# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 07:37:05 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: ~{N}4-(3-cyclopropyl-1~{H}-pyrazol-5-yl)-~{N}2-(phenylmethyl)thieno[3,2-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC1c2cc([nH]n2)Nc3nc(NCc4ccccc4)nc5ccsc35
#
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
 39I  39I  "~{N}4-(3-cyclopropyl-1~{H}-pyrazol-5-yl)-~{N}2-(phenylmethyl)thieno[3,2-d]pyrimidine-2,4-diamine"
  ligand  44  26  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_39I
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
 39I  C18  C  CR16  0  -0.235  20.8204  -15.3053  11.0661
 39I  C16  C  CR16  0  -0.272  21.7354  -14.3605  10.6160
 39I  C14  C  CR16  0  -0.239  23.0853  -14.6779  10.5925
 39I  C15  C  CR16  0  -0.303  23.5211  -15.9295  11.0141
 39I  C17  C  CR16  0  -0.283  21.2577  -16.5529  11.4829
 39I  C13  C  CR6   0   0.074  22.6123  -16.8809  11.4603
 39I  C12  C  CH2   0  -0.326  23.0295  -18.2583  11.9293
 39I  N    N  NH1   0  -0.668  24.4318  -18.5454  11.8427
 39I  C    C  CR6   0   0.584  25.0762  -18.9205  10.7172
 39I  N2   N  N     0  -0.512  24.3269  -19.0573   9.6099
 39I  C5   C  CR6   0   0.588  24.9150  -19.4464   8.4978
 39I  C2   C  CR56  0  -0.386  26.2992  -19.6970   8.4876
 39I  S    S  S2    0   0.214  27.3528  -20.1970   7.2089
 39I  C3   C  CR15  0  -0.442  28.6999  -20.1633   8.2834
 39I  C4   C  CR15  0  -0.203  28.3829  -19.7920   9.5447
 39I  C1   C  CR56  0   0.309  26.9842  -19.5129   9.6900
 39I  N1   N  N     0  -0.517  26.3839  -19.1245  10.8188
 39I  N3   N  NH1   0  -0.780  24.1778  -19.6012   7.3679
 39I  C11  C  CR5   0   0.634  22.8319  -19.3385   7.2095
 39I  C10  C  CR15  0  -0.564  21.8925  -18.6447   7.9443
 39I  N4   N  NR15  0  -0.523  22.2024  -19.7857   6.1060
 39I  N5   N  N     0  -0.313  20.9149  -19.4257   6.0636
 39I  C9   C  CR5   0   0.331  20.7143  -18.7367   7.1696
 39I  C7   C  CH1   0  -0.352  19.3874  -18.1676   7.4572
 39I  C8   C  CH2   0  -0.478  18.9114  -18.0235   8.8759
 39I  C6   C  CH2   0  -0.475  19.2661  -16.8069   8.0888
 39I  H1   H  HCR6  0   0.251  19.7636  -15.0717  11.0874
 39I  H2   H  HCR6  0   0.251  21.3973  -13.3866  10.2863
 39I  H3   H  HCR6  0   0.250  23.8074  -13.9499  10.2450
 39I  H4   H  HCR6  0   0.248  24.5796  -16.1563  10.9951
 39I  H5   H  HCR6  0   0.245  20.5360  -17.2841  11.8298
 39I  H6   H  HCH2  0   0.273  22.7402  -18.3784  12.9749
 39I  H7   H  HCH2  0   0.256  22.4649  -19.0083  11.3718
 39I  H8   H  HNH1  0   0.393  25.0057  -18.3943  12.6551
 39I  H9   H  HCR5  0   0.307  29.6765  -20.4275   7.9063
 39I  H10  H  HCR5  0   0.273  29.0972  -19.7138  10.3513
 39I  H11  H  HNH1  0   0.423  24.6568  -19.9427   6.5480
 39I  H12  H  HCR5  0   0.280  22.0343  -18.1420   8.8838
 39I  H13  H  HNR5  0   0.416  22.5953  -20.3375   5.3592
 39I  H14  H  HCH1  0   0.257  18.6363  -18.4236   6.7189
