# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:13:36 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: 4-(5-azaspiro[2.5]octan-5-yl)-7H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CC2(C1)CC2)c3ncnc4[nH]ccc34
#
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
 W5G  W5G  4-(5-azaspiro[2.5]octan-5-yl)-7H-pyrrolo[2,3-d]pyrimidine  ligand  33  17  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W5G
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
 W5G  N12   N  N     0  -0.456  -45.2013  -28.8524   6.6775
 W5G  C13   C  CR56  0   0.467  -46.2864  -29.1501   5.9594
 W5G  C15   C  CR15  0  -0.014  -48.3730  -29.7257   5.4648
 W5G  C17   C  CR56  0  -0.085  -46.3659  -29.2750   4.5583
 W5G  C01   C  CH2   0  -0.494  -42.1830  -31.2937   1.3665
 W5G  C02   C  CH2   0  -0.483  -43.0324  -31.6795   2.5462
 W5G  C03   C  CT    0   0.006  -43.5493  -30.7125   1.5253
 W5G  C04   C  CH2   0  -0.446  -44.6611  -31.1643   0.6032
 W5G  C05   C  CH2   0  -0.431  -46.0295  -30.8063   1.1816
 W5G  C06   C  CH2   0  -0.347  -46.0522  -29.3390   1.5920
 W5G  C08   C  CH2   0  -0.336  -43.6742  -29.2613   1.9342
 W5G  C09   C  CR6   0   0.510  -45.1432  -29.0423   3.8731
 W5G  C11   C  CR16  0   0.035  -44.1358  -28.6888   5.9223
 W5G  C16   C  CR15  0  -0.449  -47.7210  -29.6551   4.2713
 W5G  N07   N  NT    0  -0.469  -44.9863  -29.0432   2.5293
 W5G  N10   N  N     0  -0.494  -44.0529  -28.7696   4.6021
 W5G  N14   N  NR15  0  -0.656  -47.5061  -29.4159   6.4777
 W5G  H151  H  HCR5  0   0.287  -49.3988  -29.9784   5.6752
 W5G  H011  H  HCH2  0   0.246  -42.0305  -32.0268   0.5826
 W5G  H012  H  HCH2  0   0.246  -41.3262  -30.6541   1.5443
 W5G  H021  H  HCH2  0   0.244  -43.4591  -32.6755   2.5606
 W5G  H022  H  HCH2  0   0.246  -42.7521  -31.3017   3.5217
 W5G  H042  H  HCH2  0   0.234  -44.5917  -32.2404   0.4261
 W5G  H041  H  HCH2  0   0.226  -44.5381  -30.6793  -0.3704
 W5G  H052  H  HCH2  0   0.238  -46.8159  -30.9932   0.4470
 W5G  H051  H  HCH2  0   0.229  -46.2486  -31.4310   2.0529
 W5G  H061  H  HCH2  0   0.255  -45.8883  -28.7124   0.7095
 W5G  H062  H  HCH2  0   0.266  -47.0122  -29.0328   1.9921
 W5G  H082  H  HCH2  0   0.267  -42.8986  -28.9751   2.6386
 W5G  H081  H  HCH2  0   0.246  -43.5888  -28.6105   1.0580
 W5G  H111  H  HCR6  0   0.241  -43.2084  -28.4571   6.4373
 W5G  H161  H  HCR5  0   0.256  -48.1809  -29.8684   3.3220
 W5G  H141  H  HNR5  0   0.412  -47.7295  -29.4058   7.4597

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
 W5G  C04  C05   single    1.528  0.020  1.528
 W5G  C04  C03   single    1.513  0.020  1.513
 W5G  C05  C06   single    1.524  0.020  1.524
 W5G  C01  C03   single    1.493  0.020  1.493
 W5G  C01  C02   single    1.504  0.020  1.504
 W5G  C03  C08   single    1.513  0.020  1.513
 W5G  C03  C02   single    1.498  0.020  1.498
 W5G  C06  N07   single    1.450  0.020  1.450
 W5G  C08  N07   single    1.457  0.020  1.457
