# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:16:40 2021
#   Inital geometry file: a 92 line input string
#   Ligand name: 4-[5-(3-chlorophenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]morpholine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(c1)c2c[nH]c3ncnc(N4CCOCC4)c23
#
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
 OJ5  OJ5  4-[5-(3-chlorophenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]morpholine  ligand  37  22  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OJ5
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
 OJ5  N1   N   N     0  -0.440   0.1479  3.2318  19.1134
 OJ5  C2   C   CR16  0  -0.242   6.1691  6.6235  18.7993
 OJ5  N3   N   NT    0  -0.496   2.0522  6.7860  20.1045
 OJ5  C4   C   CR6   0   0.008   4.2830  5.5969  17.6936
 OJ5  C5   C   CR5   0  -0.033   3.0668  4.7809  17.7435
 OJ5  C6   C   CR15  0  -0.040   2.8328  3.7115  16.9201
 OJ5  C    C   CR6   0  -0.021   5.9673  6.7584  16.4300
 OJ5  C15  C   CR16  0  -0.269   4.7840  6.0397  16.4687
 OJ5  C3   C   CR16  0  -0.300   4.9907  5.8972  18.8590
 OJ5  C1   C   CR16  0  -0.233   6.6729  7.0633  17.5829
 OJ5  C14  C   CR56  0  -0.073   1.9899  4.7830  18.6986
 OJ5  C7   C   CR56  0   0.489   1.1935  3.6600  18.4093
 OJ5  N    N   NR15  0  -0.659   1.7050  3.0528  17.3137
 OJ5  C9   C   CR6   0   0.438   1.5232  5.5653  19.7788
 OJ5  N2   N   N     0  -0.474   0.5236  5.1018  20.5248
 OJ5  C8   C   CR16  0   0.037  -0.0893  3.9742  20.1738
 OJ5  C13  C   CH2   0  -0.336   2.1825  7.7805  19.0426
 OJ5  C12  C   CH2   0  -0.187   3.1065  8.8978  19.4812
 OJ5  O    O   O2    0  -0.483   2.6743  9.4851  20.6876
 OJ5  C11  C   CH2   0  -0.191   2.5928  8.5183  21.7101
 OJ5  C10  C   CH2   0  -0.314   1.6339  7.3963  21.3576
 OJ5  H1   H   HCR6  0   0.269   6.7085  6.8476  19.7102
 OJ5  H2   H   HCR5  0   0.299   3.4258  3.3426  16.0988
 OJ5  H3   H   HCR6  0   0.273   4.2433  5.8350  15.5538
 OJ5  H4   H   HCR6  0   0.257   4.6188  5.5583  19.8162
 OJ5  H5   H   HCR6  0   0.279   7.5924  7.6304  17.5366
 OJ5  H6   H   HNR5  0   0.418   1.3479  2.2065  16.8993
 OJ5  H7   H   HCR6  0   0.250  -0.8932  3.6487  20.8257
 OJ5  H8   H   HCH2  0   0.242   1.1931  8.1924  18.7995
 OJ5  H9   H   HCH2  0   0.274   2.5755  7.3326  18.1342
 OJ5  H10  H   HCH2  0   0.213   4.1278  8.5085  19.5842
 OJ5  H11  H   HCH2  0   0.243   3.1193  9.6781  18.7193
 OJ5  H12  H   HCH2  0   0.205   3.5851  8.0966  21.9232
 OJ5  H13  H   HCH2  0   0.243   2.2442  9.0233  22.6122
 OJ5  H14  H   HCH2  0   0.226   0.6088  7.7831  21.2920
 OJ5  H15  H   HCH2  0   0.259   1.6515  6.6532  22.1529
 OJ5  CL   CL  CL    0  -0.132   6.5713  7.3011  14.8962

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
 OJ5  CL   C    single    1.735  0.020  1.735
 OJ5  C    C15  aromatic  1.385  0.020  1.385
 OJ5  C    C1   aromatic  1.386  0.020  1.386
 OJ5  C15  C4   aromatic  1.395  0.020  1.395
 OJ5  C6   N    aromatic  1.364  0.020  1.364
 OJ5  C6   C5   aromatic  1.370  0.020  1.370
 OJ5  C1   C2   aromatic  1.388  0.020  1.388
 OJ5  N    C7   aromatic  1.353  0.020  1.353
 OJ5  C4   C5   single    1.465  0.020  1.465
 OJ5  C4   C3   aromatic  1.396  0.020  1.396
 OJ5  C5   C14  aromatic  1.439  0.020  1.439
 OJ5  C7   C14  aromatic  1.407  0.020  1.407
 OJ5  C7   N1   aromatic  1.331  0.020  1.331
 OJ5  C2   C3   aromatic  1.386  0.020  1.386