 39I  H15  H  HCH2  0   0.251  19.5874  -18.3321   9.6640
 39I  H16  H  HCH2  0   0.256  17.8672  -18.2236   9.0780
 39I  H17  H  HCH2  0   0.252  20.1828  -16.2894   8.3430
 39I  H18  H  HCH2  0   0.255  18.4679  -16.1623   7.7442

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
 39I  N5   N4   aromatic  1.338  0.020  1.338
 39I  N5   C9   aromatic  1.318  0.020  1.318
 39I  N4   C11  aromatic  1.347  0.020  1.347
 39I  C9   C7   single    1.472  0.020  1.472
 39I  C9   C10  aromatic  1.413  0.020  1.413
 39I  C11  N3   single    1.380  0.020  1.380
 39I  C11  C10  aromatic  1.380  0.020  1.380
 39I  N3   C5   single    1.358  0.020  1.358
 39I  C6   C7   single    1.505  0.020  1.505
 39I  C6   C8   single    1.492  0.020  1.492
 39I  C7   C8   single    1.503  0.020  1.503
 39I  S    C2   aromatic  1.731  0.020  1.731
 39I  S    C3   aromatic  1.723  0.020  1.723
 39I  C5   C2   aromatic  1.407  0.020  1.407
 39I  C5   N2   aromatic  1.317  0.020  1.317
 39I  C2   C1   aromatic  1.396  0.020  1.396
 39I  C3   C4   aromatic  1.352  0.020  1.352
 39I  N2   C    aromatic  1.344  0.020  1.344
 39I  C1   C4   aromatic  1.434  0.020  1.434
 39I  C1   N1   aromatic  1.336  0.020  1.336
 39I  C14  C15  aromatic  1.391  0.020  1.391
 39I  C14  C16  aromatic  1.387  0.020  1.387
 39I  C15  C13  aromatic  1.389  0.020  1.389
 39I  C    N1   aromatic  1.327  0.020  1.327
 39I  C    N    single    1.350  0.020  1.350
 39I  C16  C18  aromatic  1.390  0.020  1.390
 39I  C13  C12  single    1.514  0.020  1.514
 39I  C13  C17  aromatic  1.394  0.020  1.394
 39I  C12  N    single    1.434  0.020  1.434
 39I  C18  C17  aromatic  1.386  0.020  1.386
 39I  C18  H1   single    0.930  0.020  1.080
 39I  C16  H2   single    0.930  0.020  1.080
 39I  C14  H3   single    0.930  0.020  1.080
 39I  C15  H4   single    0.930  0.020  1.080
 39I  C17  H5   single    0.930  0.020  1.080
 39I  C12  H6   single    0.970  0.020  1.090
 39I  C12  H7   single    0.970  0.020  1.090
 39I  N    H8   single    0.860  0.020  1.020
 39I  C3   H9   single    0.930  0.020  1.080
 39I  C4   H10  single    0.930  0.020  1.080
 39I  N3   H11  single    0.860  0.020  1.020
 39I  C10  H12  single    0.930  0.020  1.080
 39I  N4   H13  single    0.860  0.020  1.020
 39I  C7   H14  single    0.970  0.020  1.090
 39I  C8   H15  single    0.970  0.020  1.090
 39I  C8   H16  single    0.970  0.020  1.090
 39I  C6   H17  single    0.970  0.020  1.090
 39I  C6   H18  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
 39I  H1   C18  C17  119.75  3.000
 39I  H1   C18  C16  120.15  3.000
 39I  C17  C18  C16  120.09  3.000
 39I  H2   C16  C14  120.32  3.000
 39I  H2   C16  C18  120.30  3.000
 39I  C14  C16  C18  119.38  3.000
 39I  H3   C14  C15  119.57  3.000
 39I  H3   C14  C16  120.04  3.000
 39I  C15  C14  C16  120.39  3.000
 39I  H4   C15  C13  120.11  3.000
 39I  H4   C15  C14  119.31  3.000
 39I  C13  C15  C14  120.57  3.000
