 WH1  CONST_03  C7   N1   C3   C4      0.00   0.0  0
 WH1  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 WH1  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 WH1  CONST_06  C3   N1   C7   C6      0.00   0.0  0
 WH1  CONST_07  C13  C14  C9   C10     0.00   0.0  0
 WH1  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 WH1  CONST_09  C14  C9   C10  C11     0.00   0.0  0
 WH1  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 WH1  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 WH1  CONST_12  C9   C14  C13  C12     0.00   0.0  0
 WH1  CONST_13  C2   C3   C4   C5    180.00   0.0  0
 WH1  CONST_14  C2   C3   N1   C7    180.00   0.0  0
 WH1  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 WH1  CONST_16  C13  C14  C9   C8    180.00   0.0  0
 WH1  CONST_17  H9   C6   C7   N1    180.00   0.0  0
 WH1  CONST_18  H7   C4   C3   N1    180.00   0.0  0
 WH1  CONST_19  H10  C7   C6   C5    180.00   0.0  0
 WH1  CONST_20  H8   C5   C6   C7    180.00   0.0  0
 WH1  CONST_21  H15  C14  C9   C10   180.00   0.0  0
 WH1  CONST_22  H13  C12  C11  C10   180.00   0.0  0
 WH1  CONST_23  H12  C11  C12  C13   180.00   0.0  0
 WH1  CONST_24  H14  C13  C12  C11   180.00   0.0  0
 WH1  CONST_25  H11  C10  C11  C12   180.00   0.0  0
 WH1  CONST_26  C9   C8   N    C       0.00   0.0  0
 WH1  CONST_27  C9   C8   N    C1    180.00   0.0  0
 WH1  CONST_28  O    C8   N    C     180.00   0.0  0
 WH1  CONST_29  C1   N    C8   O       0.00   0.0  0
 WH1  Var_01    C1   C2   C3   N1    -76.20  30.0  2
 WH1  Var_02    N    C8   C9   C10  -130.45  30.0  2
 WH1  Var_03    C3   C2   C1   N     -59.31  30.0  1
 WH1  Var_04    C2   C1   N    C8    106.48  30.0  3
 WH1  Var_05    H2   C    N    C8     23.86  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
 WH1  plan-1  N1   0.020
 WH1  plan-1  C4   0.020
 WH1  plan-1  C5   0.020
 WH1  plan-1  C6   0.020
 WH1  plan-1  C7   0.020
 WH1  plan-1  C3   0.020
 WH1  plan-1  H7   0.020
 WH1  plan-1  H8   0.020
 WH1  plan-1  H9   0.020
 WH1  plan-1  H10  0.020
 WH1  plan-1  C2   0.020
 WH1  plan-2  C8   0.020
 WH1  plan-2  C10  0.020
 WH1  plan-2  C13  0.020
 WH1  plan-2  C11  0.020
 WH1  plan-2  C12  0.020
 WH1  plan-2  C14  0.020
 WH1  plan-2  C9   0.020
 WH1  plan-2  H14  0.020
 WH1  plan-2  H12  0.020
 WH1  plan-2  H13  0.020
 WH1  plan-2  H15  0.020
 WH1  plan-2  H11  0.020
 WH1  plan-3  C8   0.020
 WH1  plan-3  N    0.020
 WH1  plan-3  C    0.020
 WH1  plan-3  O    0.020
 WH1  plan-3  C1   0.020
 WH1  plan-3  C9   0.020

