# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:24:54 2021
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-[(2R)-2-cyclobutylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC(C1)[C@H]2CCCN2c3ncnc4[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
 W7Y  W7Y  4-[(2R)-2-cyclobutylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine  ligand  36  18  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_W7Y
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
 W7Y  C10   C  CR6   0   0.498  -45.5024  -29.2960   3.9947
 W7Y  C17   C  CR15  0  -0.439  -48.0409  -28.7300   4.5974
 W7Y  C01   C  C     0  -0.448  -43.0769  -32.8559   0.9875
 W7Y  C02   C  C     0  -0.445  -44.4782  -32.2255   1.0980
 W7Y  C03   C  C     0  -0.227  -43.8428  -31.1013   1.9432
 W7Y  C04   C  C     0  -0.441  -42.4813  -31.4771   1.3293
 W7Y  C05   C  CH1   0  -0.058  -44.3023  -29.6510   1.8739
 W7Y  C06   C  CH2   0  -0.491  -44.7028  -29.1591   0.4828
 W7Y  C07   C  CH2   0  -0.481  -46.2091  -29.3913   0.4129
 W7Y  C08   C  CH2   0  -0.275  -46.6847  -29.1282   1.8366
 W7Y  C12   C  CR16  0   0.032  -44.2605  -29.3769   5.9359
 W7Y  C14   C  CR56  0   0.466  -46.4068  -28.9358   6.1660
 W7Y  C16   C  CR15  0  -0.021  -48.5667  -28.5293   5.8382
 W7Y  C18   C  CR56  0  -0.080  -46.6443  -28.9971   4.7818
 W7Y  N09   N  NT    0  -0.496  -45.5189  -29.4125   2.6583
 W7Y  N11   N  N     0  -0.497  -44.3258  -29.4729   4.6135
 W7Y  N13   N  N     0  -0.458  -45.2354  -29.1197   6.7824
 W7Y  N15   N  NR15  0  -0.656  -47.5782  -28.6549   6.7794
 W7Y  H171  H  HCR5  0   0.256  -48.5999  -28.6826   3.6789
 W7Y  H012  H  H     0   0.224  -42.8957  -33.5808   1.7826
 W7Y  H021  H  H     0   0.224  -44.8120  -31.8711   0.1211
 W7Y  H022  H  H     0   0.228  -45.2785  -32.8140   1.5484
 W7Y  H031  H  H     0   0.245  -43.8410  -31.4070   2.9916
 W7Y  H042  H  H     0   0.228  -41.6053  -31.4364   1.9782
 W7Y  H041  H  H     0   0.221  -42.2686  -30.9033   0.4234
 W7Y  H051  H  HCH1  0   0.247  -43.4931  -29.0379   2.2806
 W7Y  H062  H  HCH2  0   0.248  -44.1582  -29.6678  -0.3133
 W7Y  H061  H  HCH2  0   0.248  -44.4833  -28.0932   0.3928
 W7Y  H071  H  HCH2  0   0.255  -46.7053  -28.7389  -0.3043
 W7Y  H072  H  HCH2  0   0.243  -46.4329  -30.4189   0.1256
 W7Y  H081  H  HCH2  0   0.239  -46.9997  -28.0875   1.9623
 W7Y  H082  H  HCH2  0   0.248  -47.5280  -29.7664   2.1049
 W7Y  H121  H  HCR6  0   0.239  -43.2757  -29.5311   6.3668
 W7Y  H161  H  HCR5  0   0.284  -49.5788  -28.3043   6.1304
 W7Y  H151  H  HNR5  0   0.411  -47.7005  -28.5580   7.7743
 W7Y  H011  H  H     0   0.226  -42.7991  -33.3076   0.0349

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
 W7Y  C07  C06   single    1.526  0.020  1.526
 W7Y  C07  C08   single    1.524  0.020  1.524
 W7Y  C06  C05   single    1.529  0.020  1.529
 W7Y  C04  C01   single    1.540  0.020  1.540
 W7Y  C04  C03   single    1.540  0.020  1.540
 W7Y  C01  C02   single    1.541  0.020  1.541
 W7Y  C02  C03   single    1.543  0.020  1.543
 W7Y  C08  N09   single    1.454  0.020  1.454
 W7Y  C05  C03   single    1.523  0.020  1.523