 39I  H5   C17  C13  119.56  3.000
 39I  H5   C17  C18  119.54  3.000
 39I  C13  C17  C18  120.90  3.000
 39I  C12  C13  C17  118.49  3.000
 39I  C17  C13  C15  118.67  3.000
 39I  C12  C13  C15  122.84  3.000
 39I  H7   C12  H6   106.05  3.000
 39I  H7   C12  N    109.72  3.000
 39I  H6   C12  N    107.15  3.000
 39I  H7   C12  C13  108.93  3.000
 39I  H6   C12  C13  108.90  3.000
 39I  N    C12  C13  115.66  3.000
 39I  H8   N    C    116.27  3.000
 39I  H8   N    C12  118.62  3.000
 39I  C    N    C12  124.94  3.000
 39I  N1   C    N2   126.63  3.000
 39I  N1   C    N    116.69  3.000
 39I  N2   C    N    116.68  3.000
 39I  C5   N2   C    118.48  3.000
 39I  N3   C5   C2   120.52  3.000
 39I  C2   C5   N2   119.88  3.000
 39I  N3   C5   N2   119.60  3.000
 39I  C1   C2   S    112.07  3.000
 39I  C1   C2   C5   116.94  3.000
 39I  S    C2   C5   130.98  3.000
 39I  C3   S    C2    90.54  3.000
 39I  H9   C3   C4   127.22  3.000
 39I  H9   C3   S    118.97  3.000
 39I  C4   C3   S    113.80  3.000
 39I  H10  C4   C1   123.74  3.000
 39I  H10  C4   C3   124.14  3.000
 39I  C1   C4   C3   112.12  3.000
 39I  N1   C1   C4   125.48  3.000
 39I  N1   C1   C2   123.06  3.000
 39I  C4   C1   C2   111.46  3.000
 39I  C1   N1   C    115.00  3.000
 39I  H11  N3   C11  115.72  3.000
 39I  H11  N3   C5   117.19  3.000
 39I  C11  N3   C5   127.09  3.000
 39I  N4   C11  C10  106.57  3.000
 39I  C10  C11  N3   134.30  3.000
 39I  N4   C11  N3   119.11  3.000
 39I  H12  C10  C9   128.28  3.000
 39I  H12  C10  C11  127.65  3.000
 39I  C9   C10  C11  104.06  3.000
 39I  H13  N4   N5   119.92  3.000
 39I  H13  N4   C11  127.34  3.000
 39I  N5   N4   C11  112.74  3.000
 39I  C9   N5   N4   105.10  3.000
 39I  C7   C9   N5   120.20  3.000
 39I  C7   C9   C10  128.26  3.000
 39I  N5   C9   C10  111.53  3.000
 39I  H14  C7   C6   116.33  3.000
 39I  H14  C7   C8   116.50  3.000
 39I  C6   C7   C8    59.46  3.000
 39I  H14  C7   C9   113.59  3.000
 39I  C8   C7   C9   120.45  3.000
 39I  C6   C7   C9   120.27  3.000
 39I  H16  C8   H15  114.43  3.000
 39I  H16  C8   C6   118.60  3.000
 39I  H15  C8   C6   117.89  3.000
 39I  H16  C8   C7   117.64  3.000
 39I  H15  C8   C7   117.50  3.000
 39I  C6   C8   C7    60.33  3.000
 39I  H18  C6   H17  114.48  3.000
 39I  H18  C6   C8   118.58  3.000
 39I  H17  C6   C8   117.85  3.000
 39I  H18  C6   C7   117.66  3.000
 39I  H17  C6   C7   117.54  3.000
 39I  C8   C6   C7    60.21  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
 39I  CONST_01  C15  C14  C16  C18     0.00   0.0  0
 39I  CONST_02  C15  C13  C17  C18     0.00   0.0  0
 39I  CONST_03  C13  C15  C14  C16     0.00   0.0  0
 39I  CONST_04  C13  C17  C18  C16     0.00   0.0  0
 39I  CONST_05  C17  C13  C15  C14     0.00   0.0  0
 39I  CONST_06  C17  C18  C16  C14     0.00   0.0  0
 39I  CONST_07  C2   C5   N2   C       0.00   0.0  0
 39I  CONST_08  C2   C1   N1   C       0.00   0.0  0
