# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 23:26:11 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-(5-chloro-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1c[nH]c2ncnc(N3CCc4[nH]cnc4C3)c12
#
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
 CQW  CQW  5-(5-chloro-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine  ligand  30  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CQW
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
 CQW  C7    C   CR56  0   0.477   3.1287  -0.5857   0.1596
 CQW  C9    C   CR16  0   0.045   2.3105  -2.3708   1.1581
 CQW  C13   C   CR56  0   0.056   1.8484  -0.0676  -0.1253
 CQW  C21   C   CR5   0   0.299  -3.1129   0.1760  -0.3698
 CQW  N5    N   NR15  0  -0.660   4.0570   0.3096  -0.2414
 CQW  C18   C   CH2   0  -0.501  -2.1133   0.7724  -1.2882
 CQW  C2    C   CR5   0  -0.269   2.0891   1.2341  -0.6725
 CQW  C3    C   CR15  0   0.035   3.4368   1.4212  -0.7340
 CQW  N8    N   N     0  -0.441   3.3957  -1.7344   0.7790
 CQW  C12   C   CR6   0   0.497   0.7733  -0.9135   0.2464
 CQW  N11   N   N     0  -0.482   1.0478  -2.0264   0.9232
 CQW  N14   N   NT    0  -0.501  -0.5398  -0.6529  -0.0147
 CQW  C28   C   CH2   0  -0.346  -1.5305  -1.4872   0.6604
 CQW  C27   C   CR5   0   0.075  -2.8663  -0.8456   0.4953
 CQW  N26   N   N     0  -0.462  -3.9961  -1.1784   1.1869
 CQW  C24   C   CR15  0   0.067  -4.9174  -0.3590   0.7443
 CQW  N22   N   NR15  0  -0.625  -4.4313   0.4812  -0.1949
 CQW  C15   C   CH2   0  -0.333  -0.9490  -0.2110  -1.3485
 CQW  H9    H   HCR6  0   0.252   2.4536  -3.2931   1.7109
 CQW  HN5   H   HNR5  0   0.422   5.0536   0.1946  -0.1439
 CQW  H18   H   HCH2  0   0.259  -2.5128   0.9109  -2.2956
 CQW  H18A  H   HCH2  0   0.251  -1.7807   1.7510  -0.9352
 CQW  H3    H   HCR5  0   0.312   3.9963   2.2772  -1.0718
 CQW  H28   H   HCH2  0   0.239  -1.5305  -2.5119   0.2661
 CQW  H28A  H   HCH2  0   0.262  -1.2735  -1.5614   1.7172
 CQW  H24   H   HCR5  0   0.274  -5.9466  -0.3276   1.0668
 CQW  HN22  H   HNR5  0   0.416  -4.9571   1.1871  -0.6855
 CQW  H15   H   HCH2  0   0.254  -1.2613  -1.0911  -1.9241
 CQW  H15A  H   HCH2  0   0.266  -0.1054   0.2186  -1.8779
 CQW  CL1   CL  CL    0  -0.139   0.9645   2.4620  -1.0897

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
 CQW  C7   C13   aromatic  1.410  0.020  1.410
 CQW  C7   N5    aromatic  1.351  0.020  1.351
 CQW  C7   N8    aromatic  1.332  0.020  1.332
 CQW  C9   N8    aromatic  1.314  0.020  1.314
 CQW  C9   N11   aromatic  1.330  0.020  1.330
 CQW  C13  C2    aromatic  1.432  0.020  1.432
 CQW  C13  C12   aromatic  1.418  0.020  1.418
 CQW  C21  C18   single    1.483  0.020  1.483
 CQW  C21  C27   aromatic  1.361  0.020  1.361
 CQW  C21  N22   aromatic  1.364  0.020  1.364
 CQW  N5   C3    aromatic  1.365  0.020  1.365
 CQW  C18  C15   single    1.525  0.020  1.525
 CQW  CL1  C2    single    1.717  0.020  1.717
