# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 02:24:09 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: ~{N}-(4-methoxyphenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2ncnc3[nH]ccc23)cc1
#
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
 9IO  9IO  "~{N}-(4-methoxyphenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine"
  ligand  30  18  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9IO
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
 9IO  N1   N  N     0  -0.489  72.3826  39.7625  -1.1515
 9IO  C2   C  CR16  0  -0.326  68.1677  41.9880  -3.4236
 9IO  N3   N  NR15  0  -0.658  72.3098  36.4613   1.1068
 9IO  C4   C  CR6   0   0.342  69.7937  40.8545  -2.0313
 9IO  C5   C  CR6   0   0.502  71.2242  39.2134  -0.8013
 9IO  C6   C  CR16  0   0.044  73.5155  39.1906  -0.7381
 9IO  C    C  CH3   0  -0.434  69.4942  45.1240  -4.6848
 9IO  C1   C  CR6   0   0.365  69.0682  43.0261  -3.6681
 9IO  C12  C  CR16  0  -0.371  70.3266  42.9673  -3.0816
 9IO  C11  C  CR16  0  -0.291  70.6851  41.8962  -2.2687
 9IO  C3   C  CR16  0  -0.339  68.5280  40.9231  -2.6245
 9IO  N    N  NH1   0  -0.768  70.0503  39.7510  -1.2093
 9IO  C10  C  CR56  0  -0.100  71.2233  38.0533   0.0000
 9IO  C9   C  CR15  0  -0.440  70.2579  37.1785   0.5820
 9IO  C8   C  CR15  0  -0.008  70.9668  36.2221   1.2480
 9IO  C7   C  CR56  0   0.479  72.4891  37.5700   0.3520
 9IO  N2   N  N     0  -0.446  73.6589  38.1119   0.0003
 9IO  H1   H  HCR6  0   0.262  67.1815  42.0171  -3.8699
 9IO  H2   H  HNR5  0   0.412  73.0477  35.9006   1.5023
 9IO  H3   H  HCR6  0   0.245  74.4279  39.6833  -1.0575
 9IO  H4   H  HCH3  0   0.257  68.9539  45.8173  -5.3249
 9IO  H5   H  HCH3  0   0.225  69.7481  45.6329  -3.7507
 9IO  H6   H  HCH3  0   0.225  70.4211  44.8334  -5.1871
 9IO  H7   H  HCR6  0   0.276  71.0561  43.7508  -3.2368
 9IO  H8   H  HCR6  0   0.277  71.6680  41.8834  -1.8272
 9IO  H9   H  HCR6  0   0.267  67.8109  40.1275  -2.4565
 9IO  H10  H  HNH1  0   0.418  69.2293  39.2247  -0.9511
 9IO  H11  H  HCR5  0   0.256  69.1827  37.2391   0.5236
 9IO  H12  H  HCR5  0   0.288  70.6179  35.3787   1.8207
 9IO  O    O  O2    0  -0.470  68.6386  44.0215  -4.4705

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
 9IO  C    O    single    1.412  0.020  1.412
 9IO  O    C1   single    1.349  0.020  1.349
 9IO  C2   C1   aromatic  1.396  0.020  1.396
 9IO  C2   C3   aromatic  1.379  0.020  1.379
 9IO  C1   C12  aromatic  1.390  0.020  1.390
 9IO  C3   C4   aromatic  1.399  0.020  1.399
 9IO  C12  C11  aromatic  1.392  0.020  1.392
 9IO  C4   C11  aromatic  1.391  0.020  1.391
 9IO  C4   N    single    1.400  0.020  1.400
 9IO  N1   C6   aromatic  1.335  0.020  1.335
 9IO  N1   C5   aromatic  1.329  0.020  1.329
 9IO  C6   N2   aromatic  1.315  0.020  1.315
 9IO  N    C5   single    1.354  0.020  1.354
 9IO  C5   C10  aromatic  1.410  0.020  1.410
 9IO  N2   C7   aromatic  1.336  0.020  1.336
 9IO  C10  C7   aromatic  1.400  0.020  1.400
 9IO  C10  C9   aromatic  1.427  0.020  1.427
 9IO  C7   N3   aromatic  1.353  0.020  1.353
 9IO  C9   C8   aromatic  1.364  0.020  1.364
 9IO  N3   C8   aromatic  1.371  0.020  1.371
