# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 02:30:38 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: ~{N}-(4-phenoxyphenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [nH]1ccc2c1ncnc2Nc3ccc(Oc4ccccc4)cc3
#
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
 9IK  9IK  "~{N}-(4-phenoxyphenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine"
  ligand  37  23  .  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_9IK
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
 9IK  N1   N  N     0  -0.480  22.5086  -27.1717  43.7262
 9IK  C2   C  CR16  0  -0.302  17.8894  -24.3882  37.3586
 9IK  N3   N  NR15  0  -0.658  25.2237  -30.0445  44.3397
 9IK  C4   C  CR6   0   0.353  19.4802  -25.1058  40.0580
 9IK  C5   C  CR16  0  -0.326  19.4074  -25.5125  41.3861
 9IK  C6   C  CR16  0  -0.279  20.3149  -26.4241  41.8966
 9IK  C17  C  CR16  0  -0.252  19.3203  -22.0723  36.7948
 9IK  C    C  CR16  0  -0.255  18.6214  -22.7185  35.7835
 9IK  C16  C  CR16  0  -0.301  19.3120  -22.5787  38.0875
 9IK  C3   C  CR6   0   0.302  18.5919  -23.7326  38.3590
 9IK  C1   C  CR16  0  -0.252  17.9049  -23.8735  36.0692
 9IK  O    O  O2    0  -0.512  18.5412  -24.2079  39.6454
 9IK  C15  C  CR16  0  -0.334  20.4736  -25.6237  39.2383
 9IK  C14  C  CR16  0  -0.328  21.3903  -26.5249  39.7598
 9IK  C7   C  CR6   0   0.341  21.3302  -26.9370  41.0880
 9IK  N    N  NH1   0  -0.765  22.2615  -27.8880  41.5260
 9IK  C8   C  CR6   0   0.488  22.8371  -28.0074  42.7470
 9IK  C13  C  CR56  0  -0.091  23.7934  -29.0141  42.9857
 9IK  C12  C  CR15  0  -0.440  24.4138  -30.0715  42.2551
 9IK  C11  C  CR15  0  -0.008  25.2798  -30.6721  43.1212
 9IK  C10  C  CR56  0   0.479  24.3266  -29.0335  44.2807
 9IK  N2   N  N     0  -0.446  24.0012  -28.2003  45.2729
 9IK  C9   C  CR16  0   0.040  23.0975  -27.3140  44.9145
 9IK  H2   H  HNR5  0   0.412  25.7663  -30.2944  45.1513
 9IK  H3   H  HCR6  0   0.267  18.6270  -25.1190  42.0254
 9IK  H4   H  HCR6  0   0.270  20.2257  -26.7307  42.9268
 9IK  H5   H  HCR6  0   0.262  19.8770  -21.1697  36.5793
 9IK  H6   H  HCR6  0   0.259  18.6310  -22.3204  34.7775
 9IK  H7   H  HCR6  0   0.271  19.8535  -22.0784  38.8807
 9IK  H8   H  HCR6  0   0.262  17.3551  -24.3794  35.2864
 9IK  H9   H  HCR6  0   0.279  20.5579  -25.3342  38.1994
 9IK  H10  H  HCR6  0   0.269  22.1671  -26.9136  39.1118
 9IK  H11  H  HNH1  0   0.416  22.6519  -28.4691  40.8004
 9IK  H12  H  HCR5  0   0.256  24.2478  -30.3582  41.2288
 9IK  H13  H  HCR5  0   0.288  25.9406  -31.5090  42.9663
 9IK  H14  H  HCR6  0   0.244  22.7889  -26.6039  45.6748
 9IK  H1   H  HCR6  0   0.271  17.3325  -25.2880  37.5882

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
 9IK  C    C1   aromatic  1.389  0.020  1.389
 9IK  C    C17  aromatic  1.389  0.020  1.389
 9IK  C1   C2   aromatic  1.388  0.020  1.388
 9IK  C17  C16  aromatic  1.388  0.020  1.388
 9IK  C2   C3   aromatic  1.387  0.020  1.387
 9IK  C16  C3   aromatic  1.387  0.020  1.387
