# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 16:47:11 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 9-(dimethylamino)-2-[(3-hydroxyphenyl)amino]-5,6-dihydrothieno[3,4-h]quinazoline-7-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1sc(C#N)c2CCc3cnc(Nc4cccc(O)c4)nc3c12
#
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
 EK7  EK7  9-(dimethylamino)-2-[(3-hydroxyphenyl)amino]-5,6-dihydrothieno[3,4-h]quinazoline-7-carbonitrile  ligand  43  26  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EK7
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
 EK7  N5   N  NS    0  -0.254  -6.8776  -1.2791  -0.0712
 EK7  C19  C  CSP   0   0.028  -5.8156  -0.8243  -0.0668
 EK7  C1   C  CR5   0  -0.367  -4.5260  -0.2682  -0.0594
 EK7  C2   C  CR56  0   0.216  -3.3466  -0.9378   0.1144
 EK7  C9   C  C     0  -0.526  -3.1938  -2.3936   0.4027
 EK7  C8   C  C     0  -0.511  -2.0154  -2.9539  -0.3857
 EK7  C7   C  CR66  0  -0.049  -0.7951  -2.0996  -0.2205
 EK7  C4   C  CR66  0   0.284  -0.8837  -0.7035  -0.0657
 EK7  C3   C  CR56  0   0.126  -2.2096  -0.0956  -0.0172
 EK7  C16  C  CR5   0   0.025  -2.5516   1.2333  -0.2480
 EK7  N4   N  NT    0  -0.454  -1.7541   2.3280  -0.3770
 EK7  C18  C  CH3   0  -0.561  -2.2989   3.4666  -1.0906
 EK7  C17  C  CH3   0  -0.527  -0.9459   2.7216   0.7712
 EK7  S    S  S2    0   0.267  -4.2791   1.4209  -0.3428
 EK7  C6   C  CR16  0  -0.037   0.4874  -2.6033  -0.2680
 EK7  N2   N  N     0  -0.466   1.5843  -1.8552  -0.1950
 EK7  C5   C  CR6   0   0.598   1.3869  -0.5505  -0.0799
 EK7  N1   N  N     0  -0.498   0.1986   0.0525  -0.0052
 EK7  N3   N  NH1   0  -0.779   2.4424   0.3124  -0.0159
 EK7  C10  C  CR6   0   0.385   3.8138   0.1073  -0.0744
 EK7  C15  C  CR16  0  -0.344   4.4292  -1.1322  -0.2763
 EK7  C14  C  CR16  0  -0.233   5.8146  -1.1923  -0.3247
 EK7  C13  C  CR16  0  -0.406   6.6099  -0.0677  -0.1792
 EK7  C12  C  CR6   0   0.366   5.9913   1.1646   0.0231
 EK7  O    O  OH1   0  -0.635   6.6878   2.3085   0.1776
 EK7  C11  C  CR16  0  -0.451   4.6071   1.2496   0.0747
 EK7  H4   H  H     0   0.276  -3.0131  -2.5166   1.4754
 EK7  H5   H  H     0   0.270  -4.1068  -2.9414   0.1682
 EK7  H2   H  H     0   0.268  -1.8073  -3.9770  -0.0698
 EK7  H3   H  H     0   0.264  -2.2851  -3.0020  -1.4456
 EK7  H16  H  HCH3  0   0.234  -3.0552   4.0087  -0.5079
 EK7  H15  H  HCH3  0   0.267  -1.4892   4.1620  -1.3062
 EK7  H17  H  HCH3  0   0.263  -2.7356   3.1556  -2.0385
 EK7  H14  H  HCH3  0   0.266  -0.5799   1.8541   1.3054
 EK7  H12  H  HCH3  0   0.244  -0.0860   3.2949   0.4262
 EK7  H13  H  HCH3  0   0.230  -1.5307   3.3462   1.4550
 EK7  H1   H  HCR6  0   0.267   0.6444  -3.6726  -0.3727
 EK7  H6   H  HNH1  0   0.406   2.1524   1.2711   0.1038
 EK7  H11  H  HCR6  0   0.280   3.8400  -2.0261  -0.3915
 EK7  H10  H  HCR6  0   0.258   6.2878  -2.1530  -0.4833
