# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:47:32 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 3-propyl-5-pyridin-3-yl-1H-pyrazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC1=NC(=CNC1=O)c2cccnc2
#
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
 V2Z  V2Z  3-propyl-5-pyridin-3-yl-1H-pyrazin-2-one  ligand  29  16  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V2Z
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
 V2Z  N10   N  N     0  -0.393  -0.5372  -0.1850   0.0195
 V2Z  C11   C  CR6   0   0.088  -1.7579   0.2263   0.0130
 V2Z  C12   C  CR6   0   0.522  -2.1041   1.6527   0.0068
 V2Z  C14   C  CH3   0  -0.665  -3.6616  -3.1506   0.0036
 V2Z  C15   C  CH2   0  -0.416  -2.4653  -2.2104  -0.0140
 V2Z  C16   C  CH2   0  -0.483  -2.8902  -0.7506   0.0127
 V2Z  C7    C  CR6   0   0.160   0.5147   0.6836   0.0201
 V2Z  C6    C  CR16  0  -0.003   0.2744   2.0214   0.0042
 V2Z  C8    C  CR6   0  -0.043   1.8611   0.0908   0.0312
 V2Z  C9    C  CR16  0  -0.182   2.0307  -1.2909  -0.0515
 V2Z  C4    C  CR16  0  -0.120   3.0230   0.8609   0.1274
 V2Z  N3    N  N     0  -0.398   4.2481   0.3588   0.1387
 V2Z  C2    C  CR16  0  -0.076   4.3889  -0.9599   0.0565
 V2Z  C1    C  CR16  0  -0.309   3.3087  -1.8226  -0.0385
 V2Z  O6    O  O     0  -0.471  -3.2442   2.0940   0.0074
 V2Z  N7    N  NR16  0  -0.639  -1.0032   2.4654  -0.0023
 V2Z  H161  H  HCH2  0   0.253  -3.5169  -0.5584   0.8914
 V2Z  H162  H  HCH2  0   0.252  -3.5397  -0.5342  -0.8430
 V2Z  H7    H  HNR6  0   0.434  -1.1645   3.4647  -0.0089
 V2Z  H141  H  HCH3  0   0.218  -4.3101  -2.9909  -0.8597
 V2Z  H142  H  HCH3  0   0.230  -3.3407  -4.1925  -0.0155
 V2Z  H143  H  HCH3  0   0.218  -4.2679  -3.0102   0.9004
 V2Z  H151  H  HCH2  0   0.221  -1.8166  -2.4210   0.8389
 V2Z  H152  H  HCH2  0   0.221  -1.8607  -2.3990  -0.9040
 V2Z  H6    H  HCR6  0   0.315   1.0353   2.7863  -0.0065
 V2Z  H9    H  HCR6  0   0.275   1.1683  -1.9389  -0.1253
 V2Z  H4    H  HCR6  0   0.255   2.9646   1.9413   0.2039
 V2Z  H1    H  HCR6  0   0.271   3.4654  -2.8907  -0.1017
 V2Z  H2    H  HCR6  0   0.265   5.4027  -1.3435   0.0687

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
 V2Z  N10  C11   double    1.288  0.020  1.288
 V2Z  N10  C7    single    1.364  0.020  1.364
 V2Z  C11  C12   single    1.468  0.020  1.468
 V2Z  C11  C16   single    1.495  0.020  1.495
 V2Z  C12  O6    double    1.223  0.020  1.223
 V2Z  C12  N7    single    1.368  0.020  1.368
 V2Z  C14  C15   single    1.522  0.020  1.522
 V2Z  C15  C16   single    1.521  0.020  1.521
 V2Z  C7   C6    double    1.359  0.020  1.359
 V2Z  C7   C8    single    1.471  0.020  1.471
 V2Z  C6   N7    single    1.353  0.020  1.353
 V2Z  C8   C9    aromatic  1.395  0.020  1.395
 V2Z  C8   C4    aromatic  1.397  0.020  1.397
 V2Z  C9   C1    aromatic  1.384  0.020  1.384
 V2Z  C4   N3    aromatic  1.324  0.020  1.324
 V2Z  N3   C2    aromatic  1.329  0.020  1.329
 V2Z  C2   C1    aromatic  1.386  0.020  1.386
 V2Z  C16  H161  single    0.970  0.020  1.090
 V2Z  C16  H162  single    0.970  0.020  1.090
 V2Z  N7   H7    single    0.860  0.020  1.020
 V2Z  C14  H141  single    0.970  0.020  1.090
 V2Z  C14  H142  single    0.970  0.020  1.090
 V2Z  C14  H143  single    0.970  0.020  1.090
 V2Z  C15  H151  single    0.970  0.020  1.090
 V2Z  C15  H152  single    0.970  0.020  1.090
 V2Z  C6   H6    single    0.930  0.020  1.080
 V2Z  C9   H9    single    0.930  0.020  1.080
 V2Z  C4   H4    single    0.930  0.020  1.080
 V2Z  C1   H1    single    0.930  0.020  1.080
