# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 22:49:11 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: ~{N}1-(7,8-dihydro-6~{H}-cyclopenta[2,3]thieno[2,4-~{c}]pyrimidin-1-yl)-~{N}4,~{N}4-dimethyl-cyclohexane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)[C@H]1CC[C@@H](CC1)Nc2ncnc3sc4CCCc4c23
#
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
 6QX  6QX  ~{N}1-(7,8-dihydro-6~{H}-cyclopenta[2,3]thieno[2,4-~{c}]pyrimidin-1-yl)-~{N}4,~{N}4-dimethyl-cyclohexane-1,4-diamine  ligand  46  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6QX
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
 6QX  C1   C  CH3   0  -0.530   6.6281   1.0929  -0.5456
 6QX  C3   C  CH3   0  -0.529   6.5149  -0.5504   1.1538
 6QX  C7   C  CH2   0  -0.460   2.2978   1.1450  -0.8571
 6QX  C8   C  CH1   0  -0.037   1.5543  -0.0734  -0.3313
 6QX  C10  C  CH2   0  -0.433   2.1874  -0.5321   0.9771
 6QX  C11  C  CH2   0  -0.469   3.6677  -0.8446   0.7892
 6QX  C13  C  CR6   0   0.511  -0.8386  -0.6666  -0.1614
 6QX  C14  C  CR56  0  -0.014  -2.1986  -0.2812  -0.0365
 6QX  C15  C  CR55  0   0.179  -2.8478   0.9874   0.0547
 6QX  C16  C  CR55  0  -0.223  -4.1913   0.8744   0.1455
 6QX  C20  C  CR16  0   0.037  -1.5122  -2.8519  -0.2398
 6QX  C22  C  CH2   0  -0.479  -4.8979   2.1792   0.2985
 6QX  C24  C  CH2   0  -0.535  -2.4260   2.4246   0.1248
 6QX  N19  N  N     0  -0.440  -2.8050  -2.6265  -0.1165
 6QX  N2   N  NT    0  -0.419   5.8516  -0.0136  -0.0191
 6QX  C18  C  CR56  0  -0.036  -3.1132  -1.3336  -0.0181
 6QX  N12  N  NH1   0  -0.689   0.1446   0.2412  -0.1961
 6QX  C6   C  CH2   0  -0.463   3.7800   0.8479  -1.0483
 6QX  S17  S  S2    0   0.205  -4.7503  -0.7607   0.1292
 6QX  C4   C  CH1   0  -0.007   4.4556   0.3456   0.2324
 6QX  C23  C  CH2   0  -0.461  -3.7676   3.1747  -0.0579
 6QX  N21  N  N     0  -0.475  -0.5287  -1.9596  -0.2651
 6QX  H1   H  HCH3  0   0.234   7.6639   0.7781  -0.6746
 6QX  H2   H  HCH3  0   0.237   6.2693   1.4057  -1.5245
 6QX  H3   H  HCH3  0   0.189   6.6301   1.9766   0.1129
 6QX  H4   H  HCH3  0   0.189   6.4851   0.1285   2.0213
 6QX  H5   H  HCH3  0   0.237   6.0848  -1.5030   1.4571
 6QX  H6   H  HCH3  0   0.234   7.5634  -0.7373   0.9205
 6QX  H7   H  HCH2  0   0.248   1.8634   1.4716  -1.8051
 6QX  H8   H  HCH2  0   0.225   2.1801   1.9734  -0.1479
 6QX  H9   H  HCH1  0   0.237   1.6471  -0.8814  -1.0628
 6QX  H10  H  HCH2  0   0.217   2.0616   0.2545   1.7295
 6QX  H11  H  HCH2  0   0.244   1.6680  -1.4165   1.3503
 6QX  H12  H  HCH2  0   0.245   4.0710  -1.1608   1.7516
 6QX  H13  H  HCH2  0   0.218   3.7812  -1.6918   0.1030
 6QX  H14  H  HCR6  0   0.253  -1.2101  -3.8901  -0.3277
 6QX  H15  H  HCH2  0   0.257  -5.7613   2.2852  -0.3592
 6QX  H16  H  HCH2  0   0.256  -5.2565   2.3124   1.3232
 6QX  H17  H  HCH2  0   0.255  -1.9677   2.6496   1.0928
 6QX  H18  H  HCH2  0   0.248  -1.7044   2.7061  -0.6452
 6QX  H20  H  HNH1  0   0.406  -0.0944   1.2020  -0.0127
 6QX  H21  H  HCH2  0   0.220   3.9085   0.0925  -1.8316
 6QX  H22  H  HCH2  0   0.246   4.2601   1.7583  -1.4073
 6QX  H23  H  HCH1  0   0.178   4.4015   1.1616   0.9813
