# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:34:15 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 2-methoxy-3-(1-methylethyl)pyrazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1nccnc1C(C)C
#
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
 IPZ  IPZ  2-methoxy-3-(1-methylethyl)pyrazine  ligand  23  11  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IPZ
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
 IPZ  C9    C  CH3   0  -0.646   0.4459  -1.2574  -2.5318
 IPZ  C8    C  CH1   0  -0.307   0.6755   0.0121  -1.7117
 IPZ  C10   C  CH3   0  -0.646   0.4415   1.2633  -2.5574
 IPZ  C2    C  CR6   0   0.180  -0.2204   0.0208  -0.4989
 IPZ  N1    N  N     0  -0.364  -1.5216   0.0420  -0.6941
 IPZ  C6    C  CR16  0  -0.157  -2.3390   0.0482   0.3595
 IPZ  C5    C  CR16  0  -0.102  -1.8377   0.0335   1.6410
 IPZ  N4    N  N     0  -0.416  -0.5252   0.0111   1.8697
 IPZ  C3    C  CR6   0   0.465   0.2722   0.0039   0.8285
 IPZ  O7    O  O2    0  -0.465   1.5918  -0.0197   1.0034
 IPZ  C11   C  CH3   0  -0.415   2.0907  -0.0301   2.3347
 IPZ  H91   H  HCH3  0   0.232   1.1220  -1.2841  -3.3874
 IPZ  H92   H  HCH3  0   0.232   0.6235  -2.1560  -1.9392
 IPZ  H93   H  HCH3  0   0.223  -0.5768  -1.2983  -2.9090
 IPZ  H8    H  HCH1  0   0.250   1.7147   0.0172  -1.3816
 IPZ  H101  H  HCH3  0   0.223  -0.5811   1.2942  -2.9350
 IPZ  H102  H  HCH3  0   0.232   0.6171   2.1745  -1.9840
 IPZ  H103  H  HCH3  0   0.232   1.1172   1.2740  -3.4138
 IPZ  H6    H  HCR6  0   0.266  -3.4050   0.0657   0.1709
 IPZ  H5    H  HCR6  0   0.271  -2.4933   0.0394   2.5033
 IPZ  H111  H  HCH3  0   0.248   3.1735  -0.0498   2.2451
 IPZ  H112  H  HCH3  0   0.232   1.7884   0.8617   2.8847
 IPZ  H113  H  HCH3  0   0.232   1.7561  -0.9113   2.8832

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
 IPZ  C9   C8    single    1.529  0.020  1.529
 IPZ  C9   H91   single    0.970  0.020  1.090
 IPZ  C9   H92   single    0.970  0.020  1.090
 IPZ  C9   H93   single    0.970  0.020  1.090
 IPZ  C8   C10   single    1.528  0.020  1.528
 IPZ  C8   C2    single    1.508  0.020  1.508
 IPZ  C8   H8    single    0.970  0.020  1.090
 IPZ  C10  H101  single    0.970  0.020  1.090
 IPZ  C10  H102  single    0.970  0.020  1.090
 IPZ  C10  H103  single    0.970  0.020  1.090
 IPZ  C2   N1    aromatic  1.316  0.020  1.316
 IPZ  C2   C3    aromatic  1.416  0.020  1.416
 IPZ  N1   C6    aromatic  1.334  0.020  1.334
 IPZ  C6   C5    aromatic  1.376  0.020  1.376
 IPZ  C6   H6    single    0.930  0.020  1.080
 IPZ  C5   N4    aromatic  1.332  0.020  1.332
 IPZ  C5   H5    single    0.930  0.020  1.080
 IPZ  N4   C3    aromatic  1.312  0.020  1.312
 IPZ  C3   O7    single    1.331  0.020  1.331
 IPZ  O7   C11   single    1.422  0.020  1.422