 9IO  C2   H1   single    0.930  0.020  1.080
 9IO  N3   H2   single    0.860  0.020  1.020
 9IO  C6   H3   single    0.930  0.020  1.080
 9IO  C    H4   single    0.970  0.020  1.090
 9IO  C    H5   single    0.970  0.020  1.090
 9IO  C    H6   single    0.970  0.020  1.090
 9IO  C12  H7   single    0.930  0.020  1.080
 9IO  C11  H8   single    0.930  0.020  1.080
 9IO  C3   H9   single    0.930  0.020  1.080
 9IO  N    H10  single    0.860  0.020  1.020
 9IO  C9   H11  single    0.930  0.020  1.080
 9IO  C8   H12  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
 9IO  C6   N1   C5   118.77  3.000
 9IO  H1   C2   C3   119.83  3.000
 9IO  H1   C2   C1   119.69  3.000
 9IO  C3   C2   C1   120.48  3.000
 9IO  H2   N3   C7   125.29  3.000
 9IO  H2   N3   C8   125.43  3.000
 9IO  C7   N3   C8   109.28  3.000
 9IO  N    C4   C3   116.96  3.000
 9IO  N    C4   C11  124.96  3.000
 9IO  C3   C4   C11  118.06  3.000
 9IO  C10  C5   N    119.83  3.000
 9IO  C10  C5   N1   119.36  3.000
 9IO  N    C5   N1   120.82  3.000
 9IO  H3   C6   N2   116.50  3.000
 9IO  H3   C6   N1   115.34  3.000
 9IO  N2   C6   N1   128.17  3.000
 9IO  H6   C    H5   108.61  3.000
 9IO  H6   C    H4   108.67  3.000
 9IO  H5   C    H4   108.75  3.000
 9IO  H6   C    O    112.08  3.000
 9IO  H5   C    O    111.99  3.000
 9IO  H4   C    O    106.63  3.000
 9IO  C12  C1   O    124.80  3.000
 9IO  C12  C1   C2   118.61  3.000
 9IO  O    C1   C2   116.59  3.000
 9IO  H7   C12  C11  117.88  3.000
 9IO  H7   C12  C1   121.30  3.000
 9IO  C11  C12  C1   120.82  3.000
 9IO  H8   C11  C12  118.91  3.000
 9IO  H8   C11  C4   120.37  3.000
 9IO  C12  C11  C4   120.72  3.000
 9IO  H9   C3   C4   119.77  3.000
 9IO  H9   C3   C2   118.92  3.000
 9IO  C4   C3   C2   121.31  3.000
 9IO  H10  N    C5   114.92  3.000
 9IO  H10  N    C4   114.36  3.000
 9IO  C5   N    C4   130.46  3.000
 9IO  C7   C10  C9   107.31  3.000
 9IO  C9   C10  C5   137.45  3.000
 9IO  C7   C10  C5   115.24  3.000
 9IO  H11  C9   C8   125.72  3.000
 9IO  H11  C9   C10  128.17  3.000
 9IO  C8   C9   C10  106.10  3.000
 9IO  H12  C8   C9   129.79  3.000
 9IO  H12  C8   N3   120.55  3.000
 9IO  C9   C8   N3   109.65  3.000
 9IO  N2   C7   C10  125.82  3.000
 9IO  C10  C7   N3   107.65  3.000
 9IO  N2   C7   N3   126.52  3.000
 9IO  C7   N2   C6   112.64  3.000
 9IO  C1   O    C    118.26  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
 9IO  CONST_01  C7   N2   C6   N1      0.00   0.0  0
 9IO  CONST_02  C7   C10  C5   N1      0.00   0.0  0
 9IO  CONST_03  C9   C10  C5   N1    180.00   0.0  0
 9IO  CONST_04  C11  C12  C1   C2      0.00   0.0  0
 9IO  CONST_05  C11  C4   C3   C2      0.00   0.0  0
 9IO  CONST_06  C6   N2   C7   N3    180.00   0.0  0
 9IO  CONST_07  C5   C10  C7   N3    180.00   0.0  0
 9IO  CONST_08  C9   C10  C7   N3      0.00   0.0  0
 9IO  CONST_09  C10  C9   C8   N3      0.00   0.0  0
 9IO  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 9IO  CONST_11  C1   C12  C11  C4      0.00   0.0  0
 9IO  CONST_12  N2   C6   N1   C5      0.00   0.0  0
 9IO  CONST_13  N2   C7   C10  C5      0.00   0.0  0
 9IO  CONST_14  C8   C9   C10  C5    180.00   0.0  0
