# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 13:35:41 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: 3-methylpyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccnc1
#
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
 3MP  3MP  '3-methylpyridine         '  ligand  14  7  .  2021-08-04  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3MP
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
 3MP  CB   C  CH3   0  -0.723   0.0087  -0.0153   2.4601
 3MP  CG   C  CR6   0   0.010   0.0305  -0.0173   0.9622
 3MP  CD1  C  CR16  0  -0.181   1.2226   0.0424   0.2456
 3MP  CD2  C  CR16  0  -0.105  -1.1452  -0.0720   0.2193
 3MP  CE1  C  CR16  0  -0.319   1.1880   0.0465  -1.1388
 3MP  CZ   C  CR16  0  -0.077  -0.0461  -0.0094  -1.7712
 3MP  NE2  N  N     0  -0.400  -1.1936  -0.0679  -1.1081
 3MP  HB1  H  HCH3  0   0.250   0.6913  -0.7624   2.8660
 3MP  HB2  H  HCH3  0   0.252   0.3177   0.9533   2.8564
 3MP  HB3  H  HCH3  0   0.246  -0.9881  -0.2280   2.8444
 3MP  HD1  H  HCR6  0   0.265   2.1707   0.0844   0.7691
 3MP  HD2  H  HCR6  0   0.253  -2.1005  -0.1245   0.7342
 3MP  HE1  H  HCR6  0   0.269   2.0978   0.0910  -1.7219
 3MP  HZ   H  HCR6  0   0.260  -0.1077  -0.0082  -2.8539

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
 3MP  CB   CG   single    1.498  0.020  1.498
 3MP  CB   HB1  single    0.970  0.020  1.090
 3MP  CB   HB2  single    0.970  0.020  1.090
 3MP  CB   HB3  single    0.970  0.020  1.090
 3MP  CG   CD1  aromatic  1.392  0.020  1.392
 3MP  CG   CD2  aromatic  1.392  0.020  1.392
 3MP  CD1  CE1  aromatic  1.385  0.020  1.385
 3MP  CD1  HD1  single    0.930  0.020  1.080
 3MP  CD2  NE2  aromatic  1.328  0.020  1.328
 3MP  CD2  HD2  single    0.930  0.020  1.080
 3MP  CE1  CZ   aromatic  1.388  0.020  1.388
 3MP  CE1  HE1  single    0.930  0.020  1.080
 3MP  CZ   NE2  aromatic  1.327  0.020  1.327
 3MP  CZ   HZ   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
 3MP  HB3  CB   HB2  107.72  3.000
 3MP  HB3  CB   HB1  107.93  3.000
 3MP  HB2  CB   HB1  107.20  3.000
 3MP  HB3  CB   CG   111.45  3.000
 3MP  HB2  CB   CG   111.11  3.000
 3MP  HB1  CB   CG   111.24  3.000
 3MP  CD2  CG   CD1  116.76  3.000
 3MP  CD2  CG   CB   121.43  3.000
 3MP  CD1  CG   CB   121.80  3.000
 3MP  HD1  CD1  CE1  120.30  3.000
 3MP  HD1  CD1  CG   120.14  3.000
 3MP  CE1  CD1  CG   119.56  3.000
 3MP  HD2  CD2  NE2  116.21  3.000
 3MP  HD2  CD2  CG   119.45  3.000
 3MP  NE2  CD2  CG   124.34  3.000
 3MP  HE1  CE1  CZ   120.27  3.000
 3MP  HE1  CE1  CD1  121.20  3.000
 3MP  CZ   CE1  CD1  118.53  3.000
 3MP  HZ   CZ   NE2  116.74  3.000
 3MP  HZ   CZ   CE1  120.36  3.000
 3MP  NE2  CZ   CE1  122.90  3.000
 3MP  CZ   NE2  CD2  117.91  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
 3MP  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 3MP  CONST_02  CZ   NE2  CD2  CG     0.00   0.0  0
 3MP  CONST_03  NE2  CD2  CG   CD1    0.00   0.0  0
 3MP  CONST_04  NE2  CZ   CE1  CD1    0.00   0.0  0
 3MP  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 3MP  CONST_06  CE1  CZ   NE2  CD2    0.00   0.0  0
 3MP  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 3MP  CONST_08  NE2  CD2  CG   CB   180.00   0.0  0
 3MP  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 3MP  CONST_10  HD2  CD2  CG   CD1  180.00   0.0  0
 3MP  CONST_11  HZ   CZ   CE1  CD1  180.00   0.0  0
 3MP  CONST_12  HD1  CD1  CG   CD2  180.00   0.0  0
 3MP  Var_01    HB1  CB   CG   CD1  -50.30  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
 3MP  plan-1  CB   0.020
 3MP  plan-1  CG   0.020
 3MP  plan-1  CD1  0.020
 3MP  plan-1  CD2  0.020
 3MP  plan-1  CE1  0.020
 3MP  plan-1  CZ   0.020
 3MP  plan-1  NE2  0.020
 3MP  plan-1  HD1  0.020
 3MP  plan-1  HD2  0.020
 3MP  plan-1  HE1  0.020
 3MP  plan-1  HZ   0.020

