# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 05:33:52 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: ~{N}-[4-(2-chloranylphenoxy)phenyl]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1Oc2ccc(Nc3ncnc4[nH]ccc34)cc2
#
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
 9IV  9IV  "~{N}-[4-(2-chloranylphenoxy)phenyl]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-amine"
  ligand  37  24  .  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_9IV
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
 9IV  N1   N   N     0  -0.477  72.1252  39.7922  -0.8674
 9IV  C2   C   CR16  0  -0.260  66.3315  44.6051  -7.2133
 9IV  N3   N   NR15  0  -0.658  71.9421  36.4429   1.3114
 9IV  C4   C   CR16  0  -0.308  68.5688  44.0769  -6.5099
 9IV  C5   C   CR6   0   0.369  68.2283  44.3775  -5.2000
 9IV  C6   C   CR6   0   0.357  69.2805  43.1770  -3.4707
 9IV  C    C   CR6   0  -0.107  66.9324  44.7856  -4.9009
 9IV  C3   C   CR16  0  -0.247  67.6224  44.1954  -7.5168
 9IV  C1   C   CR16  0  -0.223  65.9832  44.9036  -5.9042
 9IV  O    O   O2    0  -0.499  69.1721  44.3159  -4.2197
 9IV  C17  C   CR16  0  -0.330  68.5094  42.0421  -3.6709
 9IV  C16  C   CR16  0  -0.322  68.7196  40.9257  -2.8737
 9IV  C9   C   CR6   0   0.339  69.6774  40.9272  -1.8651
 9IV  C8   C   CR16  0  -0.275  70.4275  42.0853  -1.6590
 9IV  C7   C   CR16  0  -0.324  70.2345  43.1957  -2.4605
 9IV  N    N   NH1   0  -0.764  69.8081  39.7838  -1.0646
 9IV  C10  C   CR6   0   0.482  70.9530  39.2288  -0.5956
 9IV  C15  C   CR56  0  -0.086  70.9110  38.0511   0.1752
 9IV  C14  C   CR15  0  -0.439  69.9190  37.1587   0.6812
 9IV  C13  C   CR15  0  -0.009  70.5944  36.1926   1.3673
 9IV  C12  C   CR56  0   0.479  72.1582  37.5679   0.5915
 9IV  N2   N   N     0  -0.445  73.3419  38.1252   0.3237
 9IV  C11  C   CR16  0   0.038  73.2350  39.2192  -0.3996
 9IV  H1   H   HCR6  0   0.270  65.5904  44.6992  -7.9955
 9IV  H2   H   HNR5  0   0.412  72.6597  35.8770   1.7360
 9IV  H3   H   HCR6  0   0.281  69.5798  43.7608  -6.7338
 9IV  H4   H   HCR6  0   0.269  67.8955  43.9655  -8.5378
 9IV  H5   H   HCR6  0   0.284  64.9791  45.2247  -5.6616
 9IV  H6   H   HCR6  0   0.283  67.7553  41.9971  -4.4456
 9IV  H7   H   HCR6  0   0.270  68.1230  40.0383  -3.0478
 9IV  H8   H   HCR6  0   0.268  71.1616  42.1306  -0.8695
 9IV  H9   H   HCR6  0   0.269  70.8231  44.0888  -2.2923
 9IV  H10  H   HNH1  0   0.415  68.9736  39.2272  -0.9634
 9IV  H11  H   HCR5  0   0.256  68.8490  37.2160   0.5609
 9IV  H12  H   HCR5  0   0.288  70.2187  35.3347   1.9002
 9IV  H13  H   HCR6  0   0.244  74.1617  39.7233  -0.6537
 9IV  CL   CL  CL    0  -0.099  66.5206  45.1536  -3.2658

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
 9IV  C3   C2   aromatic  1.388  0.020  1.388
 9IV  C3   C4   aromatic  1.387  0.020  1.387
 9IV  C2   C1   aromatic  1.387  0.020  1.387
 9IV  C4   C5   aromatic  1.386  0.020  1.386
 9IV  C1   C    aromatic  1.386  0.020  1.386
 9IV  C5   C    aromatic  1.391  0.020  1.391