 39I  CONST_09  C4   C1   N1   C     180.00   0.0  0
 39I  CONST_10  S    C2   C5   N2    180.00   0.0  0
 39I  CONST_11  C1   C2   C5   N2      0.00   0.0  0
 39I  CONST_12  C1   N1   C    N2      0.00   0.0  0
 39I  CONST_13  C3   S    C2   C5    180.00   0.0  0
 39I  CONST_14  C4   C1   C2   C5    180.00   0.0  0
 39I  CONST_15  N1   C1   C2   C5      0.00   0.0  0
 39I  CONST_16  N1   C    N2   C5      0.00   0.0  0
 39I  CONST_17  C4   C3   S    C2      0.00   0.0  0
 39I  CONST_18  C3   C4   C1   C2      0.00   0.0  0
 39I  CONST_19  C4   C1   C2   S       0.00   0.0  0
 39I  CONST_20  N1   C1   C2   S     180.00   0.0  0
 39I  CONST_21  C1   C4   C3   S       0.00   0.0  0
 39I  CONST_22  C1   C2   S    C3      0.00   0.0  0
 39I  CONST_23  N1   C1   C4   C3    180.00   0.0  0
 39I  CONST_24  C9   N5   N4   C11     0.00   0.0  0
 39I  CONST_25  N5   C9   C10  C11     0.00   0.0  0
 39I  CONST_26  N4   N5   C9   C10     0.00   0.0  0
 39I  CONST_27  N5   N4   C11  C10     0.00   0.0  0
 39I  CONST_28  C9   C10  C11  N4      0.00   0.0  0
 39I  CONST_29  C7   C9   C10  C11   180.00   0.0  0
 39I  CONST_30  C7   C9   N5   N4    180.00   0.0  0
 39I  CONST_31  C12  C13  C17  C18   180.00   0.0  0
 39I  CONST_32  C12  C13  C15  C14   180.00   0.0  0
 39I  CONST_33  C5   N2   C    N     180.00   0.0  0
 39I  CONST_34  C1   N1   C    N     180.00   0.0  0
 39I  CONST_35  N3   C5   N2   C     180.00   0.0  0
 39I  CONST_36  N3   C5   C2   S       0.00   0.0  0
 39I  CONST_37  N3   C5   C2   C1    180.00   0.0  0
 39I  CONST_38  N5   N4   C11  N3    180.00   0.0  0
 39I  CONST_39  C9   C10  C11  N3    180.00   0.0  0
 39I  CONST_40  H3   C14  C16  C18   180.00   0.0  0
 39I  CONST_41  H4   C15  C14  C16   180.00   0.0  0
 39I  CONST_42  H5   C17  C18  C16   180.00   0.0  0
 39I  CONST_43  H1   C18  C16  C14   180.00   0.0  0
 39I  CONST_44  H2   C16  C14  C15   180.00   0.0  0
 39I  CONST_45  H5   C17  C13  C15   180.00   0.0  0
 39I  CONST_46  H4   C15  C13  C17   180.00   0.0  0
 39I  CONST_47  H2   C16  C18  C17   180.00   0.0  0
 39I  CONST_48  H3   C14  C15  C13   180.00   0.0  0
 39I  CONST_49  H1   C18  C17  C13   180.00   0.0  0
 39I  CONST_50  H9   C3   S    C2    180.00   0.0  0
 39I  CONST_51  H10  C4   C1   C2    180.00   0.0  0
 39I  CONST_52  H10  C4   C3   S     180.00   0.0  0
 39I  CONST_53  H9   C3   C4   C1    180.00   0.0  0
 39I  CONST_54  H10  C4   C1   N1      0.00   0.0  0
 39I  CONST_55  H13  N4   C11  C10   180.00   0.0  0
 39I  CONST_56  H12  C10  C11  N4    180.00   0.0  0
 39I  CONST_57  H12  C10  C9   N5    180.00   0.0  0
 39I  CONST_58  H13  N4   N5   C9    180.00   0.0  0
 39I  CONST_59  H12  C10  C9   C7      0.00   0.0  0
 39I  CONST_60  N2   C    N    C12     0.00   0.0  0
 39I  CONST_61  N1   C    N    C12   180.00   0.0  0
 39I  CONST_62  H8   N    C    N2    180.00   0.0  0
 39I  CONST_63  H8   N    C    N1      0.00   0.0  0