 CQW  C2   C3    aromatic  1.362  0.020  1.362
 CQW  C12  N11   aromatic  1.331  0.020  1.331
 CQW  C12  N14   single    1.364  0.020  1.364
 CQW  N14  C28   single    1.461  0.020  1.461
 CQW  N14  C15   single    1.463  0.020  1.463
 CQW  C28  C27   single    1.491  0.020  1.491
 CQW  C27  N26   aromatic  1.366  0.020  1.366
 CQW  N26  C24   aromatic  1.310  0.020  1.310
 CQW  C24  N22   aromatic  1.351  0.020  1.351
 CQW  C9   H9    single    0.930  0.020  1.080
 CQW  N5   HN5   single    0.860  0.020  1.020
 CQW  C18  H18   single    0.970  0.020  1.090
 CQW  C18  H18A  single    0.970  0.020  1.090
 CQW  C3   H3    single    0.930  0.020  1.080
 CQW  C28  H28   single    0.970  0.020  1.090
 CQW  C28  H28A  single    0.970  0.020  1.090
 CQW  C24  H24   single    0.930  0.020  1.080
 CQW  N22  HN22  single    0.860  0.020  1.020
 CQW  C15  H15   single    0.970  0.020  1.090
 CQW  C15  H15A  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
 CQW  N8    C7   N5   124.89  3.000
 CQW  N8    C7   C13  126.35  3.000
 CQW  N5    C7   C13  108.69  3.000
 CQW  H9    C9   N11  115.82  3.000
 CQW  H9    C9   N8   116.74  3.000
 CQW  N11   C9   N8   127.43  3.000
 CQW  C12   C13  C2   140.34  3.000
 CQW  C12   C13  C7   114.60  3.000
 CQW  C2    C13  C7   104.99  3.000
 CQW  N22   C21  C27  105.15  3.000
 CQW  N22   C21  C18  129.86  3.000
 CQW  C27   C21  C18  124.99  3.000
 CQW  HN5   N5   C3   125.25  3.000
 CQW  HN5   N5   C7   125.11  3.000
 CQW  C3    N5   C7   109.56  3.000
 CQW  H18A  C18  H18  107.21  3.000
 CQW  H18A  C18  C15  110.98  3.000
 CQW  H18   C18  C15  108.93  3.000
 CQW  H18A  C18  C21  111.44  3.000
 CQW  H18   C18  C21  112.06  3.000
 CQW  C15   C18  C21  106.25  3.000
 CQW  C3    C2   CL1  122.61  3.000
 CQW  C3    C2   C13  107.96  3.000
 CQW  CL1   C2   C13  129.26  3.000
 CQW  H3    C3   C2   129.60  3.000
 CQW  H3    C3   N5   121.63  3.000
 CQW  C2    C3   N5   108.75  3.000
 CQW  C9    N8   C7   112.72  3.000
 CQW  N14   C12  N11  117.11  3.000
 CQW  N14   C12  C13  124.47  3.000
 CQW  N11   C12  C13  118.41  3.000
 CQW  C12   N11  C9   120.15  3.000
 CQW  C15   N14  C28  113.83  3.000
 CQW  C15   N14  C12  120.09  3.000
 CQW  C28   N14  C12  117.09  3.000
 CQW  H28A  C28  H28  106.53  3.000
 CQW  H28A  C28  C27  110.35  3.000
 CQW  H28   C28  C27  111.22  3.000
 CQW  H28A  C28  N14  109.09  3.000
 CQW  H28   C28  N14  111.54  3.000
 CQW  C27   C28  N14  108.10  3.000
 CQW  N26   C27  C28  125.46  3.000
 CQW  N26   C27  C21  110.78  3.000
 CQW  C28   C27  C21  123.75  3.000
 CQW  C24   N26  C27  104.96  3.000
 CQW  H24   C24  N22  122.21  3.000
 CQW  H24   C24  N26  126.02  3.000
 CQW  N22   C24  N26  111.77  3.000
 CQW  HN22  N22  C24  125.91  3.000
 CQW  HN22  N22  C21  126.76  3.000
 CQW  C24   N22  C21  107.33  3.000
 CQW  H15A  C15  H15  106.44  3.000
 CQW  H15A  C15  N14  110.30  3.000
 CQW  H15   C15  N14  108.40  3.000