 9IV  C5   O    single    1.362  0.020  1.362
 9IV  C    CL   single    1.726  0.020  1.726
 9IV  O    C6   single    1.367  0.020  1.367
 9IV  C17  C6   aromatic  1.387  0.020  1.387
 9IV  C17  C16  aromatic  1.388  0.020  1.388
 9IV  C6   C7   aromatic  1.390  0.020  1.390
 9IV  C16  C9   aromatic  1.391  0.020  1.391
 9IV  C7   C8   aromatic  1.383  0.020  1.383
 9IV  C9   C8   aromatic  1.395  0.020  1.395
 9IV  C9   N    single    1.402  0.020  1.402
 9IV  N1   C11  aromatic  1.334  0.020  1.334
 9IV  N1   C10  aromatic  1.329  0.020  1.329
 9IV  C11  N2   aromatic  1.316  0.020  1.316
 9IV  N    C10  single    1.356  0.020  1.356
 9IV  C10  C15  aromatic  1.408  0.020  1.408
 9IV  N2   C12  aromatic  1.335  0.020  1.335
 9IV  C15  C12  aromatic  1.401  0.020  1.401
 9IV  C15  C14  aromatic  1.427  0.020  1.427
 9IV  C12  N3   aromatic  1.353  0.020  1.353
 9IV  C14  C13  aromatic  1.364  0.020  1.364
 9IV  N3   C13  aromatic  1.372  0.020  1.372
 9IV  C2   H1   single    0.930  0.020  1.080
 9IV  N3   H2   single    0.860  0.020  1.020
 9IV  C4   H3   single    0.930  0.020  1.080
 9IV  C3   H4   single    0.930  0.020  1.080
 9IV  C1   H5   single    0.930  0.020  1.080
 9IV  C17  H6   single    0.930  0.020  1.080
 9IV  C16  H7   single    0.930  0.020  1.080
 9IV  C8   H8   single    0.930  0.020  1.080
 9IV  C7   H9   single    0.930  0.020  1.080
 9IV  N    H10  single    0.860  0.020  1.020
 9IV  C14  H11  single    0.930  0.020  1.080
 9IV  C13  H12  single    0.930  0.020  1.080
 9IV  C11  H13  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
 9IV  C11  N1   C10  118.70  3.000
 9IV  H1   C2   C1   119.45  3.000
 9IV  H1   C2   C3   120.32  3.000
 9IV  C1   C2   C3   120.23  3.000
 9IV  H2   N3   C12  125.26  3.000
 9IV  H2   N3   C13  125.45  3.000
 9IV  C12  N3   C13  109.29  3.000
 9IV  H3   C4   C3   120.79  3.000
 9IV  H3   C4   C5   119.21  3.000
 9IV  C3   C4   C5   119.99  3.000
 9IV  O    C5   C    120.26  3.000
 9IV  O    C5   C4   120.00  3.000
 9IV  C    C5   C4   119.70  3.000
 9IV  C7   C6   C17  119.85  3.000
 9IV  C7   C6   O    116.19  3.000
 9IV  C17  C6   O    123.96  3.000
 9IV  C1   C    CL   120.27  3.000
 9IV  CL   C    C5   119.25  3.000
 9IV  C1   C    C5   120.48  3.000
 9IV  H4   C3   C4   119.66  3.000
 9IV  H4   C3   C2   120.27  3.000
 9IV  C4   C3   C2   120.07  3.000
 9IV  H5   C1   C    119.91  3.000
 9IV  H5   C1   C2   120.57  3.000
 9IV  C    C1   C2   119.52  3.000
 9IV  C6   O    C5   119.13  3.000
 9IV  H6   C17  C16  118.91  3.000
 9IV  H6   C17  C6   121.66  3.000
 9IV  C16  C17  C6   119.43  3.000
 9IV  H7   C16  C9   119.78  3.000
 9IV  H7   C16  C17  118.89  3.000
 9IV  C9   C16  C17  121.33  3.000
 9IV  N    C9   C8   122.86  3.000
 9IV  N    C9   C16  118.52  3.000
 9IV  C8   C9   C16  118.57  3.000
 9IV  H8   C8   C7   119.03  3.000
 9IV  H8   C8   C9   120.58  3.000
 9IV  C7   C8   C9   120.39  3.000
 9IV  H9   C7   C8   119.76  3.000
 9IV  H9   C7   C6   119.82  3.000
