# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:22:17 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(N)nc2ncc(cc12)c3ccccc3
#
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
 PIQ  PIQ  1-methyl-6-phenyl-1H-imidazo[4,5-b]pyridin-2-amine  ligand  29  17  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PIQ
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
 PIQ  N    N  NH2   0  -0.852   0.3123  -0.0157   4.9155
 PIQ  C2   C  CR5   0   0.646  -0.0102   0.0030   3.6089
 PIQ  N1   N  NR5   0  -0.567   0.9446   0.1462   2.6427
 PIQ  C7A  C  CR56  0   0.306   0.2872   0.0413   1.4404
 PIQ  C7   C  CR16  0  -0.280   0.6815   0.1009   0.1268
 PIQ  C6   C  CR6   0  -0.013  -0.3312  -0.0382  -0.8322
 PIQ  C1'  C  CR6   0   0.085  -0.0211  -0.0009  -2.2731
 PIQ  C2'  C  CR16  0  -0.315  -0.8805   0.6253  -3.1786
 PIQ  C3'  C  CR16  0  -0.239  -0.5900   0.6497  -4.5350
 PIQ  C4'  C  CR16  0  -0.269   0.5704   0.0559  -5.0138
 PIQ  C5'  C  CR16  0  -0.239   1.4369  -0.5640  -4.1227
 PIQ  C6'  C  CR16  0  -0.314   1.1428  -0.5940  -2.7676
 PIQ  N3   N  N     0  -0.520  -1.2252  -0.1680   3.1338
 PIQ  CM   C  CH3   0  -0.553   2.3644   0.2995   2.8536
 PIQ  C3A  C  CR56  0   0.275  -1.0692  -0.1496   1.7798
 PIQ  N4   N  N     0  -0.427  -2.0269  -0.2842   0.8793
 PIQ  C5   C  CR16  0  -0.147  -1.6458  -0.2284  -0.3933
 PIQ  HN1  H  HNH2  0   0.407  -0.4535   0.0745   5.5624
 PIQ  HN2  H  HNH2  0   0.409   1.1672   0.4190   5.2208
 PIQ  H7   H  HCR6  0   0.273   1.7116   0.2657  -0.1653
 PIQ  H2'  H  HCR6  0   0.253  -1.7762   1.1178  -2.8205
 PIQ  H3'  H  HCR6  0   0.257  -1.2689   1.1441  -5.2179
 PIQ  H4'  H  HCR6  0   0.256   0.7987   0.0772  -6.0714
 PIQ  H5'  H  HCR6  0   0.257   2.3422  -1.0345  -4.4841
 PIQ  H6'  H  HCR6  0   0.253   1.8181  -1.1026  -2.0901
 PIQ  HM1  H  HCH3  0   0.267   2.8133  -0.6229   3.2209
 PIQ  HM2  H  HCH3  0   0.275   2.8386   0.5638   1.9127
 PIQ  HM3  H  HCH3  0   0.265   2.5670   1.1035   3.5600
 PIQ  H5   H  HCR6  0   0.250  -2.4329  -0.3642  -1.1275

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
 PIQ  N    C2   single    1.346  0.020  1.346
 PIQ  N    HN1  single    0.890  0.020  1.040
 PIQ  N    HN2  single    0.890  0.020  1.040
 PIQ  C2   N1   aromatic  1.366  0.020  1.366
 PIQ  C2   N3   aromatic  1.316  0.020  1.316
 PIQ  N1   C7A  aromatic  1.374  0.020  1.374
 PIQ  N1   CM   single    1.444  0.020  1.444
 PIQ  C7A  C7   aromatic  1.373  0.020  1.373
 PIQ  C7A  C3A  aromatic  1.411  0.020  1.411
 PIQ  C7   C6   aromatic  1.402  0.020  1.402
 PIQ  C7   H7   single    0.930  0.020  1.080
 PIQ  C6   C1'  single    1.474  0.020  1.474
 PIQ  C6   C5   aromatic  1.399  0.020  1.399
 PIQ  C1'  C2'  aromatic  1.397  0.020  1.397
 PIQ  C1'  C6'  aromatic  1.397  0.020  1.397