 9IO  CONST_15  C10  C5   N1   C6      0.00   0.0  0
 9IO  CONST_16  C10  C7   N2   C6      0.00   0.0  0
 9IO  CONST_17  C3   C2   C1   C12     0.00   0.0  0
 9IO  CONST_18  C3   C4   C11  C12     0.00   0.0  0
 9IO  CONST_19  C8   N3   C7   C10     0.00   0.0  0
 9IO  CONST_20  N2   C7   C10  C9    180.00   0.0  0
 9IO  CONST_21  C7   N3   C8   C9      0.00   0.0  0
 9IO  CONST_22  C7   C10  C9   C8      0.00   0.0  0
 9IO  CONST_23  N2   C7   N3   C8    180.00   0.0  0
 9IO  CONST_24  N    C4   C3   C2    180.00   0.0  0
 9IO  CONST_25  N    C5   N1   C6    180.00   0.0  0
 9IO  CONST_26  C3   C2   C1   O     180.00   0.0  0
 9IO  CONST_27  C11  C12  C1   O     180.00   0.0  0
 9IO  CONST_28  N    C4   C11  C12   180.00   0.0  0
 9IO  CONST_29  C7   C10  C5   N     180.00   0.0  0
 9IO  CONST_30  C9   C10  C5   N       0.00   0.0  0
 9IO  CONST_31  H7   C12  C1   C2    180.00   0.0  0
 9IO  CONST_32  H11  C9   C8   N3    180.00   0.0  0
 9IO  CONST_33  H1   C2   C3   C4    180.00   0.0  0
 9IO  CONST_34  H7   C12  C11  C4    180.00   0.0  0
 9IO  CONST_35  H3   C6   N1   C5    180.00   0.0  0
 9IO  CONST_36  H11  C9   C10  C5      0.00   0.0  0
 9IO  CONST_37  H9   C3   C2   C1    180.00   0.0  0
 9IO  CONST_38  H8   C11  C12  C1    180.00   0.0  0
 9IO  CONST_39  H1   C2   C1   C12   180.00   0.0  0
 9IO  CONST_40  H9   C3   C4   C11   180.00   0.0  0
 9IO  CONST_41  H8   C11  C4   C3    180.00   0.0  0
 9IO  CONST_42  H2   N3   C7   C10   180.00   0.0  0
 9IO  CONST_43  H12  C8   C9   C10   180.00   0.0  0
 9IO  CONST_44  H2   N3   C8   C9    180.00   0.0  0
 9IO  CONST_45  H3   C6   N2   C7    180.00   0.0  0
 9IO  CONST_46  H11  C9   C10  C7    180.00   0.0  0
 9IO  CONST_47  H12  C8   N3   C7    180.00   0.0  0
 9IO  CONST_48  H2   N3   C7   N2      0.00   0.0  0
 9IO  Var_01    C4   N    C5   N1      2.00  30.0  1
 9IO  Var_02    C10  C5   N    C4   -177.71  30.0  2
 9IO  Var_03    C3   C4   N    C5    159.94  30.0  2
 9IO  Var_04    C11  C4   N    C5    -21.92  30.0  2
 9IO  Var_05    C    O    C1   C2    176.71  30.0  2
 9IO  Var_06    C12  C1   O    C      -3.38  30.0  2
 9IO  Var_07    H10  N    C5   N1    175.60  30.0  1
 9IO  Var_08    H10  N    C4   C11   164.45  30.0  2
 9IO  Var_09    H10  N    C4   C3    -13.69  30.0  2
 9IO  Var_10    H10  N    C5   C10    -4.10  30.0  1
 9IO  Var_11    H4   C    O    C1   -178.23  30.0  3
 9IO  Var_12    H5   C    O    C1    -59.39  30.0  3
 9IO  Var_13    H6   C    O    C1     62.97  30.0  3

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
 9IO  plan-1  C2   0.020
 9IO  plan-1  C4   0.020
 9IO  plan-1  C1   0.020
 9IO  plan-1  C12  0.020
 9IO  plan-1  C11  0.020
 9IO  plan-1  C3   0.020
 9IO  plan-1  N    0.020
 9IO  plan-1  H1   0.020
 9IO  plan-1  H7   0.020
 9IO  plan-1  H8   0.020
 9IO  plan-1  H9   0.020
 9IO  plan-1  O    0.020
 9IO  plan-2  N1   0.020
 9IO  plan-2  N3   0.020
 9IO  plan-2  C5   0.020
 9IO  plan-2  C6   0.020
 9IO  plan-2  N    0.020
 9IO  plan-2  C10  0.020
 9IO  plan-2  C9   0.020
 9IO  plan-2  C8   0.020
 9IO  plan-2  C7   0.020
 9IO  plan-2  N2   0.020
 9IO  plan-2  H2   0.020
 9IO  plan-2  H3   0.020
 9IO  plan-2  H11  0.020
 9IO  plan-2  H12  0.020

