# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 04:12:22 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCN1)c2ncnc3[nH]ccc23
#
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
 6J9  6J9  4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine  ligand  28  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6J9
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
 6J9  C4   C  CR6   0   0.504  -0.1183   0.5330   0.0736
 6J9  C5   C  CR56  0  -0.079  -1.1849  -0.4044   0.0161
 6J9  C6   C  CR56  0   0.468  -2.4637   0.1685  -0.1157
 6J9  N1   N  NH1   0  -0.600   3.9223  -0.5140   0.1360
 6J9  C7   C  CR15  0  -0.448  -1.3827  -1.8254   0.0028
 6J9  C8   C  CR15  0  -0.012  -2.7236  -2.0359  -0.1142
 6J9  N2   N  N     0  -0.497  -0.4124   1.8326  -0.0372
 6J9  C9   C  CR16  0   0.037  -1.6751   2.2218  -0.1696
 6J9  N    N  NT    0  -0.494   1.1901   0.2082   0.2026
 6J9  C1   C  CH2   0  -0.308   1.6559  -1.0195   0.8227
 6J9  C    C  CH2   0  -0.298   2.2221   1.2324   0.1486
 6J9  C2   C  CH2   0  -0.299   3.4586   0.6819  -0.5411
 6J9  C3   C  CH2   0  -0.291   2.8966  -1.5382   0.1187
 6J9  N4   N  N     0  -0.452  -2.7526   1.4689  -0.2019
 6J9  N3   N  NR15  0  -0.655  -3.3706  -0.8325  -0.1794
 6J9  H3   H  HCR5  0   0.256  -0.6520  -2.6141   0.0498
 6J9  H4   H  HCR5  0   0.288  -3.2736  -2.9611  -0.1621
 6J9  H5   H  HCR6  0   0.243  -1.8293   3.2932  -0.2513
 6J9  H6   H  HCH2  0   0.237   1.8933  -0.8241   1.8759
 6J9  H7   H  HCH2  0   0.261   0.8871  -1.7803   0.8063
 6J9  H8   H  HCH2  0   0.265   1.8524   2.0943  -0.3979
 6J9  H9   H  HCH2  0   0.225   2.4775   1.5648   1.1624
 6J9  H10  H  HCH2  0   0.241   4.2411   1.4420  -0.5098
 6J9  H11  H  HCH2  0   0.198   3.2162   0.5053  -1.6010
 6J9  H12  H  HCH2  0   0.200   2.6188  -1.8534  -0.8993
 6J9  H13  H  HCH2  0   0.242   3.2534  -2.4228   0.6488
 6J9  H14  H  HNR5  0   0.413  -4.3656  -0.7057  -0.2713
 6J9  H1   H  HNH1  0   0.357   4.7582  -0.8589  -0.3167

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
 6J9  C2  N1   single    1.450  0.020  1.450
 6J9  C2  C    single    1.519  0.020  1.519
 6J9  C1  N    single    1.452  0.020  1.452
 6J9  C1  C3   single    1.518  0.020  1.518
 6J9  N1  C3   single    1.450  0.020  1.450
 6J9  N2  C9   aromatic  1.328  0.020  1.328
 6J9  N2  C4   aromatic  1.337  0.020  1.337
 6J9  N   C    single    1.455  0.020  1.455
 6J9  N   C4   single    1.354  0.020  1.354
 6J9  C9  N4   aromatic  1.315  0.020  1.315
 6J9  C4  C5   aromatic  1.421  0.020  1.421
 6J9  N4  C6   aromatic  1.335  0.020  1.335
 6J9  C5  C6   aromatic  1.407  0.020  1.407
 6J9  C5  C7   aromatic  1.435  0.020  1.435
 6J9  C6  N3   aromatic  1.352  0.020  1.352
 6J9  C7  C8   aromatic  1.362  0.020  1.362
 6J9  N3  C8   aromatic  1.368  0.020  1.368
 6J9  N1  H1   single    0.890  0.020  1.040
 6J9  C7  H3   single    0.930  0.020  1.080
 6J9  C8  H4   single    0.930  0.020  1.080
 6J9  C9  H5   single    0.930  0.020  1.080
 6J9  C1  H6   single    0.970  0.020  1.090
 6J9  C1  H7   single    0.970  0.020  1.090
 6J9  C   H8   single    0.970  0.020  1.090
 6J9  C   H9   single    0.970  0.020  1.090
 6J9  C2  H10  single    0.970  0.020  1.090
 6J9  C2  H11  single    0.970  0.020  1.090
 6J9  C3  H12  single    0.970  0.020  1.090
 6J9  C3  H13  single    0.970  0.020  1.090
 6J9  N3  H14  single    0.860  0.020  1.020

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
 6J9  N    C4  N2   116.97  3.000
 6J9  N    C4  C5   124.81  3.000
 6J9  N2   C4  C5   118.21  3.000
 6J9  C7   C5  C6   106.08  3.000
 6J9  C7   C5  C4   139.21  3.000