 9IV  C8   C7   C6   120.42  3.000
 9IV  H10  N    C10  115.98  3.000
 9IV  H10  N    C9   115.50  3.000
 9IV  C10  N    C9   127.60  3.000
 9IV  C15  C10  N    120.43  3.000
 9IV  C15  C10  N1   119.53  3.000
 9IV  N    C10  N1   120.04  3.000
 9IV  C12  C15  C14  107.33  3.000
 9IV  C14  C15  C10  137.55  3.000
 9IV  C12  C15  C10  115.13  3.000
 9IV  H11  C14  C13  125.81  3.000
 9IV  H11  C14  C15  128.10  3.000
 9IV  C13  C14  C15  106.09  3.000
 9IV  H12  C13  C14  129.79  3.000
 9IV  H12  C13  N3   120.53  3.000
 9IV  C14  C13  N3   109.68  3.000
 9IV  N2   C12  C15  125.85  3.000
 9IV  C15  C12  N3   107.62  3.000
 9IV  N2   C12  N3   126.53  3.000
 9IV  C11  N2   C12  112.65  3.000
 9IV  H13  C11  N2   116.46  3.000
 9IV  H13  C11  N1   115.40  3.000
 9IV  N2   C11  N1   128.14  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
 9IV  CONST_01  C12  N2   C11  N1      0.00   0.0  0
 9IV  CONST_02  C12  C15  C10  N1      0.00   0.0  0
 9IV  CONST_03  C14  C15  C10  N1    180.00   0.0  0
 9IV  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 9IV  CONST_05  C5   C    C1   C2      0.00   0.0  0
 9IV  CONST_06  C11  N2   C12  N3    180.00   0.0  0
 9IV  CONST_07  C10  C15  C12  N3    180.00   0.0  0
 9IV  CONST_08  C14  C15  C12  N3      0.00   0.0  0
 9IV  CONST_09  C15  C14  C13  N3      0.00   0.0  0
 9IV  CONST_10  C1   C2   C3   C4      0.00   0.0  0
 9IV  CONST_11  C1   C    C5   C4      0.00   0.0  0
 9IV  CONST_12  C9   C16  C17  C6      0.00   0.0  0
 9IV  CONST_13  C9   C8   C7   C6      0.00   0.0  0
 9IV  CONST_14  C3   C2   C1   C       0.00   0.0  0
 9IV  CONST_15  C3   C4   C5   C       0.00   0.0  0
 9IV  CONST_16  C8   C7   C6   C17     0.00   0.0  0
 9IV  CONST_17  C8   C9   C16  C17     0.00   0.0  0
 9IV  CONST_18  C7   C6   C17  C16     0.00   0.0  0
 9IV  CONST_19  C7   C8   C9   C16     0.00   0.0  0
 9IV  CONST_20  N2   C11  N1   C10     0.00   0.0  0
 9IV  CONST_21  N2   C12  C15  C10     0.00   0.0  0
 9IV  CONST_22  C13  C14  C15  C10   180.00   0.0  0
 9IV  CONST_23  C11  N1   C10  C15     0.00   0.0  0
 9IV  CONST_24  C11  N2   C12  C15     0.00   0.0  0
 9IV  CONST_25  C13  N3   C12  C15     0.00   0.0  0
 9IV  CONST_26  N2   C12  C15  C14   180.00   0.0  0
 9IV  CONST_27  C12  N3   C13  C14     0.00   0.0  0
 9IV  CONST_28  C12  C15  C14  C13     0.00   0.0  0
 9IV  CONST_29  N2   C12  N3   C13   180.00   0.0  0
 9IV  CONST_30  CL   C    C1   C2    180.00   0.0  0
 9IV  CONST_31  CL   C    C5   C4    180.00   0.0  0
 9IV  CONST_32  O    C5   C4   C3    180.00   0.0  0
 9IV  CONST_33  O    C5   C    C1    180.00   0.0  0
 9IV  CONST_34  C16  C17  C6   O     180.00   0.0  0
 9IV  CONST_35  C8   C7   C6   O     180.00   0.0  0
 9IV  CONST_36  N    C9   C16  C17   180.00   0.0  0
 9IV  CONST_37  N    C9   C8   C7    180.00   0.0  0
 9IV  CONST_38  C11  N1   C10  N     180.00   0.0  0
 9IV  CONST_39  C12  C15  C10  N     180.00   0.0  0
 9IV  CONST_40  C14  C15  C10  N       0.00   0.0  0