 9IK  C3   O    single    1.372  0.020  1.372
 9IK  C15  C14  aromatic  1.387  0.020  1.387
 9IK  C15  C4   aromatic  1.388  0.020  1.388
 9IK  O    C4   single    1.363  0.020  1.363
 9IK  C14  C7   aromatic  1.392  0.020  1.392
 9IK  C4   C5   aromatic  1.391  0.020  1.391
 9IK  C7   N    single    1.401  0.020  1.401
 9IK  C7   C6   aromatic  1.396  0.020  1.396
 9IK  C5   C6   aromatic  1.384  0.020  1.384
 9IK  N    C8   single    1.355  0.020  1.355
 9IK  C12  C13  aromatic  1.427  0.020  1.427
 9IK  C12  C11  aromatic  1.364  0.020  1.364
 9IK  C8   C13  aromatic  1.409  0.020  1.409
 9IK  C8   N1   aromatic  1.329  0.020  1.329
 9IK  C13  C10  aromatic  1.401  0.020  1.401
 9IK  C11  N3   aromatic  1.372  0.020  1.372
 9IK  N1   C9   aromatic  1.334  0.020  1.334
 9IK  C10  N3   aromatic  1.353  0.020  1.353
 9IK  C10  N2   aromatic  1.336  0.020  1.336
 9IK  C9   N2   aromatic  1.316  0.020  1.316
 9IK  C2   H1   single    0.930  0.020  1.080
 9IK  N3   H2   single    0.860  0.020  1.020
 9IK  C5   H3   single    0.930  0.020  1.080
 9IK  C6   H4   single    0.930  0.020  1.080
 9IK  C17  H5   single    0.930  0.020  1.080
 9IK  C    H6   single    0.930  0.020  1.080
 9IK  C16  H7   single    0.930  0.020  1.080
 9IK  C1   H8   single    0.930  0.020  1.080
 9IK  C15  H9   single    0.930  0.020  1.080
 9IK  C14  H10  single    0.930  0.020  1.080
 9IK  N    H11  single    0.860  0.020  1.020
 9IK  C12  H12  single    0.930  0.020  1.080
 9IK  C11  H13  single    0.930  0.020  1.080
 9IK  C9   H14  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
 9IK  C9   N1   C8   118.71  3.000
 9IK  H1   C2   C1   120.71  3.000
 9IK  H1   C2   C3   120.02  3.000
 9IK  C1   C2   C3   119.27  3.000
 9IK  H2   N3   C10  125.27  3.000
 9IK  H2   N3   C11  125.45  3.000
 9IK  C10  N3   C11  109.28  3.000
 9IK  C15  C4   O    124.05  3.000
 9IK  O    C4   C5   116.47  3.000
 9IK  C15  C4   C5   119.48  3.000
 9IK  H3   C5   C6   119.61  3.000
 9IK  H3   C5   C4   119.68  3.000
 9IK  C6   C5   C4   120.70  3.000
 9IK  H4   C6   C7   120.60  3.000
 9IK  H4   C6   C5   119.04  3.000
 9IK  C7   C6   C5   120.36  3.000
 9IK  H5   C17  C16  119.52  3.000
 9IK  H5   C17  C    120.13  3.000
 9IK  C16  C17  C    120.35  3.000
 9IK  H6   C    C1   120.12  3.000
 9IK  H6   C    C17  120.10  3.000
 9IK  C1   C    C17  119.79  3.000
 9IK  H7   C16  C3   120.04  3.000
 9IK  H7   C16  C17  120.70  3.000
 9IK  C3   C16  C17  119.26  3.000
 9IK  O    C3   C16  119.39  3.000
 9IK  O    C3   C2   119.58  3.000
 9IK  C16  C3   C2   120.99  3.000
 9IK  H8   C1   C    120.14  3.000
 9IK  H8   C1   C2   119.53  3.000
 9IK  C    C1   C2   120.34  3.000
 9IK  C3   O    C4   119.11  3.000
 9IK  H9   C15  C14  118.91  3.000
 9IK  H9   C15  C4   121.53  3.000
 9IK  C14  C15  C4   119.56  3.000
 9IK  H10  C14  C7   119.69  3.000
 9IK  H10  C14  C15  118.81  3.000
 9IK  C7   C14  C15  121.50  3.000
 9IK  N    C7   C14  118.07  3.000
 9IK  N    C7   C6   123.49  3.000