 EK7  H9   H  HCR6  0   0.267   7.6900  -0.1460  -0.2207
 EK7  H8   H  HOH1  0   0.474   7.6334   2.1316   0.1240
 EK7  H7   H  HCR6  0   0.269   4.1431   2.2164   0.2365

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
 EK7  C8   C9   single    1.524  0.020  1.524
 EK7  C8   C7   single    1.499  0.020  1.499
 EK7  C6   C7   aromatic  1.379  0.020  1.379
 EK7  C6   N2   aromatic  1.330  0.020  1.330
 EK7  C9   C2   single    1.492  0.020  1.492
 EK7  C7   C4   aromatic  1.408  0.020  1.408
 EK7  N2   C5   aromatic  1.325  0.020  1.325
 EK7  N5   C19  triple    1.155  0.020  1.155
 EK7  C2   C1   aromatic  1.367  0.020  1.367
 EK7  C2   C3   aromatic  1.421  0.020  1.421
 EK7  C19  C1   single    1.404  0.020  1.404
 EK7  C4   C3   aromatic  1.459  0.020  1.459
 EK7  C4   N1   aromatic  1.322  0.020  1.322
 EK7  C1   S    aromatic  1.730  0.020  1.730
 EK7  C5   N1   aromatic  1.335  0.020  1.335
 EK7  C5   N3   single    1.365  0.020  1.365
 EK7  C3   C16  aromatic  1.391  0.020  1.391
 EK7  N3   C10  single    1.388  0.020  1.388
 EK7  C16  S    aromatic  1.740  0.020  1.740
 EK7  C16  N4   single    1.361  0.020  1.361
 EK7  C17  N4   single    1.458  0.020  1.458
 EK7  N4   C18  single    1.450  0.020  1.450
 EK7  C10  C11  aromatic  1.399  0.020  1.399
 EK7  C10  C15  aromatic  1.398  0.020  1.398
 EK7  C11  C12  aromatic  1.388  0.020  1.388
 EK7  C15  C14  aromatic  1.388  0.020  1.388
 EK7  C12  O    single    1.348  0.020  1.348
 EK7  C12  C13  aromatic  1.394  0.020  1.394
 EK7  C14  C13  aromatic  1.385  0.020  1.385
 EK7  C9   H4   single    0.970  0.020  1.090
 EK7  C9   H5   single    0.970  0.020  1.090
 EK7  C8   H2   single    0.970  0.020  1.090
 EK7  C8   H3   single    0.970  0.020  1.090
 EK7  C18  H16  single    0.970  0.020  1.090
 EK7  C18  H15  single    0.970  0.020  1.090
 EK7  C18  H17  single    0.970  0.020  1.090
 EK7  C17  H14  single    0.970  0.020  1.090
 EK7  C17  H12  single    0.970  0.020  1.090
 EK7  C17  H13  single    0.970  0.020  1.090
 EK7  C6   H1   single    0.930  0.020  1.080
 EK7  N3   H6   single    0.860  0.020  1.020
 EK7  C15  H11  single    0.930  0.020  1.080
 EK7  C14  H10  single    0.930  0.020  1.080
 EK7  C13  H9   single    0.930  0.020  1.080
 EK7  O    H8   single    0.850  0.020  0.980
 EK7  C11  H7   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
 EK7  C1   C19  N5   180.00  3.000
 EK7  S    C1   C2   112.08  3.000
 EK7  S    C1   C19  121.10  3.000
 EK7  C2   C1   C19  126.78  3.000
 EK7  C3   C2   C9   120.95  3.000
 EK7  C3   C2   C1   112.84  3.000
 EK7  C9   C2   C1   126.21  3.000
 EK7  H5   C9   H4   107.01  3.000
 EK7  H5   C9   C8   110.58  3.000
 EK7  H4   C9   C8   109.75  3.000
 EK7  H5   C9   C2   111.28  3.000
 EK7  H4   C9   C2   108.42  3.000
 EK7  C8   C9   C2   109.74  3.000
 EK7  H3   C8   H2   106.62  3.000
