# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 02:55:22 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: ~{N}-methylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cccnc1
#
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
 PJH  PJH  ~{N}-methylpyridine-3-carboxamide  ligand  18  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PJH
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
 PJH  C01  C  CH3   0  -0.515  32.7643  47.4864  15.7020
 PJH  C03  C  C     0   0.524  32.9685  49.8708  15.2556
 PJH  C04  C  CR6   0  -0.125  33.5163  51.1838  15.7132
 PJH  C05  C  CR16  0  -0.079  33.7519  51.4873  17.0514
 PJH  C07  C  CR16  0  -0.056  34.4801  53.5836  16.5545
 PJH  C08  C  CR16  0  -0.318  34.2679  53.3934  15.1963
 PJH  C09  C  CR16  0  -0.152  33.7677  52.1760  14.7711
 PJH  N02  N  NH1   0  -0.635  33.2351  48.8120  16.0305
 PJH  N06  N  N     0  -0.399  34.2204  52.6561  17.4679
 PJH  O10  O  O     0  -0.489  32.3162  49.7886  14.2231
 PJH  H1   H  HCH3  0   0.253  33.0712  46.8088  16.4931
 PJH  H2   H  HCH3  0   0.243  31.6776  47.4587  15.6275
 PJH  H3   H  HCH3  0   0.240  33.1826  47.1288  14.7602
 PJH  H4   H  HCR6  0   0.266  33.5321  50.7659  17.8314
 PJH  H5   H  HCR6  0   0.274  34.8709  54.5264  16.9194
 PJH  H6   H  HCR6  0   0.278  34.4890  54.1840  14.4930
 PJH  H7   H  HCR6  0   0.278  33.5828  51.9925  13.7209
 PJH  H8   H  HNH1  0   0.412  33.8786  48.9039  16.7980

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
 PJH  O10  C03  double    1.224  0.020  1.224
 PJH  C09  C08  aromatic  1.383  0.020  1.383
 PJH  C09  C04  aromatic  1.391  0.020  1.391
 PJH  C08  C07  aromatic  1.388  0.020  1.388
 PJH  C03  C04  single    1.494  0.020  1.494
 PJH  C03  N02  single    1.339  0.020  1.339
 PJH  C04  C05  aromatic  1.392  0.020  1.392
 PJH  C01  N02  single    1.444  0.020  1.444
 PJH  C07  N06  aromatic  1.327  0.020  1.327
 PJH  C05  N06  aromatic  1.326  0.020  1.326
 PJH  C01  H1   single    0.970  0.020  1.090
 PJH  C01  H2   single    0.970  0.020  1.090
 PJH  C01  H3   single    0.970  0.020  1.090
 PJH  C05  H4   single    0.930  0.020  1.080
 PJH  C07  H5   single    0.930  0.020  1.080
 PJH  C08  H6   single    0.930  0.020  1.080
 PJH  C09  H7   single    0.930  0.020  1.080
 PJH  N02  H8   single    0.860  0.020  1.020

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
 PJH  H3   C01  H2   108.36  3.000
 PJH  H3   C01  H1   108.42  3.000
 PJH  H2   C01  H1   108.41  3.000
 PJH  H3   C01  N02  111.85  3.000
 PJH  H2   C01  N02  111.34  3.000
 PJH  H1   C01  N02  108.35  3.000
 PJH  O10  C03  N02  122.76  3.000
 PJH  N02  C03  C04  116.40  3.000
 PJH  O10  C03  C04  120.84  3.000
 PJH  C09  C04  C05  117.70  3.000
 PJH  C05  C04  C03  123.22  3.000
 PJH  C09  C04  C03  119.04  3.000
 PJH  H4   C05  N06  115.57  3.000
 PJH  H4   C05  C04  120.78  3.000
 PJH  N06  C05  C04  123.62  3.000
 PJH  H5   C07  N06  116.53  3.000
 PJH  H5   C07  C08  120.25  3.000
 PJH  N06  C07  C08  123.22  3.000
 PJH  H6   C08  C09  121.18  3.000
 PJH  H6   C08  C07  120.35  3.000
 PJH  C09  C08  C07  118.47  3.000
 PJH  H7   C09  C08  120.63  3.000
 PJH  H7   C09  C04  120.36  3.000
 PJH  C08  C09  C04  119.01  3.000
 PJH  H8   N02  C03  119.78  3.000
 PJH  H8   N02  C01  117.77  3.000
 PJH  C03  N02  C01  121.96  3.000
 PJH  C07  N06  C05  117.95  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
 PJH  CONST_01  C07  C08  C09  C04     0.00   0.0  0
 PJH  CONST_02  C07  N06  C05  C04     0.00   0.0  0
 PJH  CONST_03  C08  C09  C04  C05     0.00   0.0  0
 PJH  CONST_04  C08  C07  N06  C05     0.00   0.0  0
 PJH  CONST_05  N06  C07  C08  C09     0.00   0.0  0
 PJH  CONST_06  N06  C05  C04  C09     0.00   0.0  0
 PJH  CONST_07  C08  C09  C04  C03   180.00   0.0  0
 PJH  CONST_08  N06  C05  C04  C03   180.00   0.0  0
 PJH  CONST_09  H6   C08  C09  C04   180.00   0.0  0
 PJH  CONST_10  H7   C09  C04  C05   180.00   0.0  0
 PJH  CONST_11  H5   C07  N06  C05   180.00   0.0  0
 PJH  CONST_12  H4   C05  N06  C07   180.00   0.0  0
 PJH  CONST_13  C04  C03  N02  C01   180.00   0.0  0
 PJH  CONST_14  H8   N02  C03  C04     0.00   0.0  0
 PJH  CONST_15  O10  C03  N02  C01     0.00   0.0  0
 PJH  Var_01    O10  C03  C04  C05   152.09  30.0  2
 PJH  Var_02    H1   C01  N02  C03  -177.83  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
 PJH  plan-1  C03  0.020
 PJH  plan-1  C04  0.020
 PJH  plan-1  C05  0.020
 PJH  plan-1  C07  0.020
 PJH  plan-1  C08  0.020
 PJH  plan-1  C09  0.020
 PJH  plan-1  N06  0.020
 PJH  plan-1  H4   0.020
 PJH  plan-1  H5   0.020
 PJH  plan-1  H6   0.020
 PJH  plan-1  H7   0.020
 PJH  plan-2  C01  0.020
 PJH  plan-2  C03  0.020
 PJH  plan-2  C04  0.020
 PJH  plan-2  N02  0.020
 PJH  plan-2  O10  0.020
 PJH  plan-2  H8   0.020

