# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 16:40:17 2021
#   Inital geometry file: a 46 line input string
#   Ligand name: 2,4-dimethylpyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(C)c1
#
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
 RVV  RVV  '2,4-dimethylpyridine     '  ligand  17  8  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RVV
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
 RVV  C01   C  CH3   0  -0.723  -5.4516  2.3246  28.4174
 RVV  C02   C  CR6   0   0.192  -5.5445  2.1018  26.9395
 RVV  C03   C  CR16  0  -0.374  -4.8424  2.8963  26.0426
 RVV  C04   C  CR6   0   0.243  -4.9633  2.6827  24.6710
 RVV  C06   C  CR16  0  -0.071  -6.4184  0.9633  25.0274
 RVV  C07   C  CR16  0  -0.374  -6.3551  1.1043  26.4018
 RVV  C08   C  CH3   0  -0.731  -4.1945  3.5299  23.7012
 RVV  N05   N  N     0  -0.435  -5.7437  1.7265  24.1729
 RVV  H013  H  HCH3  0   0.258  -6.1288  3.1237  28.7251
 RVV  H011  H  HCH3  0   0.249  -5.7268  1.4305  28.9750
 RVV  H012  H  HCH3  0   0.251  -4.4462  2.6208  28.7137
 RVV  H031  H  HCR6  0   0.253  -4.1953  3.6871  26.4049
 RVV  H061  H  HCR6  0   0.256  -7.0448  0.1926  24.5906
 RVV  H071  H  HCR6  0   0.259  -6.9284  0.4467  27.0426
 RVV  H082  H  HCH3  0   0.247  -4.4827  3.3045  22.6766
 RVV  H081  H  HCH3  0   0.248  -4.3636  4.5919  23.8828
 RVV  H083  H  HCH3  0   0.251  -3.1211  3.3565  23.7981

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
 RVV  C08  C04   single    1.500  0.020  1.500
 RVV  N05  C04   aromatic  1.331  0.020  1.331
 RVV  N05  C06   aromatic  1.330  0.020  1.330
 RVV  C04  C03   aromatic  1.393  0.020  1.393
 RVV  C06  C07   aromatic  1.383  0.020  1.383
 RVV  C03  C02   aromatic  1.389  0.020  1.389
 RVV  C07  C02   aromatic  1.393  0.020  1.393
 RVV  C02  C01   single    1.498  0.020  1.498
 RVV  C01  H013  single    0.970  0.020  1.090
 RVV  C01  H011  single    0.970  0.020  1.090
 RVV  C01  H012  single    0.970  0.020  1.090
 RVV  C03  H031  single    0.930  0.020  1.080
 RVV  C06  H061  single    0.930  0.020  1.080
 RVV  C07  H071  single    0.930  0.020  1.080
 RVV  C08  H082  single    0.970  0.020  1.090
 RVV  C08  H081  single    0.970  0.020  1.090
 RVV  C08  H083  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
 RVV  H012  C01  H011  108.50  3.000
 RVV  H012  C01  H013  107.26  3.000
 RVV  H011  C01  H013  107.45  3.000
 RVV  H012  C01  C02   111.48  3.000
 RVV  H011  C01  C02   111.56  3.000
 RVV  H013  C01  C02   110.40  3.000
 RVV  C07   C02  C03   117.03  3.000
 RVV  C07   C02  C01   121.56  3.000
 RVV  C03   C02  C01   121.40  3.000
 RVV  H031  C03  C04   119.50  3.000
 RVV  H031  C03  C02   120.22  3.000
 RVV  C04   C03  C02   120.28  3.000
 RVV  N05   C04  C08   117.67  3.000
 RVV  N05   C04  C03   121.96  3.000
 RVV  C08   C04  C03   120.36  3.000
 RVV  H061  C06  N05   116.23  3.000
 RVV  H061  C06  C07   119.93  3.000
 RVV  N05   C06  C07   123.84  3.000
 RVV  H071  C07  C06   120.14  3.000
 RVV  H071  C07  C02   120.97  3.000
 RVV  C06   C07  C02   118.89  3.000
 RVV  H083  C08  H081  107.00  3.000
 RVV  H083  C08  H082  108.13  3.000
 RVV  H081  C08  H082  108.51  3.000
 RVV  H083  C08  C04   110.91  3.000
 RVV  H081  C08  C04   111.27  3.000
 RVV  H082  C08  C04   110.86  3.000
 RVV  C06   N05  C04   118.00  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
 RVV  CONST_01  N05   C04  C03  C02     0.00   0.0  0
 RVV  CONST_02  N05   C06  C07  C02     0.00   0.0  0
 RVV  CONST_03  C06   N05  C04  C03     0.00   0.0  0
 RVV  CONST_04  C06   C07  C02  C03     0.00   0.0  0
 RVV  CONST_05  C07   C06  N05  C04     0.00   0.0  0
 RVV  CONST_06  C07   C02  C03  C04     0.00   0.0  0
 RVV  CONST_07  C04   C03  C02  C01   180.00   0.0  0
 RVV  CONST_08  C06   C07  C02  C01   180.00   0.0  0
 RVV  CONST_09  C08   C04  C03  C02   180.00   0.0  0
 RVV  CONST_10  C08   C04  N05  C06   180.00   0.0  0
 RVV  CONST_11  H061  C06  C07  C02   180.00   0.0  0
 RVV  CONST_12  H071  C07  C02  C03   180.00   0.0  0
 RVV  CONST_13  H031  C03  C02  C07   180.00   0.0  0
 RVV  Var_01    H082  C08  C04  C03  -173.93  30.0  2
 RVV  Var_02    H013  C01  C02  C03    82.47  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
 RVV  plan-1  C01   0.020
 RVV  plan-1  C02   0.020
 RVV  plan-1  C03   0.020
 RVV  plan-1  C04   0.020
 RVV  plan-1  C06   0.020
 RVV  plan-1  C07   0.020
 RVV  plan-1  C08   0.020
 RVV  plan-1  N05   0.020
 RVV  plan-1  H031  0.020
 RVV  plan-1  H061  0.020
 RVV  plan-1  H071  0.020