 9IK  C14  C7   C6   118.38  3.000
 9IK  H11  N    C8   115.66  3.000
 9IK  H11  N    C7   115.06  3.000
 9IK  C8   N    C7   128.59  3.000
 9IK  C13  C8   N    120.26  3.000
 9IK  C13  C8   N1   119.50  3.000
 9IK  N    C8   N1   120.24  3.000
 9IK  C10  C13  C12  107.31  3.000
 9IK  C10  C13  C8   115.15  3.000
 9IK  C12  C13  C8   137.54  3.000
 9IK  H12  C12  C11  125.79  3.000
 9IK  H12  C12  C13  128.12  3.000
 9IK  C11  C12  C13  106.09  3.000
 9IK  H13  C11  C12  129.80  3.000
 9IK  H13  C11  N3   120.53  3.000
 9IK  C12  C11  N3   109.67  3.000
 9IK  N2   C10  C13  125.83  3.000
 9IK  N2   C10  N3   126.53  3.000
 9IK  C13  C10  N3   107.64  3.000
 9IK  C9   N2   C10  112.66  3.000
 9IK  H14  C9   N2   116.45  3.000
 9IK  H14  C9   N1   115.39  3.000
 9IK  N2   C9   N1   128.16  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
 9IK  CONST_01  C12  C13  C8   N1    180.00   0.0  0
 9IK  CONST_02  C10  C13  C8   N1      0.00   0.0  0
 9IK  CONST_03  C10  N2   C9   N1      0.00   0.0  0
 9IK  CONST_04  C17  C    C1   C2      0.00   0.0  0
 9IK  CONST_05  C17  C16  C3   C2      0.00   0.0  0
 9IK  CONST_06  C13  C12  C11  N3      0.00   0.0  0
 9IK  CONST_07  C12  C13  C10  N3      0.00   0.0  0
 9IK  CONST_08  C8   C13  C10  N3    180.00   0.0  0
 9IK  CONST_09  C9   N2   C10  N3    180.00   0.0  0
 9IK  CONST_10  C7   C14  C15  C4      0.00   0.0  0
 9IK  CONST_11  C7   C6   C5   C4      0.00   0.0  0
 9IK  CONST_12  C14  C15  C4   C5      0.00   0.0  0
 9IK  CONST_13  C14  C7   C6   C5      0.00   0.0  0
 9IK  CONST_14  C15  C14  C7   C6      0.00   0.0  0
 9IK  CONST_15  C15  C4   C5   C6      0.00   0.0  0
 9IK  CONST_16  C3   C2   C1   C       0.00   0.0  0
 9IK  CONST_17  C3   C16  C17  C       0.00   0.0  0
 9IK  CONST_18  C1   C    C17  C16     0.00   0.0  0
 9IK  CONST_19  C1   C2   C3   C16     0.00   0.0  0
 9IK  CONST_20  C11  C12  C13  C8    180.00   0.0  0
 9IK  CONST_21  N2   C10  C13  C8      0.00   0.0  0
 9IK  CONST_22  N2   C9   N1   C8      0.00   0.0  0
 9IK  CONST_23  C9   N1   C8   C13     0.00   0.0  0
 9IK  CONST_24  C11  N3   C10  C13     0.00   0.0  0
 9IK  CONST_25  C9   N2   C10  C13     0.00   0.0  0
 9IK  CONST_26  N2   C10  C13  C12   180.00   0.0  0
 9IK  CONST_27  C10  N3   C11  C12     0.00   0.0  0
 9IK  CONST_28  C10  C13  C12  C11     0.00   0.0  0
 9IK  CONST_29  N2   C10  N3   C11   180.00   0.0  0
 9IK  CONST_30  N    C7   C6   C5    180.00   0.0  0
 9IK  CONST_31  O    C4   C5   C6    180.00   0.0  0
 9IK  CONST_32  O    C3   C16  C17   180.00   0.0  0
 9IK  CONST_33  O    C3   C2   C1    180.00   0.0  0
 9IK  CONST_34  C14  C15  C4   O     180.00   0.0  0
 9IK  CONST_35  N    C7   C14  C15   180.00   0.0  0
 9IK  CONST_36  C12  C13  C8   N       0.00   0.0  0
 9IK  CONST_37  C10  C13  C8   N     180.00   0.0  0
 9IK  CONST_38  C9   N1   C8   N     180.00   0.0  0
 9IK  CONST_39  H6   C    C1   C2    180.00   0.0  0
 9IK  CONST_40  H7   C16  C3   C2    180.00   0.0  0