 W5G  N07  C09   single    1.353  0.020  1.353
 W5G  C09  C17   aromatic  1.421  0.020  1.421
 W5G  C09  N10   aromatic  1.340  0.020  1.340
 W5G  C16  C17   aromatic  1.436  0.020  1.436
 W5G  C16  C15   aromatic  1.362  0.020  1.362
 W5G  C17  C13   aromatic  1.409  0.020  1.409
 W5G  N10  C11   aromatic  1.325  0.020  1.325
 W5G  C15  N14   aromatic  1.369  0.020  1.369
 W5G  C13  N14   aromatic  1.352  0.020  1.352
 W5G  C13  N12   aromatic  1.335  0.020  1.335
 W5G  C11  N12   aromatic  1.316  0.020  1.316
 W5G  C15  H151  single    0.930  0.020  1.080
 W5G  C01  H011  single    0.970  0.020  1.090
 W5G  C01  H012  single    0.970  0.020  1.090
 W5G  C02  H021  single    0.970  0.020  1.090
 W5G  C02  H022  single    0.970  0.020  1.090
 W5G  C04  H042  single    0.970  0.020  1.090
 W5G  C04  H041  single    0.970  0.020  1.090
 W5G  C05  H052  single    0.970  0.020  1.090
 W5G  C05  H051  single    0.970  0.020  1.090
 W5G  C06  H061  single    0.970  0.020  1.090
 W5G  C06  H062  single    0.970  0.020  1.090
 W5G  C08  H082  single    0.970  0.020  1.090
 W5G  C08  H081  single    0.970  0.020  1.090
 W5G  C11  H111  single    0.930  0.020  1.080
 W5G  C16  H161  single    0.930  0.020  1.080
 W5G  N14  H141  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
 W5G  C11   N12  C13   112.16  3.000
 W5G  N14   C13  C17   108.23  3.000
 W5G  N14   C13  N12   124.83  3.000
 W5G  C17   C13  N12   126.92  3.000
 W5G  H151  C15  N14   120.78  3.000
 W5G  H151  C15  C16   129.74  3.000
 W5G  N14   C15  C16   109.49  3.000
 W5G  C16   C17  C09   139.36  3.000
 W5G  C16   C17  C13   105.99  3.000
 W5G  C09   C17  C13   114.61  3.000
 W5G  H012  C01  H011  113.98  3.000
 W5G  H012  C01  C03   118.43  3.000
 W5G  H011  C01  C03   117.95  3.000
 W5G  H012  C01  C02   117.98  3.000
 W5G  H011  C01  C02   118.24  3.000
 W5G  C03   C01  C02    59.98  3.000
 W5G  H022  C02  H021  114.24  3.000
 W5G  H022  C02  C03   118.55  3.000
 W5G  H021  C02  C03   117.80  3.000
 W5G  H022  C02  C01   118.09  3.000
 W5G  H021  C02  C01   117.94  3.000
 W5G  C03   C02  C01    59.65  3.000
 W5G  C08   C03  C04   112.98  3.000
 W5G  C08   C03  C02   117.61  3.000
 W5G  C04   C03  C02   118.42  3.000
 W5G  C02   C03  C01    60.36  3.000
 W5G  C08   C03  C01   118.53  3.000
 W5G  C04   C03  C01   119.42  3.000
 W5G  H041  C04  H042  106.56  3.000
 W5G  H041  C04  C05   109.48  3.000
 W5G  H042  C04  C05   110.43  3.000
 W5G  H041  C04  C03   109.09  3.000
 W5G  H042  C04  C03   110.25  3.000
 W5G  C05   C04  C03   110.93  3.000
 W5G  H051  C05  H052  107.08  3.000
 W5G  H051  C05  C06   109.40  3.000
 W5G  H052  C05  C06   109.58  3.000
 W5G  H051  C05  C04   110.30  3.000
 W5G  H052  C05  C04   110.49  3.000
 W5G  C06   C05  C04   109.93  3.000
 W5G  H062  C06  H061  105.57  3.000
 W5G  H062  C06  N07   110.78  3.000
 W5G  H061  C06  N07   107.12  3.000
 W5G  H062  C06  C05   112.61  3.000
 W5G  H061  C06  C05   109.38  3.000