 OJ5  C14  C9   aromatic  1.413  0.020  1.413
 OJ5  C13  C12  single    1.515  0.020  1.515
 OJ5  C13  N3   single    1.461  0.020  1.461
 OJ5  N1   C8   aromatic  1.316  0.020  1.316
 OJ5  C12  O    single    1.410  0.020  1.410
 OJ5  C9   N3   single    1.370  0.020  1.370
 OJ5  C9   N2   aromatic  1.331  0.020  1.331
 OJ5  C8   N2   aromatic  1.331  0.020  1.331
 OJ5  N3   C10  single    1.455  0.020  1.455
 OJ5  O    C11  single    1.410  0.020  1.410
 OJ5  C10  C11  single    1.517  0.020  1.517
 OJ5  C2   H1   single    0.930  0.020  1.080
 OJ5  C6   H2   single    0.930  0.020  1.080
 OJ5  C15  H3   single    0.930  0.020  1.080
 OJ5  C3   H4   single    0.930  0.020  1.080
 OJ5  C1   H5   single    0.930  0.020  1.080
 OJ5  N    H6   single    0.860  0.020  1.020
 OJ5  C8   H7   single    0.930  0.020  1.080
 OJ5  C13  H8   single    0.970  0.020  1.090
 OJ5  C13  H9   single    0.970  0.020  1.090
 OJ5  C12  H10  single    0.970  0.020  1.090
 OJ5  C12  H11  single    0.970  0.020  1.090
 OJ5  C11  H12  single    0.970  0.020  1.090
 OJ5  C11  H13  single    0.970  0.020  1.090
 OJ5  C10  H14  single    0.970  0.020  1.090
 OJ5  C10  H15  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
 OJ5  C8   N1   C7   112.72  3.000
 OJ5  H1   C2   C1   119.41  3.000
 OJ5  H1   C2   C3   119.75  3.000
 OJ5  C1   C2   C3   120.84  3.000
 OJ5  C10  N3   C13  111.48  3.000
 OJ5  C10  N3   C9   117.88  3.000
 OJ5  C13  N3   C9   117.92  3.000
 OJ5  C3   C4   C15  118.85  3.000
 OJ5  C3   C4   C5   120.79  3.000
 OJ5  C15  C4   C5   120.30  3.000
 OJ5  C14  C5   C6   105.79  3.000
 OJ5  C14  C5   C4   130.00  3.000
 OJ5  C6   C5   C4   123.78  3.000
 OJ5  H2   C6   N    120.62  3.000
 OJ5  H2   C6   C5   129.13  3.000
 OJ5  N    C6   C5   110.17  3.000
 OJ5  C1   C    C15  121.73  3.000
 OJ5  C1   C    CL   119.30  3.000
 OJ5  C15  C    CL   118.97  3.000
 OJ5  H3   C15  C    120.10  3.000
 OJ5  H3   C15  C4   120.17  3.000
 OJ5  C    C15  C4   119.73  3.000
 OJ5  H4   C3   C4   119.82  3.000
 OJ5  H4   C3   C2   119.67  3.000
 OJ5  C4   C3   C2   120.52  3.000
 OJ5  H5   C1   C    120.85  3.000
 OJ5  H5   C1   C2   120.82  3.000
 OJ5  C    C1   C2   118.33  3.000
 OJ5  C9   C14  C7   114.34  3.000
 OJ5  C9   C14  C5   139.03  3.000
 OJ5  C7   C14  C5   106.61  3.000
 OJ5  N    C7   C14  108.10  3.000
 OJ5  C14  C7   N1   126.34  3.000
 OJ5  N    C7   N1   125.51  3.000
 OJ5  H6   N    C7   125.16  3.000
 OJ5  H6   N    C6   125.45  3.000
 OJ5  C7   N    C6   109.24  3.000
 OJ5  N2   C9   C14  118.93  3.000
 OJ5  N2   C9   N3   117.85  3.000
 OJ5  C14  C9   N3   123.21  3.000
 OJ5  C8   N2   C9   119.56  3.000
 OJ5  H7   C8   N2   115.92  3.000
 OJ5  H7   C8   N1   116.64  3.000
 OJ5  N2   C8   N1   127.42  3.000
 OJ5  H9   C13  H8   107.17  3.000
 OJ5  H9   C13  C12  109.00  3.000
 OJ5  H8   C13  C12  109.68  3.000
 OJ5  H9   C13  N3   111.07  3.000
 OJ5  H8   C13  N3   109.61  3.000
 OJ5  C12  C13  N3   110.25  3.000
 OJ5  H11  C12  H10  107.95  3.000
 OJ5  H11  C12  O    107.66  3.000
 OJ5  H10  C12  O    110.66  3.000
 OJ5  H11  C12  C13  109.43  3.000
 OJ5  H10  C12  C13  109.46  3.000
 OJ5  O    C12  C13  111.60  3.000
 OJ5  C11  O    C12  110.66  3.000
 OJ5  H13  C11  H12  107.81  3.000
 OJ5  H13  C11  C10  109.42  3.000
 OJ5  H12  C11  C10  109.38  3.000
 OJ5  H13  C11  O    107.51  3.000
 OJ5  H12  C11  O    110.58  3.000
 OJ5  C10  C11  O    112.03  3.000
