# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:01:04 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-(piperazin-1-yl)pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1cccnc1N2CCNCC2
#
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
 49O  49O  2-(piperazin-1-yl)pyridine-3-carbonitrile  ligand  26  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_49O
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
 49O  C8   C  CSP   0   0.043  -1.0761  -1.7152  -0.9963
 49O  C12  C  CR16  0  -0.353  -3.3797   0.8918   0.2014
 49O  C7   C  CR16  0  -0.127  -2.9040  -0.2249  -0.4590
 49O  C9   C  CR16  0  -0.035  -2.4496   1.6919   0.8470
 49O  C3   C  CR6   0  -0.129  -1.5350  -0.4733  -0.4810
 49O  C1   C  CR6   0   0.541  -0.6532   0.4553   0.1290
 49O  C10  C  CH2   0  -0.315   2.6957  -0.6870  -0.9303
 49O  C11  C  CH2   0  -0.321   2.8355   0.2819   1.2519
 49O  C5   C  CH2   0  -0.327   1.3914   0.0565  -1.1756
 49O  C6   C  CH2   0  -0.303   1.5274   1.0346   1.0303
 49O  N13  N  NS    0  -0.252  -0.7344  -2.7450  -1.3882
 49O  N4   N  N     0  -0.453  -1.1415   1.4915   0.8047
 49O  N14  N  NH1   0  -0.579   3.5597  -0.0225   0.0299
 49O  N2   N  NT    0  -0.500   0.7024   0.2864   0.0930
 49O  H1   H  HCR6  0   0.279  -4.4346   1.1180   0.2450
 49O  H2   H  HCR6  0   0.293  -3.5825  -0.9243  -0.9292
 49O  H3   H  HCR6  0   0.275  -2.7794   2.5497   1.4225
 49O  H4   H  HCH2  0   0.227   2.4689  -1.6923  -0.5620
 49O  H5   H  HCH2  0   0.244   3.2284  -0.8003  -1.8759
 49O  H6   H  HCH2  0   0.244   3.4766   0.8688   1.9120
 49O  H7   H  HCH2  0   0.225   2.6161  -0.6585   1.7666
 49O  H8   H  HCH2  0   0.239   1.6067   1.0262  -1.6469
 49O  H9   H  HCH2  0   0.262   0.7706  -0.5023  -1.8718
 49O  H10  H  HCH2  0   0.255   0.9999   1.1431   1.9759
 49O  H11  H  HCH2  0   0.221   1.7346   2.0449   0.6516
 49O  H12  H  HNH1  0   0.344   3.8987   0.8424  -0.3770

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
 49O  N14  C11  single    1.453  0.020  1.453
 49O  N14  C10  single    1.453  0.020  1.453
 49O  C11  C6   single    1.525  0.020  1.525
 49O  C10  C5   single    1.521  0.020  1.521
 49O  C6   N2   single    1.456  0.020  1.456
 49O  C5   N2   single    1.462  0.020  1.462
 49O  N13  C8   triple    1.154  0.020  1.154
 49O  N2   C1   single    1.367  0.020  1.367
 49O  C8   C3   single    1.421  0.020  1.421
 49O  C1   C3   aromatic  1.418  0.020  1.418
 49O  C1   N4   aromatic  1.330  0.020  1.330
 49O  C3   C7   aromatic  1.392  0.020  1.392
 49O  N4   C9   aromatic  1.324  0.020  1.324
 49O  C7   C12  aromatic  1.382  0.020  1.382
 49O  C9   C12  aromatic  1.386  0.020  1.386
 49O  C12  H1   single    0.930  0.020  1.080
 49O  C7   H2   single    0.930  0.020  1.080
 49O  C9   H3   single    0.930  0.020  1.080
 49O  C10  H4   single    0.970  0.020  1.090
 49O  C10  H5   single    0.970  0.020  1.090
 49O  C11  H6   single    0.970  0.020  1.090
 49O  C11  H7   single    0.970  0.020  1.090
 49O  C5   H8   single    0.970  0.020  1.090
 49O  C5   H9   single    0.970  0.020  1.090
 49O  C6   H10  single    0.970  0.020  1.090
 49O  C6   H11  single    0.970  0.020  1.090
 49O  N14  H12  single    0.890  0.020  1.040