 6QX  H24  H  HCH2  0   0.249  -3.8715   3.4719  -1.1018
 6QX  H25  H  HCH2  0   0.246  -3.8157   4.0802   0.5451

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
 6QX  C22  C23  single    1.548  0.020  1.548
 6QX  C22  C16  single    1.492  0.020  1.492
 6QX  C23  C24  single    1.548  0.020  1.548
 6QX  C16  S17  aromatic  1.728  0.020  1.728
 6QX  C16  C15  aromatic  1.351  0.020  1.351
 6QX  C24  C15  single    1.499  0.020  1.499
 6QX  S17  C18  aromatic  1.741  0.020  1.741
 6QX  C15  C14  aromatic  1.428  0.020  1.428
 6QX  C18  C14  aromatic  1.394  0.020  1.394
 6QX  C18  N19  aromatic  1.333  0.020  1.333
 6QX  C14  C13  aromatic  1.419  0.020  1.419
 6QX  N19  C20  aromatic  1.318  0.020  1.318
 6QX  C13  N12  single    1.339  0.020  1.339
 6QX  C13  N21  aromatic  1.334  0.020  1.334
 6QX  N12  C8   single    1.451  0.020  1.451
 6QX  C20  N21  aromatic  1.328  0.020  1.328
 6QX  C10  C8   single    1.524  0.020  1.524
 6QX  C10  C11  single    1.525  0.020  1.525
 6QX  C8   C7   single    1.521  0.020  1.521
 6QX  C11  C4   single    1.532  0.020  1.532
 6QX  C7   C6   single    1.524  0.020  1.524
 6QX  C4   C6   single    1.533  0.020  1.533
 6QX  C4   N2   single    1.463  0.020  1.463
 6QX  C1   N2   single    1.451  0.020  1.451
 6QX  N2   C3   single    1.451  0.020  1.451
 6QX  C1   H1   single    0.970  0.020  1.090
 6QX  C1   H2   single    0.970  0.020  1.090
 6QX  C1   H3   single    0.970  0.020  1.090
 6QX  C3   H4   single    0.970  0.020  1.090
 6QX  C3   H5   single    0.970  0.020  1.090
 6QX  C3   H6   single    0.970  0.020  1.090
 6QX  C7   H7   single    0.970  0.020  1.090
 6QX  C7   H8   single    0.970  0.020  1.090
 6QX  C8   H9   single    0.970  0.020  1.090
 6QX  C10  H10  single    0.970  0.020  1.090
 6QX  C10  H11  single    0.970  0.020  1.090
 6QX  C11  H12  single    0.970  0.020  1.090
 6QX  C11  H13  single    0.970  0.020  1.090
 6QX  C20  H14  single    0.930  0.020  1.080
 6QX  C22  H15  single    0.970  0.020  1.090
 6QX  C22  H16  single    0.970  0.020  1.090
 6QX  C24  H17  single    0.970  0.020  1.090
 6QX  C24  H18  single    0.970  0.020  1.090
 6QX  N12  H20  single    0.860  0.020  1.020
 6QX  C6   H21  single    0.970  0.020  1.090
 6QX  C6   H22  single    0.970  0.020  1.090
 6QX  C4   H23  single    0.970  0.020  1.090
 6QX  C23  H24  single    0.970  0.020  1.090
 6QX  C23  H25  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
 6QX  H3   C1   H2   107.91  3.000
 6QX  H3   C1   H1   107.48  3.000
 6QX  H2   C1   H1   106.84  3.000
 6QX  H3   C1   N2   113.31  3.000
 6QX  H2   C1   N2   111.67  3.000
 6QX  H1   C1   N2   109.35  3.000
 6QX  H6   C3   H5   106.84  3.000
 6QX  H6   C3   H4   107.46  3.000
 6QX  H5   C3   H4   108.01  3.000
 6QX  H6   C3   N2   109.28  3.000
 6QX  H5   C3   N2   111.63  3.000
 6QX  H4   C3   N2   113.34  3.000
 6QX  H8   C7   H7   107.01  3.000
 6QX  H8   C7   C6   109.44  3.000
 6QX  H7   C7   C6   109.64  3.000
 6QX  H8   C7   C8   109.20  3.000
 6QX  H7   C7   C8   110.18  3.000
 6QX  C6   C7   C8   111.26  3.000
 6QX  H9   C8   N12  107.75  3.000