 EK7  H3   C8   C7   109.41  3.000
 EK7  H2   C8   C7   110.33  3.000
 EK7  H3   C8   C9   109.05  3.000
 EK7  H2   C8   C9   110.02  3.000
 EK7  C7   C8   C9   111.28  3.000
 EK7  C6   C7   C4   115.14  3.000
 EK7  C4   C7   C8   121.75  3.000
 EK7  C6   C7   C8   123.05  3.000
 EK7  N1   C4   C3   120.28  3.000
 EK7  N1   C4   C7   121.39  3.000
 EK7  C3   C4   C7   118.30  3.000
 EK7  C16  C3   C4   128.00  3.000
 EK7  C16  C3   C2   112.63  3.000
 EK7  C4   C3   C2   118.89  3.000
 EK7  S    C16  N4   119.34  3.000
 EK7  N4   C16  C3   129.80  3.000
 EK7  S    C16  C3   110.86  3.000
 EK7  C17  N4   C18  112.57  3.000
 EK7  C18  N4   C16  117.27  3.000
 EK7  C17  N4   C16  117.87  3.000
 EK7  H17  C18  H15  107.96  3.000
 EK7  H17  C18  H16  109.07  3.000
 EK7  H15  C18  H16  107.58  3.000
 EK7  H17  C18  N4   110.78  3.000
 EK7  H15  C18  N4   108.63  3.000
 EK7  H16  C18  N4   112.66  3.000
 EK7  H13  C17  H12  108.60  3.000
 EK7  H13  C17  H14  109.23  3.000
 EK7  H12  C17  H14  108.13  3.000
 EK7  H13  C17  N4   110.46  3.000
 EK7  H12  C17  N4   109.28  3.000
 EK7  H14  C17  N4   111.08  3.000
 EK7  C16  S    C1    91.57  3.000
 EK7  H1   C6   N2   116.11  3.000
 EK7  H1   C6   C7   119.84  3.000
 EK7  N2   C6   C7   124.05  3.000
 EK7  C5   N2   C6   115.85  3.000
 EK7  N3   C5   N1   113.60  3.000
 EK7  N3   C5   N2   120.77  3.000
 EK7  N1   C5   N2   125.63  3.000
 EK7  C5   N1   C4   117.92  3.000
 EK7  H6   N3   C10  115.44  3.000
 EK7  H6   N3   C5   112.58  3.000
 EK7  C10  N3   C5   131.97  3.000
 EK7  C11  C10  C15  119.32  3.000
 EK7  C15  C10  N3   124.88  3.000
 EK7  C11  C10  N3   115.80  3.000
 EK7  H11  C15  C14  120.44  3.000
 EK7  H11  C15  C10  120.69  3.000
 EK7  C14  C15  C10  118.87  3.000
 EK7  H10  C14  C13  119.00  3.000
 EK7  H10  C14  C15  118.69  3.000
 EK7  C13  C14  C15  122.31  3.000
 EK7  H9   C13  C12  120.79  3.000
 EK7  H9   C13  C14  120.64  3.000
 EK7  C12  C13  C14  118.57  3.000
 EK7  C11  C12  O    117.33  3.000
 EK7  O    C12  C13  122.52  3.000
 EK7  C11  C12  C13  120.15  3.000
 EK7  H8   O    C12  110.18  3.000
 EK7  H7   C11  C12  119.13  3.000
 EK7  H7   C11  C10  120.08  3.000
 EK7  C12  C11  C10  120.78  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
 EK7  CONST_01  C4   C3   C2   C1    180.00   0.0  0
 EK7  CONST_02  C16  C3   C2   C1      0.00   0.0  0
 EK7  CONST_03  C3   C16  S    C1      0.00   0.0  0
 EK7  CONST_04  C16  S    C1   C2      0.00   0.0  0
 EK7  CONST_05  C7   C4   C3   C2      0.00   0.0  0
 EK7  CONST_06  N1   C4   C3   C2    180.00   0.0  0
 EK7  CONST_07  S    C16  C3   C2      0.00   0.0  0
 EK7  CONST_08  C5   N2   C6   C7      0.00   0.0  0
 EK7  CONST_10  C5   N1   C4   C7      0.00   0.0  0
 EK7  CONST_11  N2   C6   C7   C4      0.00   0.0  0
 EK7  CONST_12  S    C16  C3   C4    180.00   0.0  0