 W7Y  C05  N09   single    1.467  0.020  1.467
 W7Y  N09  C10   single    1.342  0.020  1.342
 W7Y  C10  N11   aromatic  1.341  0.020  1.341
 W7Y  C10  C18   aromatic  1.419  0.020  1.419
 W7Y  C17  C18   aromatic  1.434  0.020  1.434
 W7Y  C17  C16   aromatic  1.362  0.020  1.362
 W7Y  N11  C12   aromatic  1.328  0.020  1.328
 W7Y  C18  C14   aromatic  1.406  0.020  1.406
 W7Y  C16  N15   aromatic  1.371  0.020  1.371
 W7Y  C12  N13   aromatic  1.316  0.020  1.316
 W7Y  C14  N15   aromatic  1.352  0.020  1.352
 W7Y  C14  N13   aromatic  1.336  0.020  1.336
 W7Y  C17  H171  single    0.930  0.020  1.080
 W7Y  C01  H011  single    0.970  0.020  1.090
 W7Y  C01  H012  single    0.970  0.020  1.090
 W7Y  C02  H021  single    0.970  0.020  1.090
 W7Y  C02  H022  single    0.970  0.020  1.090
 W7Y  C03  H031  single    0.970  0.020  1.090
 W7Y  C04  H042  single    0.970  0.020  1.090
 W7Y  C04  H041  single    0.970  0.020  1.090
 W7Y  C05  H051  single    0.970  0.020  1.090
 W7Y  C06  H062  single    0.970  0.020  1.090
 W7Y  C06  H061  single    0.970  0.020  1.090
 W7Y  C07  H071  single    0.970  0.020  1.090
 W7Y  C07  H072  single    0.970  0.020  1.090
 W7Y  C08  H081  single    0.970  0.020  1.090
 W7Y  C08  H082  single    0.970  0.020  1.090
 W7Y  C12  H121  single    0.930  0.020  1.080
 W7Y  C16  H161  single    0.930  0.020  1.080
 W7Y  N15  H151  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
 W7Y  N11   C10  N09   117.32  3.000
 W7Y  N11   C10  C18   118.55  3.000
 W7Y  N09   C10  C18   124.13  3.000
 W7Y  H171  C17  C18   128.60  3.000
 W7Y  H171  C17  C16   124.77  3.000
 W7Y  C18   C17  C16   106.63  3.000
 W7Y  H012  C01  H011  108.61  3.000
 W7Y  H012  C01  C04   111.64  3.000
 W7Y  H011  C01  C04   117.79  3.000
 W7Y  H012  C01  C02   111.76  3.000
 W7Y  H011  C01  C02   117.64  3.000
 W7Y  C04   C01  C02    88.26  3.000
 W7Y  H022  C02  H021  108.69  3.000
 W7Y  H022  C02  C03   117.96  3.000
 W7Y  H021  C02  C03   112.31  3.000
 W7Y  H022  C02  C01   118.44  3.000
 W7Y  H021  C02  C01   110.29  3.000
 W7Y  C03   C02  C01    87.87  3.000
 W7Y  H031  C03  C05   108.11  3.000
 W7Y  H031  C03  C04   108.23  3.000
 W7Y  C05   C03  C04   118.75  3.000
 W7Y  H031  C03  C02   108.81  3.000
 W7Y  C05   C03  C02   123.00  3.000
 W7Y  C04   C03  C02    88.16  3.000
 W7Y  H041  C04  H042  108.49  3.000
 W7Y  H041  C04  C03   111.97  3.000
 W7Y  H042  C04  C03   117.62  3.000
 W7Y  H041  C04  C01   111.17  3.000
 W7Y  H042  C04  C01   118.42  3.000
 W7Y  C03   C04  C01    87.99  3.000
 W7Y  H051  C05  N09   108.88  3.000
 W7Y  H051  C05  C06   110.60  3.000
 W7Y  N09   C05  C06   102.53  3.000
 W7Y  H051  C05  C03   107.08  3.000
 W7Y  N09   C05  C03   112.37  3.000
 W7Y  C06   C05  C03   115.27  3.000
 W7Y  H061  C06  H062  107.14  3.000
 W7Y  H061  C06  C07   110.08  3.000
 W7Y  H062  C06  C07   112.87  3.000
 W7Y  H061  C06  C05   109.66  3.000
 W7Y  H062  C06  C05   112.54  3.000
 W7Y  C07   C06  C05   104.56  3.000
 W7Y  H072  C07  H071  107.31  3.000
 W7Y  H072  C07  C08   110.17  3.000
 W7Y  H071  C07  C08   111.69  3.000
 W7Y  H072  C07  C06   110.99  3.000
 W7Y  H071  C07  C06   112.88  3.000
