# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:24:09 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: N-[(pyridin-2-yl)methyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCc1ccccn1
#
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
 8UA  8UA  N-[(pyridin-2-yl)methyl]acetamide  ligand  21  11  .  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_8UA
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
 8UA  N1   N  NH1   0  -0.642  -1.4701   0.0951   0.2085
 8UA  C4   C  CR6   0   0.225   0.8715  -0.4730  -0.0704
 8UA  C5   C  CR16  0  -0.328   1.9090  -1.2960  -0.5019
 8UA  C6   C  CR16  0  -0.146   3.2111  -0.9279  -0.2187
 8UA  C7   C  CR16  0  -0.335   3.4396   0.2493   0.4843
 8UA  C8   C  CR16  0  -0.061   2.3442   0.9996   0.8707
 8UA  C1   C  CH3   0  -0.775  -3.6009   1.0107   0.8607
 8UA  C2   C  C     0   0.524  -2.7999  -0.0590   0.1622
 8UA  C3   C  CH2   0  -0.286  -0.5569  -0.8509  -0.3710
 8UA  N2   N  N     0  -0.453   1.0898   0.6480   0.6003
 8UA  O1   O  O     0  -0.514  -3.3327  -1.0125  -0.3939
 8UA  H1   H  HNH1  0   0.402  -1.0556   0.8887   0.6749
 8UA  H2   H  HCR6  0   0.270   1.6922  -2.2057  -1.0473
 8UA  H3   H  HCR6  0   0.276   4.0375  -1.5486  -0.5393
 8UA  H4   H  HCR6  0   0.273   4.4406   0.5773   0.7266
 8UA  H5   H  HCR6  0   0.267   2.4771   1.9235   1.4219
 8UA  H6   H  HCH3  0   0.248  -3.0067   1.8733   1.1563
 8UA  H7   H  HCH3  0   0.262  -4.4082   1.3485   0.2125
 8UA  H8   H  HCH3  0   0.266  -4.0583   0.5891   1.7567
 8UA  H9   H  HCH2  0   0.263  -0.7479  -1.8585   0.0102
 8UA  H10  H  HCH2  0   0.263  -0.6876  -0.9070  -1.4569

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
 8UA  C8  C7   aromatic  1.383  0.020  1.383
 8UA  C8  N2   aromatic  1.331  0.020  1.331
 8UA  C7  C6   aromatic  1.390  0.020  1.390
 8UA  N2  C4   aromatic  1.324  0.020  1.324
 8UA  C6  C5   aromatic  1.382  0.020  1.382
 8UA  C4  C5   aromatic  1.393  0.020  1.393
 8UA  C4  C3   single    1.508  0.020  1.508
 8UA  C3  N1   single    1.437  0.020  1.437
 8UA  N1  C2   single    1.339  0.020  1.339
 8UA  C2  C1   single    1.508  0.020  1.508
 8UA  C2  O1   double    1.226  0.020  1.226
 8UA  N1  H1   single    0.860  0.020  1.020
 8UA  C5  H2   single    0.930  0.020  1.080
 8UA  C6  H3   single    0.930  0.020  1.080
 8UA  C7  H4   single    0.930  0.020  1.080
 8UA  C8  H5   single    0.930  0.020  1.080
 8UA  C1  H6   single    0.970  0.020  1.090
 8UA  C1  H7   single    0.970  0.020  1.090
 8UA  C1  H8   single    0.970  0.020  1.090
 8UA  C3  H9   single    0.970  0.020  1.090
 8UA  C3  H10  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
 8UA  H1   N1  C3  116.29  3.000
 8UA  H1   N1  C2  120.93  3.000
 8UA  C3   N1  C2  122.77  3.000
 8UA  N2   C4  C3  117.99  3.000
 8UA  C3   C4  C5  119.72  3.000
 8UA  N2   C4  C5  122.29  3.000
 8UA  H2   C5  C6  121.04  3.000
 8UA  H2   C5  C4  120.23  3.000
 8UA  C6   C5  C4  118.74  3.000
 8UA  H3   C6  C7  120.67  3.000
 8UA  H3   C6  C5  120.39  3.000
 8UA  C7   C6  C5  118.94  3.000
 8UA  H4   C7  C8  120.42  3.000
 8UA  H4   C7  C6  121.50  3.000
 8UA  C8   C7  C6  118.08  3.000
 8UA  H5   C8  N2  116.36  3.000
 8UA  H5   C8  C7  120.50  3.000
 8UA  N2   C8  C7  123.14  3.000
 8UA  H8   C1  H7  107.33  3.000
 8UA  H8   C1  H6  108.18  3.000
 8UA  H7   C1  H6  108.69  3.000
 8UA  H8   C1  C2  109.21  3.000
 8UA  H7   C1  C2  109.77  3.000
 8UA  H6   C1  C2  113.46  3.000
 8UA  O1   C2  C1  122.08  3.000
 8UA  O1   C2  N1  122.46  3.000
 8UA  C1   C2  N1  115.45  3.000
 8UA  H10  C3  H9  106.11  3.000
 8UA  H10  C3  C4  108.88  3.000
 8UA  H9   C3  C4  109.07  3.000
 8UA  H10  C3  N1  110.96  3.000
 8UA  H9   C3  N1  110.78  3.000
 8UA  C4   C3  N1  110.89  3.000
 8UA  C8   N2  C4  118.81  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
 8UA  CONST_01  C7  C8  N2  C4     0.00   0.0  0
 8UA  CONST_02  C7  C6  C5  C4     0.00   0.0  0
 8UA  CONST_03  C8  C7  C6  C5     0.00   0.0  0
 8UA  CONST_04  C8  N2  C4  C5     0.00   0.0  0
 8UA  CONST_05  N2  C8  C7  C6     0.00   0.0  0
 8UA  CONST_06  N2  C4  C5  C6     0.00   0.0  0
 8UA  CONST_07  C3  C4  C5  C6   180.00   0.0  0
 8UA  CONST_08  C3  C4  N2  C8   180.00   0.0  0
 8UA  CONST_09  H5  C8  N2  C4   180.00   0.0  0
 8UA  CONST_10  H3  C6  C5  C4   180.00   0.0  0
 8UA  CONST_11  H4  C7  C6  C5   180.00   0.0  0
 8UA  CONST_12  H2  C5  C6  C7   180.00   0.0  0
 8UA  CONST_13  C3  N1  C2  C1   180.00   0.0  0
 8UA  CONST_14  O1  C2  N1  C3     0.00   0.0  0
 8UA  CONST_15  H1  N1  C2  C1     0.00   0.0  0
 8UA  Var_01    N2  C4  C3  N1    -2.72  30.0  2
 8UA  Var_02    C2  N1  C3  C4  -175.51  30.0  3
 8UA  Var_03    H6  C1  C2  N1    10.81  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
 8UA  plan-1  C4  0.020
 8UA  plan-1  C5  0.020
 8UA  plan-1  C6  0.020
 8UA  plan-1  C7  0.020
 8UA  plan-1  C8  0.020
 8UA  plan-1  C3  0.020
 8UA  plan-1  N2  0.020
 8UA  plan-1  H2  0.020
 8UA  plan-1  H3  0.020
 8UA  plan-1  H4  0.020
 8UA  plan-1  H5  0.020
 8UA  plan-2  N1  0.020
 8UA  plan-2  C1  0.020
 8UA  plan-2  C2  0.020
 8UA  plan-2  C3  0.020
 8UA  plan-2  O1  0.020
 8UA  plan-2  H1  0.020