 V2Z  C2   H2    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
 V2Z  C7    N10  C11   121.83  3.000
 V2Z  C16   C11  C12   117.14  3.000
 V2Z  C16   C11  N10   120.59  3.000
 V2Z  C12   C11  N10   122.26  3.000
 V2Z  N7    C12  O6    122.40  3.000
 V2Z  N7    C12  C11   112.80  3.000
 V2Z  O6    C12  C11   124.80  3.000
 V2Z  H143  C14  H142  107.50  3.000
 V2Z  H143  C14  H141  107.51  3.000
 V2Z  H142  C14  H141  107.51  3.000
 V2Z  H143  C14  C15   111.51  3.000
 V2Z  H142  C14  C15   111.03  3.000
 V2Z  H141  C14  C15   111.57  3.000
 V2Z  H152  C15  H151  105.92  3.000
 V2Z  H152  C15  C16   109.56  3.000
 V2Z  H151  C15  C16   109.72  3.000
 V2Z  H152  C15  C14   109.74  3.000
 V2Z  H151  C15  C14   109.81  3.000
 V2Z  C16   C15  C14   111.92  3.000
 V2Z  H162  C16  H161  104.62  3.000
 V2Z  H162  C16  C15   109.97  3.000
 V2Z  H161  C16  C15   110.01  3.000
 V2Z  H162  C16  C11   108.65  3.000
 V2Z  H161  C16  C11   108.55  3.000
 V2Z  C15   C16  C11   114.55  3.000
 V2Z  C8    C7   C6    123.95  3.000
 V2Z  C8    C7   N10   116.69  3.000
 V2Z  C6    C7   N10   119.36  3.000
 V2Z  H6    C6   N7    115.68  3.000
 V2Z  H6    C6   C7    124.97  3.000
 V2Z  N7    C6   C7    119.35  3.000
 V2Z  C4    C8   C9    116.68  3.000
 V2Z  C4    C8   C7    122.65  3.000
 V2Z  C9    C8   C7    120.67  3.000
 V2Z  H9    C9   C1    120.45  3.000
 V2Z  H9    C9   C8    120.06  3.000
 V2Z  C1    C9   C8    119.49  3.000
 V2Z  H4    C4   N3    115.27  3.000
 V2Z  H4    C4   C8    120.60  3.000
 V2Z  N3    C4   C8    124.13  3.000
 V2Z  C2    N3   C4    118.29  3.000
 V2Z  H2    C2   C1    120.63  3.000
 V2Z  H2    C2   N3    116.72  3.000
 V2Z  C1    C2   N3    122.65  3.000
 V2Z  H1    C1   C2    120.39  3.000
 V2Z  H1    C1   C9    120.84  3.000
 V2Z  C2    C1   C9    118.76  3.000
 V2Z  H7    N7   C6    118.34  3.000
 V2Z  H7    N7   C12   117.27  3.000
 V2Z  C6    N7   C12   124.39  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
 V2Z  CONST_01  C2    C1   C9   C8     0.00   0.0  0
 V2Z  CONST_02  C2    N3   C4   C8     0.00   0.0  0
 V2Z  CONST_03  N3    C4   C8   C9     0.00   0.0  0
 V2Z  CONST_04  N3    C2   C1   C9     0.00   0.0  0
 V2Z  CONST_05  C1    C9   C8   C4     0.00   0.0  0
 V2Z  CONST_06  C1    C2   N3   C4     0.00   0.0  0
 V2Z  CONST_07  C1    C9   C8   C7   180.00   0.0  0
 V2Z  CONST_08  N3    C4   C8   C7   180.00   0.0  0
 V2Z  CONST_09  C6    N7   C12  C11    0.00   0.0  0
 V2Z  CONST_10  O6    C12  N7   C6   180.00   0.0  0
 V2Z  CONST_11  H9    C9   C8   C7     0.00   0.0  0
 V2Z  CONST_12  H4    C4   C8   C7     0.00   0.0  0
 V2Z  CONST_13  H1    C1   C9   C8   180.00   0.0  0
 V2Z  CONST_14  H2    C2   C1   C9   180.00   0.0  0
 V2Z  CONST_15  H7    N7   C12  C11  180.00   0.0  0
 V2Z  Var_01    C9    C8   C7   N10    4.40  30.0  2
 V2Z  Var_02    C15   C16  C11  N10   -1.43  30.0  3
 V2Z  Var_03    C14   C15  C16  C11  179.33  30.0  2
 V2Z  Var_04    H141  C14  C15  C16   60.12  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
 V2Z  plan-1  N10  0.020
 V2Z  plan-1  C11  0.020
 V2Z  plan-1  C12  0.020
 V2Z  plan-1  C16  0.020
 V2Z  plan-1  C7   0.020
 V2Z  plan-1  C6   0.020
 V2Z  plan-1  C8   0.020
 V2Z  plan-1  O6   0.020
 V2Z  plan-1  N7   0.020
 V2Z  plan-1  H7   0.020
 V2Z  plan-1  H6   0.020
 V2Z  plan-2  C7   0.020
 V2Z  plan-2  C8   0.020
 V2Z  plan-2  C9   0.020
 V2Z  plan-2  C4   0.020
 V2Z  plan-2  N3   0.020
 V2Z  plan-2  C2   0.020
 V2Z  plan-2  C1   0.020
 V2Z  plan-2  H9   0.020
 V2Z  plan-2  H4   0.020
 V2Z  plan-2  H1   0.020
 V2Z  plan-2  H2   0.020