 39I  Var_01    C6   C7   C9   C10    38.07  30.0  2
 39I  Var_02    C8   C7   C9   C10   -32.09  30.0  2
 39I  Var_03    C6   C7   C9   N5   -141.38  30.0  2
 39I  Var_04    C8   C7   C9   N5    148.46  30.0  2
 39I  Var_05    C8   C6   C7   C9   -109.69  30.0  1
 39I  Var_06    C11  N3   C5   N2      3.01  30.0  2
 39I  Var_07    N4   C11  N3   C5   -167.31  30.0  2
 39I  Var_08    C10  C11  N3   C5     14.79  30.0  2
 39I  Var_09    C11  N3   C5   C2   -176.93  30.0  2
 39I  Var_10    H14  C7   C9   C10  -177.31  30.0  2
 39I  Var_11    H14  C7   C9   N5      3.23  30.0  2
 39I  Var_12    H17  C6   C7   C9     -1.72  30.0  1
 39I  Var_13    H18  C6   C7   C9    141.51  30.0  1
 39I  Var_14    H15  C8   C7   C9      1.31  30.0  1
 39I  Var_15    H16  C8   C7   C9   -141.73  30.0  1
 39I  Var_16    H15  C8   C6   C7    107.44  30.0  1
 39I  Var_17    H16  C8   C6   C7   -107.31  30.0  1
 39I  Var_18    H17  C6   C8   C7   -107.46  30.0  1
 39I  Var_19    H18  C6   C8   C7    107.30  30.0  1
 39I  Var_20    H14  C7   C6   C8    106.62  30.0  1
 39I  Var_21    N    C12  C13  C15    -2.06  30.0  2
 39I  Var_22    N    C12  C13  C17   178.20  30.0  2
 39I  Var_23    C    N    C12  C13   -80.51  30.0  3
 39I  Var_24    H6   C12  C13  C15   118.62  30.0  2
 39I  Var_25    H7   C12  C13  C15  -126.15  30.0  2
 39I  Var_26    H6   C12  C13  C17   -61.12  30.0  2
 39I  Var_27    H7   C12  C13  C17    54.11  30.0  2
 39I  Var_28    H11  N3   C5   N2   -177.17  30.0  2
 39I  Var_29    H11  N3   C5   C2      2.89  30.0  2
 39I  Var_30    H11  N3   C11  C10  -165.04  30.0  2
 39I  Var_31    H11  N3   C11  N4     12.86  30.0  2
 39I  Var_32    H8   N    C12  C13    94.58  30.0  3
 39I  Var_33    H6   C12  N    C     157.87  30.0  1
 39I  Var_34    H7   C12  N    C      43.17  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
 39I  chir_01  C7  C9  C6  C8  both

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
 39I  plan-1  N3   0.020
 39I  plan-1  C11  0.020
 39I  plan-1  C10  0.020
 39I  plan-1  N4   0.020
 39I  plan-1  N5   0.020
 39I  plan-1  C9   0.020
 39I  plan-1  C7   0.020
 39I  plan-1  H12  0.020
 39I  plan-1  H13  0.020
 39I  plan-2  C18  0.020
 39I  plan-2  C16  0.020
 39I  plan-2  C14  0.020
 39I  plan-2  C15  0.020
 39I  plan-2  C17  0.020
 39I  plan-2  C13  0.020
 39I  plan-2  C12  0.020
 39I  plan-2  H1   0.020
 39I  plan-2  H2   0.020
 39I  plan-2  H3   0.020
 39I  plan-2  H4   0.020
 39I  plan-2  H5   0.020
 39I  plan-3  N    0.020
 39I  plan-3  C    0.020
 39I  plan-3  N2   0.020
 39I  plan-3  C5   0.020
 39I  plan-3  C2   0.020
 39I  plan-3  S    0.020
 39I  plan-3  C3   0.020
 39I  plan-3  C4   0.020
 39I  plan-3  C1   0.020
 39I  plan-3  N1   0.020
 39I  plan-3  N3   0.020
 39I  plan-3  H9   0.020
 39I  plan-3  H10  0.020
 39I  plan-4  C12  0.020
 39I  plan-4  N    0.020
 39I  plan-4  C    0.020
 39I  plan-4  H8   0.020