 6J9  C6   C5  C4   114.66  3.000
 6J9  N3   C6  N4   124.96  3.000
 6J9  N3   C6  C5   108.21  3.000
 6J9  N4   C6  C5   126.81  3.000
 6J9  H1   N1  C3   109.79  3.000
 6J9  H1   N1  C2   109.66  3.000
 6J9  C3   N1  C2   110.53  3.000
 6J9  H3   C7  C8   123.97  3.000
 6J9  H3   C7  C5   129.19  3.000
 6J9  C8   C7  C5   106.83  3.000
 6J9  H4   C8  N3   120.79  3.000
 6J9  H4   C8  C7   129.71  3.000
 6J9  N3   C8  C7   109.49  3.000
 6J9  C9   N2  C4   120.15  3.000
 6J9  H5   C9  N4   116.54  3.000
 6J9  H5   C9  N2   115.59  3.000
 6J9  N4   C9  N2   127.87  3.000
 6J9  C    N   C1   112.55  3.000
 6J9  C    N   C4   120.86  3.000
 6J9  C1   N   C4   123.60  3.000
 6J9  H7   C1  H6   107.07  3.000
 6J9  H7   C1  C3   109.49  3.000
 6J9  H6   C1  C3   109.22  3.000
 6J9  H7   C1  N    111.11  3.000
 6J9  H6   C1  N    109.19  3.000
 6J9  C3   C1  N    110.68  3.000
 6J9  H9   C   H8   107.69  3.000
 6J9  H9   C   C2   109.87  3.000
 6J9  H8   C   C2   109.66  3.000
 6J9  H9   C   N    110.13  3.000
 6J9  H8   C   N    109.64  3.000
 6J9  C2   C   N    109.83  3.000
 6J9  H11  C2  H10  107.28  3.000
 6J9  H11  C2  C    108.41  3.000
 6J9  H10  C2  C    108.56  3.000
 6J9  H11  C2  N1   112.79  3.000
 6J9  H10  C2  N1   109.37  3.000
 6J9  C    C2  N1   110.31  3.000
 6J9  H13  C3  H12  107.43  3.000
 6J9  H13  C3  C1   108.60  3.000
 6J9  H12  C3  C1   108.69  3.000
 6J9  H13  C3  N1   109.61  3.000
 6J9  H12  C3  N1   113.06  3.000
 6J9  C1   C3  N1   109.35  3.000
 6J9  C9   N4  C6   112.26  3.000
 6J9  H14  N3  C8   125.62  3.000
 6J9  H14  N3  C6   125.00  3.000
 6J9  C8   N3  C6   109.38  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
 6J9  CONST_01  N4   C9  N2  C4     0.00   0.0  0
 6J9  CONST_02  N4   C6  C5  C4     0.00   0.0  0
 6J9  CONST_03  N3   C6  C5  C4   180.00   0.0  0
 6J9  CONST_04  C8   C7  C5  C4   180.00   0.0  0
 6J9  CONST_05  C9   N2  C4  C5     0.00   0.0  0
 6J9  CONST_06  C9   N4  C6  C5     0.00   0.0  0
 6J9  CONST_07  C8   N3  C6  C5     0.00   0.0  0
 6J9  CONST_08  N3   C8  C7  C5     0.00   0.0  0
 6J9  CONST_09  N2   C9  N4  C6     0.00   0.0  0
 6J9  CONST_10  N2   C4  C5  C6     0.00   0.0  0
 6J9  CONST_11  C8   C7  C5  C6     0.00   0.0  0
 6J9  CONST_12  C7   C8  N3  C6     0.00   0.0  0
 6J9  CONST_13  N2   C4  C5  C7   180.00   0.0  0
 6J9  CONST_14  N4   C6  C5  C7   180.00   0.0  0
 6J9  CONST_15  N3   C6  C5  C7     0.00   0.0  0
 6J9  CONST_16  N4   C6  N3  C8   180.00   0.0  0
 6J9  CONST_17  N3   C6  N4  C9   180.00   0.0  0
 6J9  CONST_18  N    C4  C5  C6   180.00   0.0  0
 6J9  CONST_19  N    C4  C5  C7     0.00   0.0  0
 6J9  CONST_20  N    C4  N2  C9   180.00   0.0  0
 6J9  CONST_21  H5   C9  N2  C4   180.00   0.0  0
 6J9  CONST_22  H3   C7  C5  C4     0.00   0.0  0
 6J9  CONST_23  H14  N3  C6  C5   180.00   0.0  0
 6J9  CONST_24  H4   C8  C7  C5   180.00   0.0  0
 6J9  Var_01    C3   C1  N   C4   144.20  30.0  1
 6J9  Var_02    C2   C   N   C4  -144.33  30.0  1
 6J9  Var_03    C1   N   C4  C5   -25.86  30.0  3
 6J9  Var_04    N    C   C2  N1   -56.36  30.0  1
 6J9  Var_05    N    C1  C3  N1    56.89  30.0  1
 6J9  Var_06    C2   N1  C3  C1   -59.92  30.0  1
 6J9  Var_07    C3   N1  C2  C     60.21  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
 6J9  plan-1  C4   0.020
 6J9  plan-1  C5   0.020
 6J9  plan-1  C6   0.020
 6J9  plan-1  C7   0.020
 6J9  plan-1  C8   0.020
 6J9  plan-1  N2   0.020
 6J9  plan-1  C9   0.020
 6J9  plan-1  N    0.020
 6J9  plan-1  N4   0.020
 6J9  plan-1  N3   0.020
 6J9  plan-1  H3   0.020
 6J9  plan-1  H4   0.020
 6J9  plan-1  H5   0.020
 6J9  plan-1  H14  0.020