 IPZ  C11  H111  single    0.970  0.020  1.090
 IPZ  C11  H112  single    0.970  0.020  1.090
 IPZ  C11  H113  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
 IPZ  H93   C9   H92   108.03  3.000
 IPZ  H93   C9   H91   108.00  3.000
 IPZ  H92   C9   H91   107.76  3.000
 IPZ  H93   C9   C8    110.94  3.000
 IPZ  H92   C9   C8    111.60  3.000
 IPZ  H91   C9   C8    110.36  3.000
 IPZ  H8    C8   C2    108.83  3.000
 IPZ  H8    C8   C10   108.04  3.000
 IPZ  C2    C8   C10   110.45  3.000
 IPZ  H8    C8   C9    108.03  3.000
 IPZ  C2    C8   C9    110.31  3.000
 IPZ  C10   C8   C9    111.10  3.000
 IPZ  H103  C10  H102  107.74  3.000
 IPZ  H103  C10  H101  107.98  3.000
 IPZ  H102  C10  H101  108.02  3.000
 IPZ  H103  C10  C8    110.34  3.000
 IPZ  H102  C10  C8    111.61  3.000
 IPZ  H101  C10  C8    111.00  3.000
 IPZ  C3    C2   N1    118.90  3.000
 IPZ  C3    C2   C8    123.18  3.000
 IPZ  N1    C2   C8    117.93  3.000
 IPZ  C6    N1   C2    119.28  3.000
 IPZ  H6    C6   C5    121.40  3.000
 IPZ  H6    C6   N1    117.77  3.000
 IPZ  C5    C6   N1    120.83  3.000
 IPZ  H5    C5   N4    117.36  3.000
 IPZ  H5    C5   C6    121.39  3.000
 IPZ  N4    C5   C6    121.25  3.000
 IPZ  C3    N4   C5    117.57  3.000
 IPZ  O7    C3   N4    119.90  3.000
 IPZ  O7    C3   C2    117.92  3.000
 IPZ  N4    C3   C2    122.18  3.000
 IPZ  C11   O7   C3    118.10  3.000
 IPZ  H113  C11  H112  108.79  3.000
 IPZ  H113  C11  H111  109.43  3.000
 IPZ  H112  C11  H111  109.43  3.000
 IPZ  H113  C11  O7    111.67  3.000
 IPZ  H112  C11  O7    111.65  3.000
 IPZ  H111  C11  O7    105.81  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
 IPZ  CONST_01  C5    C6   N1  C2     0.00   0.0  0
 IPZ  CONST_02  C5    N4   C3  C2     0.00   0.0  0
 IPZ  CONST_03  N4    C3   C2  N1     0.00   0.0  0
 IPZ  CONST_04  N4    C5   C6  N1     0.00   0.0  0
 IPZ  CONST_05  C3    C2   N1  C6     0.00   0.0  0
 IPZ  CONST_06  C3    N4   C5  C6     0.00   0.0  0
 IPZ  CONST_07  C6    N1   C2  C8   180.00   0.0  0
 IPZ  CONST_08  N4    C3   C2  C8   180.00   0.0  0
 IPZ  CONST_09  O7    C3   C2  N1   180.00   0.0  0
 IPZ  CONST_10  O7    C3   N4  C5   180.00   0.0  0
 IPZ  CONST_11  H6    C6   N1  C2   180.00   0.0  0
 IPZ  CONST_12  H5    C5   C6  N1   180.00   0.0  0
 IPZ  Var_01    N1    C2   C8  C9   -62.92  30.0  2
 IPZ  Var_02    H91   C9   C8  C2  -177.71  30.0  3
 IPZ  Var_03    H101  C10  C8  C2   -62.49  30.0  3
 IPZ  Var_04    H111  C11  O7  C3   179.97  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
 IPZ  plan-1  C8  0.020
 IPZ  plan-1  C2  0.020
 IPZ  plan-1  N1  0.020
 IPZ  plan-1  C6  0.020
 IPZ  plan-1  C5  0.020
 IPZ  plan-1  N4  0.020
 IPZ  plan-1  C3  0.020
 IPZ  plan-1  O7  0.020
 IPZ  plan-1  H6  0.020
 IPZ  plan-1  H5  0.020