 PIQ  C2'  C3'  aromatic  1.387  0.020  1.387
 PIQ  C2'  H2'  single    0.930  0.020  1.080
 PIQ  C3'  C4'  aromatic  1.389  0.020  1.389
 PIQ  C3'  H3'  single    0.930  0.020  1.080
 PIQ  C4'  C5'  aromatic  1.389  0.020  1.389
 PIQ  C4'  H4'  single    0.930  0.020  1.080
 PIQ  C5'  C6'  aromatic  1.387  0.020  1.387
 PIQ  C5'  H5'  single    0.930  0.020  1.080
 PIQ  C6'  H6'  single    0.930  0.020  1.080
 PIQ  N3   C3A  aromatic  1.363  0.020  1.363
 PIQ  CM   HM1  single    0.970  0.020  1.090
 PIQ  CM   HM2  single    0.970  0.020  1.090
 PIQ  CM   HM3  single    0.970  0.020  1.090
 PIQ  C3A  N4   aromatic  1.321  0.020  1.321
 PIQ  N4   C5   aromatic  1.330  0.020  1.330
 PIQ  C5   H5   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
 PIQ  HN2  N    HN1  114.36  3.000
 PIQ  HN2  N    C2   119.47  3.000
 PIQ  HN1  N    C2   116.14  3.000
 PIQ  N3   C2   N1   113.81  3.000
 PIQ  N3   C2   N    124.75  3.000
 PIQ  N1   C2   N    121.38  3.000
 PIQ  CM   N1   C7A  127.33  3.000
 PIQ  CM   N1   C2   126.53  3.000
 PIQ  C7A  N1   C2   106.05  3.000
 PIQ  C3A  C7A  C7   120.80  3.000
 PIQ  C3A  C7A  N1   105.05  3.000
 PIQ  C7   C7A  N1   134.14  3.000
 PIQ  H7   C7   C6   121.18  3.000
 PIQ  H7   C7   C7A  122.53  3.000
 PIQ  C6   C7   C7A  116.29  3.000
 PIQ  C5   C6   C1'  120.51  3.000
 PIQ  C5   C6   C7   118.54  3.000
 PIQ  C1'  C6   C7   120.94  3.000
 PIQ  C6'  C1'  C2'  118.27  3.000
 PIQ  C6'  C1'  C6   120.70  3.000
 PIQ  C2'  C1'  C6   121.04  3.000
 PIQ  H2'  C2'  C3'  119.24  3.000
 PIQ  H2'  C2'  C1'  119.89  3.000
 PIQ  C3'  C2'  C1'  120.86  3.000
 PIQ  H3'  C3'  C4'  120.13  3.000
 PIQ  H3'  C3'  C2'  119.57  3.000
 PIQ  C4'  C3'  C2'  120.30  3.000
 PIQ  H4'  C4'  C5'  120.27  3.000
 PIQ  H4'  C4'  C3'  120.32  3.000
 PIQ  C5'  C4'  C3'  119.41  3.000
 PIQ  H5'  C5'  C6'  119.61  3.000
 PIQ  H5'  C5'  C4'  120.11  3.000
 PIQ  C6'  C5'  C4'  120.28  3.000
 PIQ  H6'  C6'  C5'  119.27  3.000
 PIQ  H6'  C6'  C1'  119.82  3.000
 PIQ  C5'  C6'  C1'  120.89  3.000
 PIQ  C3A  N3   C2   104.55  3.000
 PIQ  HM3  CM   HM2  107.51  3.000
 PIQ  HM3  CM   HM1  109.25  3.000
 PIQ  HM2  CM   HM1  108.55  3.000
 PIQ  HM3  CM   N1   110.86  3.000
 PIQ  HM2  CM   N1   109.18  3.000
 PIQ  HM1  CM   N1   111.38  3.000
 PIQ  N4   C3A  N3   126.34  3.000
 PIQ  N4   C3A  C7A  123.12  3.000
 PIQ  N3   C3A  C7A  110.53  3.000
 PIQ  C5   N4   C3A  116.12  3.000
 PIQ  H5   C5   N4   115.76  3.000
 PIQ  H5   C5   C6   119.11  3.000
 PIQ  N4   C5   C6   125.12  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
 PIQ  CONST_01  C7   C7A  N1   C2   180.00   0.0  0
 PIQ  CONST_02  C3A  C7A  N1   C2     0.00   0.0  0
 PIQ  CONST_03  C7A  C3A  N3   C2     0.00   0.0  0