 9IV  CONST_41  H3   C4   C3   C2    180.00   0.0  0
 9IV  CONST_42  H11  C14  C13  N3    180.00   0.0  0
 9IV  CONST_43  H1   C2   C3   C4    180.00   0.0  0
 9IV  CONST_44  H4   C3   C4   C5    180.00   0.0  0
 9IV  CONST_45  H5   C1   C    C5    180.00   0.0  0
 9IV  CONST_46  H7   C16  C17  C6    180.00   0.0  0
 9IV  CONST_47  H8   C8   C7   C6    180.00   0.0  0
 9IV  CONST_48  H1   C2   C1   C     180.00   0.0  0
 9IV  CONST_49  H3   C4   C5   C     180.00   0.0  0
 9IV  CONST_50  H5   C1   C2   C3    180.00   0.0  0
 9IV  CONST_51  H4   C3   C2   C1    180.00   0.0  0
 9IV  CONST_52  H9   C7   C6   C17   180.00   0.0  0
 9IV  CONST_53  H8   C8   C9   C16   180.00   0.0  0
 9IV  CONST_54  H6   C17  C16  C9    180.00   0.0  0
 9IV  CONST_55  H9   C7   C8   C9    180.00   0.0  0
 9IV  CONST_56  H7   C16  C9   C8    180.00   0.0  0
 9IV  CONST_57  H6   C17  C6   C7    180.00   0.0  0
 9IV  CONST_58  H13  C11  N1   C10   180.00   0.0  0
 9IV  CONST_59  H11  C14  C15  C10     0.00   0.0  0
 9IV  CONST_60  H2   N3   C12  C15   180.00   0.0  0
 9IV  CONST_61  H12  C13  C14  C15   180.00   0.0  0
 9IV  CONST_62  H2   N3   C13  C14   180.00   0.0  0
 9IV  CONST_63  H13  C11  N2   C12   180.00   0.0  0
 9IV  CONST_64  H11  C14  C15  C12   180.00   0.0  0
 9IV  CONST_65  H12  C13  N3   C12   180.00   0.0  0
 9IV  CONST_66  H2   N3   C12  N2      0.00   0.0  0
 9IV  Var_01    C9   N    C10  N1      1.26  30.0  1
 9IV  Var_02    C6   O    C5   C4    -95.62  30.0  2
 9IV  Var_03    C17  C6   O    C5      2.15  30.0  2
 9IV  Var_04    C7   C6   O    C5   -178.04  30.0  2
 9IV  Var_05    C    C5   O    C6     86.59  30.0  2
 9IV  Var_06    C10  N    C9   C16   140.92  30.0  2
 9IV  Var_07    C15  C10  N    C9   -178.43  30.0  2
 9IV  Var_08    C10  N    C9   C8    -41.79  30.0  2
 9IV  Var_09    H10  N    C10  N1    169.67  30.0  1
 9IV  Var_10    H10  N    C9   C16   -27.54  30.0  2
 9IV  Var_11    H10  N    C9   C8    149.75  30.0  2
 9IV  Var_12    H10  N    C10  C15   -10.01  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
 9IV  plan-1  C2   0.020
 9IV  plan-1  C4   0.020
 9IV  plan-1  C5   0.020
 9IV  plan-1  C    0.020
 9IV  plan-1  C3   0.020
 9IV  plan-1  C1   0.020
 9IV  plan-1  O    0.020
 9IV  plan-1  H1   0.020
 9IV  plan-1  H3   0.020
 9IV  plan-1  H4   0.020
 9IV  plan-1  H5   0.020
 9IV  plan-1  CL   0.020
 9IV  plan-2  C6   0.020
 9IV  plan-2  O    0.020
 9IV  plan-2  C17  0.020
 9IV  plan-2  C16  0.020
 9IV  plan-2  C9   0.020
 9IV  plan-2  C8   0.020
 9IV  plan-2  C7   0.020
 9IV  plan-2  N    0.020
 9IV  plan-2  H6   0.020
 9IV  plan-2  H7   0.020
 9IV  plan-2  H8   0.020
 9IV  plan-2  H9   0.020
 9IV  plan-3  N1   0.020
 9IV  plan-3  N3   0.020
 9IV  plan-3  N    0.020
 9IV  plan-3  C10  0.020
 9IV  plan-3  C15  0.020
 9IV  plan-3  C14  0.020
 9IV  plan-3  C13  0.020
 9IV  plan-3  C12  0.020
 9IV  plan-3  N2   0.020
 9IV  plan-3  C11  0.020
 9IV  plan-3  H2   0.020
 9IV  plan-3  H11  0.020
 9IV  plan-3  H12  0.020
 9IV  plan-3  H13  0.020