 CQW  H15A  C15  C18  110.96  3.000
 CQW  H15   C15  C18  108.71  3.000
 CQW  N14   C15  C18  111.85  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
 CQW  CONST_01  C3    C2   C13  C7      0.00   0.0  0
 CQW  CONST_02  N11   C12  C13  C7      0.00   0.0  0
 CQW  CONST_03  C2    C3   N5   C7      0.00   0.0  0
 CQW  CONST_04  N11   C9   N8   C7      0.00   0.0  0
 CQW  CONST_05  C13   C7   N8   C9      0.00   0.0  0
 CQW  CONST_06  N5    C7   N8   C9    180.00   0.0  0
 CQW  CONST_07  C13   C12  N11  C9      0.00   0.0  0
 CQW  CONST_08  C3    N5   C7   C13     0.00   0.0  0
 CQW  CONST_09  N5    C3   C2   C13     0.00   0.0  0
 CQW  CONST_10  C24   N26  C27  C21     0.00   0.0  0
 CQW  CONST_11  N26   C24  N22  C21     0.00   0.0  0
 CQW  CONST_12  C2    C13  C7   N5      0.00   0.0  0
 CQW  CONST_13  C12   C13  C7   N5    180.00   0.0  0
 CQW  CONST_14  N8    C7   C13  C2    180.00   0.0  0
 CQW  CONST_15  N11   C12  C13  C2    180.00   0.0  0
 CQW  CONST_16  N8    C7   N5   C3    180.00   0.0  0
 CQW  CONST_17  C12   C13  C2   C3    180.00   0.0  0
 CQW  CONST_18  C12   C13  C7   N8      0.00   0.0  0
 CQW  CONST_19  C12   N11  C9   N8      0.00   0.0  0
 CQW  CONST_20  C24   N22  C21  C27     0.00   0.0  0
 CQW  CONST_21  N22   C24  N26  C27     0.00   0.0  0
 CQW  CONST_22  N22   C21  C27  N26     0.00   0.0  0
 CQW  CONST_23  N14   C12  C13  C7    180.00   0.0  0
 CQW  CONST_24  N14   C12  N11  C9    180.00   0.0  0
 CQW  CONST_25  N14   C12  C13  C2      0.00   0.0  0
 CQW  CONST_26  CL1   C2   C13  C7    180.00   0.0  0
 CQW  CONST_27  CL1   C2   C3   N5    180.00   0.0  0
 CQW  CONST_28  C12   C13  C2   CL1     0.00   0.0  0
 CQW  CONST_29  H3    C3   N5   C7    180.00   0.0  0
 CQW  CONST_30  H9    C9   N8   C7    180.00   0.0  0
 CQW  CONST_31  HN5   N5   C7   C13   180.00   0.0  0
 CQW  CONST_32  H24   C24  N22  C21   180.00   0.0  0
 CQW  CONST_33  HN22  N22  C21  C18     0.00   0.0  0
 CQW  Var_01    C28   N14  C12  C13  -168.30  30.0  2
 CQW  Var_02    N14   C15  C18  C21   -47.54  30.0  1
 CQW  Var_03    N14   C28  C27  C21    12.29  30.0  1
 CQW  Var_04    C12   N14  C15  C18  -145.77  30.0  1
 CQW  Var_05    C27   C28  N14  C12   166.95  30.0  1
 CQW  Var_06    C15   C18  C21  C27    15.62  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
 CQW  plan-1  C7    0.020
 CQW  plan-1  C9    0.020
 CQW  plan-1  C13   0.020
 CQW  plan-1  N5    0.020
 CQW  plan-1  C2    0.020
 CQW  plan-1  C3    0.020
 CQW  plan-1  N8    0.020
 CQW  plan-1  C12   0.020
 CQW  plan-1  N11   0.020
 CQW  plan-1  N14   0.020
 CQW  plan-1  H9    0.020
 CQW  plan-1  HN5   0.020
 CQW  plan-1  H3    0.020
 CQW  plan-1  CL1   0.020
 CQW  plan-2  C21   0.020
 CQW  plan-2  C18   0.020
 CQW  plan-2  C28   0.020
 CQW  plan-2  C27   0.020
 CQW  plan-2  N26   0.020
 CQW  plan-2  C24   0.020
 CQW  plan-2  N22   0.020
 CQW  plan-2  H24   0.020
 CQW  plan-2  HN22  0.020