 W5G  N07   C06  C05   111.08  3.000
 W5G  H081  C08  H082  107.87  3.000
 W5G  H081  C08  N07   107.95  3.000
 W5G  H082  C08  N07   109.80  3.000
 W5G  H081  C08  C03   110.33  3.000
 W5G  H082  C08  C03   111.66  3.000
 W5G  N07   C08  C03   109.16  3.000
 W5G  N10   C09  N07   116.51  3.000
 W5G  N10   C09  C17   118.12  3.000
 W5G  N07   C09  C17   125.36  3.000
 W5G  H111  C11  N10   115.60  3.000
 W5G  H111  C11  N12   116.48  3.000
 W5G  N10   C11  N12   127.92  3.000
 W5G  H161  C16  C17   129.19  3.000
 W5G  H161  C16  C15   123.93  3.000
 W5G  C17   C16  C15   106.87  3.000
 W5G  C09   N07  C08   120.67  3.000
 W5G  C09   N07  C06   123.85  3.000
 W5G  C08   N07  C06   111.56  3.000
 W5G  C11   N10  C09   120.24  3.000
 W5G  H141  N14  C15   125.68  3.000
 W5G  H141  N14  C13   124.89  3.000
 W5G  C15   N14  C13   109.41  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
 W5G  CONST_01  C09   C17  C13  N12     0.00   0.0  0
 W5G  CONST_02  C16   C17  C13  N12   180.00   0.0  0
 W5G  CONST_03  C15   N14  C13  N12   180.00   0.0  0
 W5G  CONST_04  C09   N10  C11  N12     0.00   0.0  0
 W5G  CONST_05  N10   C09  C17  C13     0.00   0.0  0
 W5G  CONST_06  C15   C16  C17  C13     0.00   0.0  0
 W5G  CONST_07  C16   C15  N14  C13     0.00   0.0  0
 W5G  CONST_08  N10   C11  N12  C13     0.00   0.0  0
 W5G  CONST_09  C09   C17  C16  C15   180.00   0.0  0
 W5G  CONST_10  C17   C13  N14  C15     0.00   0.0  0
 W5G  CONST_11  C11   N10  C09  C17     0.00   0.0  0
 W5G  CONST_12  N14   C15  C16  C17     0.00   0.0  0
 W5G  CONST_13  C11   N12  C13  C17     0.00   0.0  0
 W5G  CONST_14  N14   C13  C17  C09   180.00   0.0  0
 W5G  CONST_15  N14   C13  N12  C11   180.00   0.0  0
 W5G  CONST_16  N10   C09  C17  C16   180.00   0.0  0
 W5G  CONST_17  N14   C13  C17  C16     0.00   0.0  0
 W5G  CONST_18  N07   C09  C17  C13   180.00   0.0  0
 W5G  CONST_19  N07   C09  N10  C11   180.00   0.0  0
 W5G  CONST_20  N07   C09  C17  C16     0.00   0.0  0
 W5G  CONST_21  H141  N14  C13  N12     0.00   0.0  0
 W5G  CONST_22  H161  C16  C17  C13   180.00   0.0  0
 W5G  CONST_23  H151  C15  N14  C13   180.00   0.0  0
 W5G  CONST_24  H111  C11  N12  C13   180.00   0.0  0
 W5G  Var_01    C06   N07  C09  C17    -2.58  30.0  3
 W5G  Var_02    C05   C04  C03  C01   162.35  30.0  1
 W5G  Var_03    N07   C08  C03  C01  -157.88  30.0  1
 W5G  Var_04    C04   C03  C02  C01   109.55  30.0  3
 W5G  Var_05    C06   C05  C04  C03    50.17  30.0  1
 W5G  Var_06    N07   C06  C05  C04   -56.17  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
 W5G  plan-1  N12   0.020
 W5G  plan-1  C13   0.020
 W5G  plan-1  C15   0.020
 W5G  plan-1  C17   0.020
 W5G  plan-1  C09   0.020
 W5G  plan-1  C11   0.020
 W5G  plan-1  C16   0.020
 W5G  plan-1  N07   0.020
 W5G  plan-1  N10   0.020
 W5G  plan-1  N14   0.020
 W5G  plan-1  H151  0.020
 W5G  plan-1  H111  0.020
 W5G  plan-1  H161  0.020
 W5G  plan-1  H141  0.020

