# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:24:22 2021
#   Inital geometry file: a 47 line input string
#   Ligand name: 2-hydrazinyl-4-methoxypyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccnc(NN)n1
#
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
 R8S  R8S  2-hydrazinyl-4-methoxypyrimidine  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 OK
;

data_comp_R8S
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
 R8S  C4  C  CR6   0   0.591  16.1958   1.7943  48.9470
 R8S  N1  N  N     0  -0.528  17.4988   1.6785  49.2559
 R8S  N2  N  NH1   0  -0.535  15.7231   0.8063  48.1616
 R8S  N3  N  NH2   0  -0.636  14.4048   0.7425  47.7640
 R8S  N   N  N     0  -0.465  15.3871   2.7708  49.3439
 R8S  C3  C  CR16  0  -0.026  15.9502   3.7043  50.1091
 R8S  C2  C  CR16  0  -0.451  17.2710   3.7007  50.4899
 R8S  C1  C  CR6   0   0.559  18.0183   2.6147  50.0119
 R8S  O   O  O2    0  -0.462  19.2984   2.5514  50.3512
 R8S  C   C  CH3   0  -0.419  20.0711   1.4527  49.8813
 R8S  H1  H  HNH1  0   0.389  16.3736   0.0828  47.8925
 R8S  H2  H  HNH2  0   0.368  14.3599   0.7275  46.7536
 R8S  H3  H  HNH2  0   0.367  13.9926  -0.1171  48.1030
 R8S  H4  H  HCR6  0   0.264  15.2975   4.5064  50.4378
 R8S  H5  H  HCR6  0   0.269  17.6998   4.4734  51.1103
 R8S  H6  H  HCH3  0   0.249  21.0729   1.6070  50.2730
 R8S  H7  H  HCH3  0   0.233  19.6826   0.5016  50.2460
 R8S  H8  H  HCH3  0   0.233  20.1092   1.4233  48.7923

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
 R8S  N3  N2  single    1.378  0.020  1.378
 R8S  N2  C4  single    1.348  0.020  1.348
 R8S  C4  N1  aromatic  1.344  0.020  1.344
 R8S  C4  N   aromatic  1.328  0.020  1.328
 R8S  N1  C1  aromatic  1.311  0.020  1.311
 R8S  N   C3  aromatic  1.332  0.020  1.332
 R8S  C   O   single    1.423  0.020  1.423
 R8S  C1  O   single    1.326  0.020  1.326
 R8S  C1  C2  aromatic  1.402  0.020  1.402
 R8S  C3  C2  aromatic  1.375  0.020  1.375
 R8S  N2  H1  single    0.860  0.020  1.020
 R8S  N3  H2  single    0.890  0.020  1.040
 R8S  N3  H3  single    0.890  0.020  1.040
 R8S  C3  H4  single    0.930  0.020  1.080
 R8S  C2  H5  single    0.930  0.020  1.080
 R8S  C   H6  single    0.970  0.020  1.090
 R8S  C   H7  single    0.970  0.020  1.090
 R8S  C   H8  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
 R8S  N   C4  N2  119.96  3.000
 R8S  N   C4  N1  125.79  3.000
 R8S  N2  C4  N1  114.25  3.000
 R8S  C1  N1  C4  117.08  3.000
 R8S  H1  N2  N3  120.42  3.000
 R8S  H1  N2  C4  117.05  3.000
 R8S  N3  N2  C4  122.51  3.000
 R8S  H3  N3  H2  107.69  3.000
 R8S  H3  N3  N2  109.41  3.000
 R8S  H2  N3  N2  109.35  3.000
 R8S  C3  N   C4  115.43  3.000
 R8S  H4  C3  C2  119.73  3.000
 R8S  H4  C3  N   115.96  3.000
 R8S  C2  C3  N   124.30  3.000
 R8S  H5  C2  C1  122.58  3.000
 R8S  H5  C2  C3  122.61  3.000
 R8S  C1  C2  C3  114.81  3.000
 R8S  O   C1  C2  117.66  3.000
 R8S  C2  C1  N1  122.58  3.000
 R8S  O   C1  N1  119.75  3.000
 R8S  C   O   C1  118.46  3.000
 R8S  H8  C   H7  108.85  3.000
 R8S  H8  C   H6  109.37  3.000
 R8S  H7  C   H6  109.38  3.000
 R8S  H8  C   O   111.70  3.000
 R8S  H7  C   O   111.69  3.000
 R8S  H6  C   O   105.78  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
 R8S  CONST_01  C2  C1  N1  C4    0.00   0.0  0
 R8S  CONST_02  C2  C3  N   C4    0.00   0.0  0
 R8S  CONST_03  C3  N   C4  N1    0.00   0.0  0
 R8S  CONST_04  C3  C2  C1  N1    0.00   0.0  0
 R8S  CONST_05  C1  N1  C4  N     0.00   0.0  0
 R8S  CONST_06  C1  C2  C3  N     0.00   0.0  0
 R8S  CONST_07  O   C1  N1  C4  180.00   0.0  0
 R8S  CONST_08  C1  N1  C4  N2  180.00   0.0  0
 R8S  CONST_09  C3  N   C4  N2  180.00   0.0  0
 R8S  CONST_10  O   C1  C2  C3  180.00   0.0  0
 R8S  CONST_11  H4  C3  N   C4  180.00   0.0  0
 R8S  CONST_12  H5  C2  C1  N1  180.00   0.0  0
 R8S  CONST_13  N3  N2  C4  N1  180.00   0.0  0
 R8S  CONST_14  N   C4  N2  N3    0.00   0.0  0
 R8S  CONST_15  H1  N2  C4  N1    0.00   0.0  0
 R8S  Var_01    H6  C   O   C1  179.84  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
 R8S  plan-1  C4  0.020
 R8S  plan-1  N1  0.020
 R8S  plan-1  N2  0.020
 R8S  plan-1  N   0.020
 R8S  plan-1  C3  0.020
 R8S  plan-1  C2  0.020
 R8S  plan-1  C1  0.020
 R8S  plan-1  O   0.020
 R8S  plan-1  H4  0.020
 R8S  plan-1  H5  0.020
 R8S  plan-2  C4  0.020
 R8S  plan-2  N2  0.020
 R8S  plan-2  N3  0.020
 R8S  plan-2  H1  0.020