 PIQ  CONST_04  N4   C3A  N3   C2   180.00   0.0  0
 PIQ  CONST_05  C3A  N3   C2   N1     0.00   0.0  0
 PIQ  CONST_06  C6   C7   C7A  N1   180.00   0.0  0
 PIQ  CONST_07  N3   C3A  C7A  N1     0.00   0.0  0
 PIQ  CONST_08  N4   C3A  C7A  N1   180.00   0.0  0
 PIQ  CONST_09  N3   C2   N1   C7A    0.00   0.0  0
 PIQ  CONST_10  C1'  C6   C7   C7A  180.00   0.0  0
 PIQ  CONST_11  C5   C6   C7   C7A    0.00   0.0  0
 PIQ  CONST_12  C5   N4   C3A  C7A    0.00   0.0  0
 PIQ  CONST_13  N3   C3A  C7A  C7   180.00   0.0  0
 PIQ  CONST_14  N4   C3A  C7A  C7     0.00   0.0  0
 PIQ  CONST_17  N4   C5   C6   C7     0.00   0.0  0
 PIQ  CONST_18  C3A  C7A  C7   C6     0.00   0.0  0
 PIQ  CONST_19  C3'  C2'  C1'  C6   180.00   0.0  0
 PIQ  CONST_20  C5'  C6'  C1'  C6   180.00   0.0  0
 PIQ  CONST_21  C3A  N4   C5   C6     0.00   0.0  0
 PIQ  CONST_22  N4   C5   C6   C1'  180.00   0.0  0
 PIQ  CONST_23  C4'  C3'  C2'  C1'    0.00   0.0  0
 PIQ  CONST_24  C4'  C5'  C6'  C1'    0.00   0.0  0
 PIQ  CONST_26  C5'  C6'  C1'  C2'    0.00   0.0  0
 PIQ  CONST_27  C5'  C4'  C3'  C2'    0.00   0.0  0
 PIQ  CONST_28  C6'  C1'  C2'  C3'    0.00   0.0  0
 PIQ  CONST_29  C6'  C5'  C4'  C3'    0.00   0.0  0
 PIQ  CONST_31  C5   N4   C3A  N3   180.00   0.0  0
 PIQ  CONST_32  C7A  N1   C2   N    180.00   0.0  0
 PIQ  CONST_33  C3A  N3   C2   N    180.00   0.0  0
 PIQ  CONST_34  CM   N1   C7A  C7     0.00   0.0  0
 PIQ  CONST_35  CM   N1   C2   N3   180.00   0.0  0
 PIQ  CONST_36  C3A  C7A  N1   CM   180.00   0.0  0
 PIQ  CONST_37  H7   C7   C7A  N1     0.00   0.0  0
 PIQ  CONST_38  H5   C5   C6   C7   180.00   0.0  0
 PIQ  CONST_39  H2'  C2'  C1'  C6     0.00   0.0  0
 PIQ  CONST_40  H6'  C6'  C1'  C6     0.00   0.0  0
 PIQ  CONST_41  H3'  C3'  C2'  C1'  180.00   0.0  0
 PIQ  CONST_42  H5'  C5'  C6'  C1'  180.00   0.0  0
 PIQ  CONST_43  H4'  C4'  C3'  C2'  180.00   0.0  0
 PIQ  CONST_44  HN1  N    C2   N1   180.00   0.0  0
 PIQ  Var_01    HM1  CM   N1   C2    69.98  30.0  2

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
 PIQ  plan-1  C6   0.020
 PIQ  plan-1  C1'  0.020
 PIQ  plan-1  C2'  0.020
 PIQ  plan-1  C3'  0.020
 PIQ  plan-1  C4'  0.020
 PIQ  plan-1  C5'  0.020
 PIQ  plan-1  C6'  0.020
 PIQ  plan-1  H2'  0.020
 PIQ  plan-1  H3'  0.020
 PIQ  plan-1  H4'  0.020
 PIQ  plan-1  H5'  0.020
 PIQ  plan-1  H6'  0.020
 PIQ  plan-2  N    0.020
 PIQ  plan-2  C2   0.020
 PIQ  plan-2  N1   0.020
 PIQ  plan-2  C7A  0.020
 PIQ  plan-2  C7   0.020
 PIQ  plan-2  C6   0.020
 PIQ  plan-2  C1'  0.020
 PIQ  plan-2  N3   0.020
 PIQ  plan-2  CM   0.020
 PIQ  plan-2  C3A  0.020
 PIQ  plan-2  N4   0.020
 PIQ  plan-2  C5   0.020
 PIQ  plan-2  H7   0.020
 PIQ  plan-2  H5   0.020
 PIQ  plan-3  N    0.020
 PIQ  plan-3  C2   0.020
 PIQ  plan-3  HN1  0.020
 PIQ  plan-3  HN2  0.020

