# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:57:16 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: N~2~-methyl-N-(4-methylpyridin-2-yl)glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC(=O)Nc1cc(C)ccn1
#
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
 W04  W04  N~2~-methyl-N-(4-methylpyridin-2-yl)glycinamide  ligand  26  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W04
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
 W04  N1   N  NH1   0  -0.713  -4.0473  14.5388   1.6979
 W04  C4   C  CR16  0  -0.426  -2.5945  14.5327  -0.2942
 W04  C5   C  CR6   0   0.199  -1.3103  14.7086  -0.7894
 W04  C6   C  CH3   0  -0.724  -1.0284  14.5855  -2.2549
 W04  C7   C  CR16  0  -0.379  -0.2905  15.0140   0.1117
 W04  C8   C  CR16  0  -0.057  -0.6098  15.1334   1.4499
 W04  O    O  O     0  -0.453  -5.4282  13.8579   0.0198
 W04  C2   C  C     0   0.538  -5.2439  14.1377   1.1861
 W04  C1   C  CH2   0  -0.426  -6.3309  14.0548   2.2493
 W04  N    N  NH1   0  -0.581  -7.6457  13.9772   1.6773
 W04  C    C  CH3   0  -0.527  -8.1514  15.2543   1.2151
 W04  C3   C  CR6   0   0.493  -2.8082  14.6736   1.0790
 W04  N2   N  N     0  -0.459  -1.8357  14.9699   1.9318
 W04  H1   H  HNH1  0   0.407  -4.0132  14.7299   2.6897
 W04  H2   H  HCR6  0   0.280  -3.4076  14.2992  -0.9621
 W04  H3   H  HCH3  0   0.257  -0.6848  15.5380  -2.6611
 W04  H4   H  HCH3  0   0.255  -0.2401  13.8553  -2.4412
 W04  H5   H  HCH3  0   0.251  -1.9131  14.2823  -2.8119
 W04  H6   H  HCR6  0   0.260   0.7289  15.1588  -0.2214
 W04  H7   H  HCR6  0   0.264   0.1589  15.3739   2.1759
 W04  H8   H  HCH2  0   0.291  -6.1400  13.1452   2.8275
 W04  H9   H  HCH2  0   0.231  -6.2017  14.8944   2.9518
 W04  H10  H  HNH1  0   0.360  -8.2754  13.5969   2.3694
 W04  H12  H  HCH3  0   0.236  -9.1846  15.1408   0.8885
 W04  H13  H  HCH3  0   0.197  -8.1228  16.0463   1.9760
 W04  H14  H  HCH3  0   0.228  -7.5775  15.6012   0.3554

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
 W04  C6  C5   single    1.497  0.020  1.497
 W04  C5  C4   aromatic  1.388  0.020  1.388
 W04  C5  C7   aromatic  1.395  0.020  1.395
 W04  C4  C3   aromatic  1.397  0.020  1.397
 W04  C7  C8   aromatic  1.381  0.020  1.381
 W04  O   C2   double    1.213  0.020  1.213
 W04  C   N    single    1.449  0.020  1.449
 W04  C3  N1   single    1.392  0.020  1.392
 W04  C3  N2   aromatic  1.327  0.020  1.327
 W04  C2  N1   single    1.362  0.020  1.362
 W04  C2  C1   single    1.523  0.020  1.523
 W04  C8  N2   aromatic  1.327  0.020  1.327
 W04  N   C1   single    1.436  0.020  1.436
 W04  N1  H1   single    0.860  0.020  1.020
 W04  C4  H2   single    0.930  0.020  1.080
 W04  C6  H3   single    0.970  0.020  1.090
 W04  C6  H4   single    0.970  0.020  1.090
 W04  C6  H5   single    0.970  0.020  1.090
 W04  C7  H6   single    0.930  0.020  1.080
 W04  C8  H7   single    0.930  0.020  1.080
 W04  C1  H8   single    0.970  0.020  1.090
 W04  C1  H9   single    0.970  0.020  1.090
 W04  N   H10  single    0.890  0.020  1.040
 W04  C   H12  single    0.970  0.020  1.090
 W04  C   H13  single    0.970  0.020  1.090