 EK7  CONST_13  N2   C5   N1   C4      0.00   0.0  0
 EK7  CONST_14  S    C1   C2   C3      0.00   0.0  0
 EK7  CONST_15  C6   C7   C4   C3    180.00   0.0  0
 EK7  CONST_16  C5   N1   C4   C3    180.00   0.0  0
 EK7  CONST_18  N1   C4   C7   C6      0.00   0.0  0
 EK7  CONST_19  N1   C5   N2   C6      0.00   0.0  0
 EK7  CONST_20  C13  C12  C11  C10     0.00   0.0  0
 EK7  CONST_21  C13  C14  C15  C10     0.00   0.0  0
 EK7  CONST_22  C12  C11  C10  C15     0.00   0.0  0
 EK7  CONST_23  C12  C13  C14  C15     0.00   0.0  0
 EK7  CONST_24  C11  C10  C15  C14     0.00   0.0  0
 EK7  CONST_25  C11  C12  C13  C14     0.00   0.0  0
 EK7  CONST_26  C9   C2   C1   C19     0.00   0.0  0
 EK7  CONST_27  C3   C2   C1   C19   180.00   0.0  0
 EK7  CONST_28  C16  S    C1   C19   180.00   0.0  0
 EK7  CONST_29  N4   C16  S    C1    180.00   0.0  0
 EK7  CONST_30  N4   C16  C3   C2    180.00   0.0  0
 EK7  CONST_31  N4   C16  C3   C4      0.00   0.0  0
 EK7  CONST_32  N3   C5   N1   C4    180.00   0.0  0
 EK7  CONST_33  N3   C5   N2   C6    180.00   0.0  0
 EK7  CONST_34  C12  C11  C10  N3    180.00   0.0  0
 EK7  CONST_35  C14  C15  C10  N3    180.00   0.0  0
 EK7  CONST_36  O    C12  C11  C10   180.00   0.0  0
 EK7  CONST_37  O    C12  C13  C14   180.00   0.0  0
 EK7  CONST_38  H1   C6   C7   C8      0.00   0.0  0
 EK7  CONST_39  H10  C14  C15  C10   180.00   0.0  0
 EK7  CONST_40  H7   C11  C10  C15   180.00   0.0  0
 EK7  CONST_41  H9   C13  C14  C15   180.00   0.0  0
 EK7  CONST_42  H11  C15  C14  C13   180.00   0.0  0
 EK7  Var_01    C8   C9   C2   C1    139.96  30.0  1
 EK7  Var_02    C7   C8   C9   C2     49.11  30.0  1
 EK7  Var_03    C6   C7   C8   C9    149.53  30.0  1
 EK7  Var_04    C10  N3   C5   N2      1.48  30.0  2
 EK7  Var_05    C11  C10  N3   C5   -177.81  30.0  2
 EK7  Var_06    H14  C17  N4   C16    36.68  30.0  3
 EK7  Var_07    H16  C18  N4   C16    73.47  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
 EK7  plan-1  N3   0.020
 EK7  plan-1  C10  0.020
 EK7  plan-1  C15  0.020
 EK7  plan-1  C14  0.020
 EK7  plan-1  C13  0.020
 EK7  plan-1  C12  0.020
 EK7  plan-1  O    0.020
 EK7  plan-1  C11  0.020
 EK7  plan-1  H11  0.020
 EK7  plan-1  H10  0.020
 EK7  plan-1  H9   0.020
 EK7  plan-1  H7   0.020
 EK7  plan-2  N5   0.020
 EK7  plan-2  C19  0.020
 EK7  plan-2  C1   0.020
 EK7  plan-2  C2   0.020
 EK7  plan-2  C9   0.020
 EK7  plan-2  C4   0.020
 EK7  plan-2  C3   0.020
 EK7  plan-2  C16  0.020
 EK7  plan-2  N4   0.020
 EK7  plan-2  S    0.020
 EK7  plan-3  C8   0.020
 EK7  plan-3  C7   0.020
 EK7  plan-3  C4   0.020
 EK7  plan-3  C3   0.020
 EK7  plan-3  C6   0.020
 EK7  plan-3  N2   0.020
 EK7  plan-3  C5   0.020
 EK7  plan-3  N1   0.020
 EK7  plan-3  N3   0.020
 EK7  plan-3  H1   0.020
 EK7  plan-4  C16  0.020
 EK7  plan-4  N4   0.020
 EK7  plan-4  C18  0.020
 EK7  plan-4  C17  0.020