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
 49O  N13  C8   C3   180.00  3.000
 49O  H1   C12  C9   121.04  3.000
 49O  H1   C12  C7   121.67  3.000
 49O  C9   C12  C7   117.26  3.000
 49O  H2   C7   C3   119.65  3.000
 49O  H2   C7   C12  120.94  3.000
 49O  C3   C7   C12  119.38  3.000
 49O  H3   C9   N4   115.92  3.000
 49O  H3   C9   C12  119.98  3.000
 49O  N4   C9   C12  124.09  3.000
 49O  C1   C3   C7   119.20  3.000
 49O  C7   C3   C8   118.66  3.000
 49O  C1   C3   C8   121.83  3.000
 49O  N2   C1   N4   118.29  3.000
 49O  N4   C1   C3   120.02  3.000
 49O  N2   C1   C3   121.63  3.000
 49O  H5   C10  H4   107.30  3.000
 49O  H5   C10  N14  109.27  3.000
 49O  H4   C10  N14  108.72  3.000
 49O  H5   C10  C5   109.25  3.000
 49O  H4   C10  C5   109.00  3.000
 49O  N14  C10  C5   113.14  3.000
 49O  H7   C11  H6   107.18  3.000
 49O  H7   C11  N14  108.39  3.000
 49O  H6   C11  N14  109.19  3.000
 49O  H7   C11  C6   108.69  3.000
 49O  H6   C11  C6   109.04  3.000
 49O  N14  C11  C6   114.12  3.000
 49O  H9   C5   H8   106.89  3.000
 49O  H9   C5   N2   111.55  3.000
 49O  H8   C5   N2   109.00  3.000
 49O  H9   C5   C10  109.98  3.000
 49O  H8   C5   C10  109.41  3.000
 49O  N2   C5   C10  109.94  3.000
 49O  H11  C6   H10  107.41  3.000
 49O  H11  C6   N2   110.96  3.000
 49O  H10  C6   N2   109.64  3.000
 49O  H11  C6   C11  110.00  3.000
 49O  H10  C6   C11  109.79  3.000
 49O  N2   C6   C11  109.02  3.000
 49O  C1   N4   C9   119.79  3.000
 49O  H12  N14  C11  108.99  3.000
 49O  H12  N14  C10  108.89  3.000
 49O  C11  N14  C10  110.82  3.000
 49O  C6   N2   C5   111.87  3.000
 49O  C5   N2   C1   120.65  3.000
 49O  C6   N2   C1   118.80  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
 49O  CONST_01  C1   C3   C7   C12     0.00   0.0  0
 49O  CONST_02  C1   N4   C9   C12     0.00   0.0  0
 49O  CONST_03  N4   C1   C3   C7      0.00   0.0  0
 49O  CONST_04  N4   C9   C12  C7      0.00   0.0  0
 49O  CONST_05  C3   C1   N4   C9      0.00   0.0  0
 49O  CONST_06  C3   C7   C12  C9      0.00   0.0  0
 49O  CONST_07  N2   C1   C3   C7    180.00   0.0  0
 49O  CONST_08  N2   C1   N4   C9    180.00   0.0  0
 49O  CONST_09  N2   C1   C3   C8      0.00   0.0  0
 49O  CONST_10  N4   C1   C3   C8    180.00   0.0  0
 49O  CONST_11  C12  C7   C3   C8    180.00   0.0  0
 49O  CONST_12  H3   C9   C12  C7    180.00   0.0  0
 49O  CONST_13  H2   C7   C12  C9    180.00   0.0  0
 49O  CONST_14  H1   C12  C7   C3    180.00   0.0  0
 49O  Var_01    C6   N2   C1   C3   -162.88  30.0  2
 49O  Var_02    C11  C6   N2   C1    155.00  30.0  1
 49O  Var_03    C10  C5   N2   C1   -154.98  30.0  1
 49O  Var_04    C6   C11  N14  C10   -51.96  30.0  1
 49O  Var_05    C5   C10  N14  C11    51.60  30.0  1
 49O  Var_06    N2   C6   C11  N14    54.59  30.0  1
 49O  Var_07    N2   C5   C10  N14   -54.71  30.0  1

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
 49O  plan-1  C8   0.020
 49O  plan-1  C12  0.020
 49O  plan-1  C7   0.020
 49O  plan-1  C9   0.020
 49O  plan-1  C3   0.020
 49O  plan-1  C1   0.020
 49O  plan-1  N13  0.020
 49O  plan-1  N4   0.020
 49O  plan-1  N2   0.020
 49O  plan-1  H1   0.020
 49O  plan-1  H2   0.020
 49O  plan-1  H3   0.020