 W04  C   H14  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
 W04  H1   N1  C3   112.84  3.000
 W04  H1   N1  C2   117.01  3.000
 W04  C3   N1  C2   130.07  3.000
 W04  H2   C4  C3   121.03  3.000
 W04  H2   C4  C5   120.30  3.000
 W04  C3   C4  C5   118.67  3.000
 W04  C7   C5  C6   120.84  3.000
 W04  C7   C5  C4   118.29  3.000
 W04  C6   C5  C4   120.87  3.000
 W04  H5   C6  H4   108.27  3.000
 W04  H5   C6  H3   107.97  3.000
 W04  H4   C6  H3   107.06  3.000
 W04  H5   C6  C5   111.76  3.000
 W04  H4   C6  C5   110.99  3.000
 W04  H3   C6  C5   110.61  3.000
 W04  H6   C7  C8   120.30  3.000
 W04  H6   C7  C5   121.27  3.000
 W04  C8   C7  C5   118.42  3.000
 W04  H7   C8  N2   116.04  3.000
 W04  H7   C8  C7   120.27  3.000
 W04  N2   C8  C7   123.69  3.000
 W04  C1   C2  O    123.38  3.000
 W04  C1   C2  N1   112.38  3.000
 W04  O    C2  N1   124.23  3.000
 W04  H9   C1  H8   106.02  3.000
 W04  H9   C1  N    113.73  3.000
 W04  H8   C1  N    108.97  3.000
 W04  H9   C1  C2   108.66  3.000
 W04  H8   C1  C2   106.83  3.000
 W04  N    C1  C2   112.23  3.000
 W04  H10  N   C    109.44  3.000
 W04  H10  N   C1   108.55  3.000
 W04  C    N   C1   113.51  3.000
 W04  H14  C   H13  107.64  3.000
 W04  H14  C   H12  107.22  3.000
 W04  H13  C   H12  107.90  3.000
 W04  H14  C   N    110.37  3.000
 W04  H13  C   N    113.91  3.000
 W04  H12  C   N    109.55  3.000
 W04  N2   C3  C4   122.83  3.000
 W04  N2   C3  N1   112.85  3.000
 W04  C4   C3  N1   124.32  3.000
 W04  C3   N2  C8   118.10  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
 W04  CONST_01  C8   C7  C5  C4     0.00   0.0  0
 W04  CONST_02  C8   N2  C3  C4     0.00   0.0  0
 W04  CONST_03  N2   C3  C4  C5     0.00   0.0  0
 W04  CONST_04  N2   C8  C7  C5     0.00   0.0  0
 W04  CONST_05  C3   C4  C5  C7     0.00   0.0  0
 W04  CONST_06  C3   N2  C8  C7     0.00   0.0  0
 W04  CONST_07  C5   C4  C3  N1   180.00   0.0  0
 W04  CONST_08  C8   N2  C3  N1   180.00   0.0  0
 W04  CONST_09  C3   C4  C5  C6   180.00   0.0  0
 W04  CONST_10  C8   C7  C5  C6   180.00   0.0  0
 W04  CONST_11  H6   C7  C5  C4   180.00   0.0  0
 W04  CONST_12  H7   C8  C7  C5   180.00   0.0  0
 W04  CONST_13  H2   C4  C5  C7   180.00   0.0  0
 W04  CONST_14  C2   N1  C3  C4     0.00   0.0  0
 W04  CONST_15  N2   C3  N1  C2   180.00   0.0  0
 W04  CONST_16  H1   N1  C3  C4   180.00   0.0  0
 W04  CONST_17  C3   N1  C2  O      0.00   0.0  0
 W04  CONST_18  C3   N1  C2  C1   180.00   0.0  0
 W04  Var_01    H3   C6  C5  C4   116.18  30.0  2
 W04  Var_02    N    C1  C2  N1   164.83  30.0  3
 W04  Var_03    C    N   C1  C2   -78.27  30.0  1
 W04  Var_04    H12  C   N   C1  -174.30  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
 W04  plan-1  N1  0.020
 W04  plan-1  C4  0.020
 W04  plan-1  C5  0.020
 W04  plan-1  C6  0.020
 W04  plan-1  C7  0.020
 W04  plan-1  C8  0.020
 W04  plan-1  C3  0.020
 W04  plan-1  N2  0.020
 W04  plan-1  H2  0.020
 W04  plan-1  H6  0.020
 W04  plan-1  H7  0.020
 W04  plan-2  N1  0.020
 W04  plan-2  O   0.020
 W04  plan-2  C2  0.020
 W04  plan-2  C1  0.020
 W04  plan-2  C3  0.020
 W04  plan-2  H1  0.020