 9IK  CONST_41  H12  C12  C11  N3    180.00   0.0  0
 9IK  CONST_42  H10  C14  C15  C4    180.00   0.0  0
 9IK  CONST_43  H4   C6   C5   C4    180.00   0.0  0
 9IK  CONST_44  H9   C15  C4   C5    180.00   0.0  0
 9IK  CONST_45  H10  C14  C7   C6    180.00   0.0  0
 9IK  CONST_46  H8   C1   C    C17   180.00   0.0  0
 9IK  CONST_47  H1   C2   C1   C     180.00   0.0  0
 9IK  CONST_48  H7   C16  C17  C     180.00   0.0  0
 9IK  CONST_49  H6   C    C17  C16   180.00   0.0  0
 9IK  CONST_50  H1   C2   C3   C16   180.00   0.0  0
 9IK  CONST_51  H8   C1   C2   C3    180.00   0.0  0
 9IK  CONST_52  H5   C17  C16  C3    180.00   0.0  0
 9IK  CONST_53  H5   C17  C    C1    180.00   0.0  0
 9IK  CONST_54  H3   C5   C4   C15   180.00   0.0  0
 9IK  CONST_55  H4   C6   C7   C14   180.00   0.0  0
 9IK  CONST_56  H9   C15  C14  C7    180.00   0.0  0
 9IK  CONST_57  H3   C5   C6   C7    180.00   0.0  0
 9IK  CONST_58  H12  C12  C13  C8      0.00   0.0  0
 9IK  CONST_59  H14  C9   N1   C8    180.00   0.0  0
 9IK  CONST_60  H13  C11  C12  C13   180.00   0.0  0
 9IK  CONST_61  H2   N3   C10  C13   180.00   0.0  0
 9IK  CONST_62  H2   N3   C11  C12   180.00   0.0  0
 9IK  CONST_63  H12  C12  C13  C10   180.00   0.0  0
 9IK  CONST_64  H13  C11  N3   C10   180.00   0.0  0
 9IK  CONST_65  H14  C9   N2   C10   180.00   0.0  0
 9IK  CONST_66  H2   N3   C10  N2      0.00   0.0  0
 9IK  Var_01    C7   N    C8   N1      1.75  30.0  1
 9IK  Var_02    C4   O    C3   C2     91.19  30.0  2
 9IK  Var_03    C16  C3   O    C4    -90.82  30.0  2
 9IK  Var_04    C3   O    C4   C5    177.64  30.0  3
 9IK  Var_05    C8   N    C7   C6    -36.39  30.0  2
 9IK  Var_06    C15  C4   O    C3     -2.65  30.0  2
 9IK  Var_07    C8   N    C7   C14   146.33  30.0  2
 9IK  Var_08    C13  C8   N    C7   -177.92  30.0  2
 9IK  Var_09    H11  N    C8   N1    171.70  30.0  1
 9IK  Var_10    H11  N    C7   C6    153.61  30.0  2
 9IK  Var_11    H11  N    C7   C14   -23.67  30.0  2
 9IK  Var_12    H11  N    C8   C13    -7.97  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
 9IK  plan-1  C2   0.020
 9IK  plan-1  C17  0.020
 9IK  plan-1  C    0.020
 9IK  plan-1  C16  0.020
 9IK  plan-1  C3   0.020
 9IK  plan-1  C1   0.020
 9IK  plan-1  O    0.020
 9IK  plan-1  H5   0.020
 9IK  plan-1  H6   0.020
 9IK  plan-1  H7   0.020
 9IK  plan-1  H8   0.020
 9IK  plan-1  H1   0.020
 9IK  plan-2  C4   0.020
 9IK  plan-2  C5   0.020
 9IK  plan-2  C6   0.020
 9IK  plan-2  O    0.020
 9IK  plan-2  C15  0.020
 9IK  plan-2  C14  0.020
 9IK  plan-2  C7   0.020
 9IK  plan-2  N    0.020
 9IK  plan-2  H3   0.020
 9IK  plan-2  H4   0.020
 9IK  plan-2  H9   0.020
 9IK  plan-2  H10  0.020
 9IK  plan-3  N1   0.020
 9IK  plan-3  N3   0.020
 9IK  plan-3  N    0.020
 9IK  plan-3  C8   0.020
 9IK  plan-3  C13  0.020
 9IK  plan-3  C12  0.020
 9IK  plan-3  C11  0.020
 9IK  plan-3  C10  0.020
 9IK  plan-3  N2   0.020
 9IK  plan-3  C9   0.020
 9IK  plan-3  H2   0.020
 9IK  plan-3  H12  0.020
 9IK  plan-3  H13  0.020
 9IK  plan-3  H14  0.020