 OJ5  H15  C10  H14  107.42  3.000
 OJ5  H15  C10  C11  108.95  3.000
 OJ5  H14  C10  C11  110.09  3.000
 OJ5  H15  C10  N3   109.77  3.000
 OJ5  H14  C10  N3   111.40  3.000
 OJ5  C11  C10  N3   109.18  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
 OJ5  CONST_01  C6   N    C7   N1    180.00   0.0  0
 OJ5  CONST_02  C5   C14  C7   N1    180.00   0.0  0
 OJ5  CONST_03  C9   C14  C7   N1      0.00   0.0  0
 OJ5  CONST_04  C9   N2   C8   N1      0.00   0.0  0
 OJ5  CONST_05  C15  C    C1   C2      0.00   0.0  0
 OJ5  CONST_06  C15  C4   C3   C2      0.00   0.0  0
 OJ5  CONST_07  C5   C4   C3   C2    180.00   0.0  0
 OJ5  CONST_08  C1   C    C15  C4      0.00   0.0  0
 OJ5  CONST_09  N    C6   C5   C4    180.00   0.0  0
 OJ5  CONST_10  C7   C14  C5   C4    180.00   0.0  0
 OJ5  CONST_11  C9   C14  C5   C4      0.00   0.0  0
 OJ5  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 OJ5  CONST_13  C7   N    C6   C5      0.00   0.0  0
 OJ5  CONST_14  C    C15  C4   C5    180.00   0.0  0
 OJ5  CONST_15  N    C7   C14  C5      0.00   0.0  0
 OJ5  CONST_16  N2   C9   C14  C5    180.00   0.0  0
 OJ5  CONST_17  C14  C7   N    C6      0.00   0.0  0
 OJ5  CONST_20  C7   C14  C5   C6      0.00   0.0  0
 OJ5  CONST_21  C9   C14  C5   C6    180.00   0.0  0
 OJ5  CONST_22  C3   C4   C15  C       0.00   0.0  0
 OJ5  CONST_23  C3   C2   C1   C       0.00   0.0  0
 OJ5  CONST_26  N    C6   C5   C14     0.00   0.0  0
 OJ5  CONST_27  C8   N1   C7   C14     0.00   0.0  0
 OJ5  CONST_28  C8   N2   C9   C14     0.00   0.0  0
 OJ5  CONST_29  N2   C9   C14  C7      0.00   0.0  0
 OJ5  CONST_30  N2   C8   N1   C7      0.00   0.0  0
 OJ5  CONST_31  C9   C14  C7   N     180.00   0.0  0
 OJ5  CONST_32  C8   N1   C7   N     180.00   0.0  0
 OJ5  CONST_33  C5   C14  C9   N3      0.00   0.0  0
 OJ5  CONST_34  C7   C14  C9   N3    180.00   0.0  0
 OJ5  CONST_35  C8   N2   C9   N3    180.00   0.0  0
 OJ5  CONST_36  CL   C    C1   C2    180.00   0.0  0
 OJ5  CONST_37  CL   C    C15  C4    180.00   0.0  0
 OJ5  CONST_38  H6   N    C7   N1      0.00   0.0  0
 OJ5  CONST_39  H2   C6   C5   C4      0.00   0.0  0
 OJ5  CONST_40  H1   C2   C3   C4    180.00   0.0  0
 OJ5  CONST_41  H3   C15  C4   C5      0.00   0.0  0
 OJ5  CONST_42  H4   C3   C4   C5      0.00   0.0  0
 OJ5  CONST_43  H5   C1   C    C15   180.00   0.0  0
 OJ5  CONST_44  H7   C8   N1   C7    180.00   0.0  0
 OJ5  Var_01    O    C12  C13  N3    -55.57  30.0  1
 OJ5  Var_02    O    C11  C10  N3     57.00  30.0  1
 OJ5  Var_03    C13  N3   C9   C14    51.05  30.0  2
 OJ5  Var_04    C12  C13  N3   C9   -164.74  30.0  1
 OJ5  Var_05    C11  C10  N3   C9    164.54  30.0  1
 OJ5  Var_06    C10  C11  O    C12   -59.09  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
 OJ5  plan-1  C2   0.020
 OJ5  plan-1  C4   0.020
 OJ5  plan-1  C5   0.020
 OJ5  plan-1  C    0.020
 OJ5  plan-1  C15  0.020
 OJ5  plan-1  C3   0.020
 OJ5  plan-1  C1   0.020
 OJ5  plan-1  H1   0.020
 OJ5  plan-1  H3   0.020
 OJ5  plan-1  H4   0.020
 OJ5  plan-1  H5   0.020
 OJ5  plan-1  CL   0.020
 OJ5  plan-2  N1   0.020
 OJ5  plan-2  N3   0.020
 OJ5  plan-2  C4   0.020
 OJ5  plan-2  C5   0.020
 OJ5  plan-2  C6   0.020
 OJ5  plan-2  C14  0.020
 OJ5  plan-2  C7   0.020
 OJ5  plan-2  N    0.020
 OJ5  plan-2  C9   0.020
 OJ5  plan-2  N2   0.020
 OJ5  plan-2  C8   0.020
 OJ5  plan-2  H2   0.020
 OJ5  plan-2  H6   0.020
 OJ5  plan-2  H7   0.020