 W7Y  C08   C07  C06   103.83  3.000
 W7Y  H082  C08  H081  107.79  3.000
 W7Y  H082  C08  N09   111.49  3.000
 W7Y  H081  C08  N09   110.59  3.000
 W7Y  H082  C08  C07   111.71  3.000
 W7Y  H081  C08  C07   111.17  3.000
 W7Y  N09   C08  C07   104.12  3.000
 W7Y  H121  C12  N13   116.37  3.000
 W7Y  H121  C12  N11   115.44  3.000
 W7Y  N13   C12  N11   128.18  3.000
 W7Y  N15   C14  N13   125.37  3.000
 W7Y  N13   C14  C18   126.60  3.000
 W7Y  N15   C14  C18   108.03  3.000
 W7Y  H161  C16  N15   120.69  3.000
 W7Y  H161  C16  C17   129.82  3.000
 W7Y  N15   C16  C17   109.49  3.000
 W7Y  C14   C18  C17   106.44  3.000
 W7Y  C14   C18  C10   114.80  3.000
 W7Y  C17   C18  C10   138.75  3.000
 W7Y  C08   N09  C05   113.23  3.000
 W7Y  C05   N09  C10   122.45  3.000
 W7Y  C08   N09  C10   123.76  3.000
 W7Y  C12   N11  C10   119.56  3.000
 W7Y  C14   N13  C12   112.30  3.000
 W7Y  H151  N15  C16   125.60  3.000
 W7Y  H151  N15  C14   124.99  3.000
 W7Y  C16   N15  C14   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
 W7Y  CONST_01  N13   C12  N11  C10    0.00   0.0  0
 W7Y  CONST_02  C16   C17  C18  C10  180.00   0.0  0
 W7Y  CONST_03  N15   C14  C18  C10  180.00   0.0  0
 W7Y  CONST_04  N13   C14  C18  C10    0.00   0.0  0
 W7Y  CONST_05  N11   C10  C18  C17  180.00   0.0  0
 W7Y  CONST_06  N15   C14  C18  C17    0.00   0.0  0
 W7Y  CONST_07  N13   C14  C18  C17  180.00   0.0  0
 W7Y  CONST_08  C14   N15  C16  C17    0.00   0.0  0
 W7Y  CONST_09  C18   C10  N11  C12    0.00   0.0  0
 W7Y  CONST_10  C18   C14  N13  C12    0.00   0.0  0
 W7Y  CONST_11  N15   C14  N13  C12  180.00   0.0  0
 W7Y  CONST_12  N11   C10  C18  C14    0.00   0.0  0
 W7Y  CONST_13  C16   C17  C18  C14    0.00   0.0  0
 W7Y  CONST_14  N11   C12  N13  C14    0.00   0.0  0
 W7Y  CONST_15  C18   C14  N15  C16    0.00   0.0  0
 W7Y  CONST_16  N13   C14  N15  C16  180.00   0.0  0
 W7Y  CONST_17  N15   C16  C17  C18    0.00   0.0  0
 W7Y  CONST_18  N09   C10  C18  C17    0.00   0.0  0
 W7Y  CONST_19  N09   C10  N11  C12  180.00   0.0  0
 W7Y  CONST_20  N09   C10  C18  C14  180.00   0.0  0
 W7Y  CONST_21  H121  C12  N11  C10  180.00   0.0  0
 W7Y  CONST_22  H171  C17  C18  C10    0.00   0.0  0
 W7Y  CONST_23  H151  N15  C16  C17  180.00   0.0  0
 W7Y  CONST_24  H161  C16  N15  C14  180.00   0.0  0
 W7Y  Var_01    C07   C08  N09  C10  179.52  30.0  1
 W7Y  Var_02    C03   C04  C01  C02   20.82  30.0  1
 W7Y  Var_03    C08   C07  C06  C05   34.69  30.0  1
 W7Y  Var_04    N11   C10  N09  C05   -3.26  30.0  2
 W7Y  Var_05    N09   C08  C07  C06  -26.07  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 W7Y  chir_01  C03  C04  C02  C05  positiv
 W7Y  chir_02  C05  N09  C06  C03  positiv

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
 W7Y  plan-1  C10   0.020
 W7Y  plan-1  C17   0.020
 W7Y  plan-1  C12   0.020
 W7Y  plan-1  C14   0.020
 W7Y  plan-1  C16   0.020
 W7Y  plan-1  C18   0.020
 W7Y  plan-1  N09   0.020
 W7Y  plan-1  N11   0.020
 W7Y  plan-1  N13   0.020
 W7Y  plan-1  N15   0.020
 W7Y  plan-1  H171  0.020
 W7Y  plan-1  H121  0.020
 W7Y  plan-1  H161  0.020
 W7Y  plan-1  H151  0.020