 6QX  H9   C8   C10  108.45  3.000
 6QX  N12  C8   C10  112.89  3.000
 6QX  H9   C8   C7   108.60  3.000
 6QX  C10  C8   C7   109.56  3.000
 6QX  N12  C8   C7   109.48  3.000
 6QX  H11  C10  H10  106.99  3.000
 6QX  H11  C10  C11  109.76  3.000
 6QX  H10  C10  C11  110.07  3.000
 6QX  H11  C10  C8   109.86  3.000
 6QX  H10  C10  C8   109.01  3.000
 6QX  C11  C10  C8   111.06  3.000
 6QX  H13  C11  H12  106.87  3.000
 6QX  H13  C11  C4   108.64  3.000
 6QX  H12  C11  C4   110.84  3.000
 6QX  H13  C11  C10  109.64  3.000
 6QX  H12  C11  C10  108.05  3.000
 6QX  C4   C11  C10  112.64  3.000
 6QX  N21  C13  N12  119.00  3.000
 6QX  N21  C13  C14  119.53  3.000
 6QX  N12  C13  C14  121.46  3.000
 6QX  C18  C14  C15  111.81  3.000
 6QX  C18  C14  C13  115.14  3.000
 6QX  C15  C14  C13  133.05  3.000
 6QX  C24  C15  C16  110.90  3.000
 6QX  C24  C15  C14  136.60  3.000
 6QX  C16  C15  C14  112.46  3.000
 6QX  S17  C16  C22  132.48  3.000
 6QX  S17  C16  C15  113.59  3.000
 6QX  C22  C16  C15  113.87  3.000
 6QX  H14  C20  N21  115.79  3.000
 6QX  H14  C20  N19  116.39  3.000
 6QX  N21  C20  N19  127.82  3.000
 6QX  H16  C22  H15  107.08  3.000
 6QX  H16  C22  C23  112.14  3.000
 6QX  H15  C22  C23  112.13  3.000
 6QX  H16  C22  C16  110.97  3.000
 6QX  H15  C22  C16  113.46  3.000
 6QX  C23  C22  C16  101.13  3.000
 6QX  H18  C24  H17  107.09  3.000
 6QX  H18  C24  C23  111.38  3.000
 6QX  H17  C24  C23  111.58  3.000
 6QX  H18  C24  C15  113.57  3.000
 6QX  H17  C24  C15  110.87  3.000
 6QX  C23  C24  C15  102.42  3.000
 6QX  C18  N19  C20  113.55  3.000
 6QX  C4   N2   C3   112.84  3.000
 6QX  C3   N2   C1   109.33  3.000
 6QX  C4   N2   C1   112.70  3.000
 6QX  S17  C18  N19  122.89  3.000
 6QX  N19  C18  C14  125.42  3.000
 6QX  S17  C18  C14  111.69  3.000
 6QX  H20  N12  C13  117.91  3.000
 6QX  H20  N12  C8   117.03  3.000
 6QX  C13  N12  C8   124.68  3.000
 6QX  H22  C6   H21  106.78  3.000
 6QX  H22  C6   C4   110.78  3.000
 6QX  H21  C6   C4   108.65  3.000
 6QX  H22  C6   C7   107.87  3.000
 6QX  H21  C6   C7   109.77  3.000
 6QX  C4   C6   C7   112.82  3.000
 6QX  C18  S17  C16   90.46  3.000
 6QX  H23  C4   C6   107.56  3.000
 6QX  H23  C4   N2   110.07  3.000
 6QX  C6   C4   N2   110.94  3.000
 6QX  H23  C4   C11  107.52  3.000
 6QX  N2   C4   C11  111.25  3.000
 6QX  C6   C4   C11  109.37  3.000
 6QX  H25  C23  H24  107.42  3.000
 6QX  H25  C23  C24  112.08  3.000
 6QX  H24  C23  C24  109.13  3.000
 6QX  H25  C23  C22  112.03  3.000
 6QX  H24  C23  C22  109.04  3.000
 6QX  C24  C23  C22  107.10  3.000
 6QX  C20  N21  C13  118.54  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
 6QX  CONST_01  C16  C15  C14  C13  180.00   0.0  0
 6QX  CONST_02  S17  C18  C14  C13  180.00   0.0  0
 6QX  CONST_03  N19  C18  C14  C13    0.00   0.0  0
 6QX  CONST_04  N19  C20  N21  C13    0.00   0.0  0
 6QX  CONST_05  S17  C16  C15  C14    0.00   0.0  0
 6QX  CONST_06  C16  S17  C18  C14    0.00   0.0  0
 6QX  CONST_07  C20  N19  C18  C14    0.00   0.0  0
 6QX  CONST_08  C20  N21  C13  C14    0.00   0.0  0
 6QX  CONST_09  C18  S17  C16  C15    0.00   0.0  0
 6QX  CONST_10  S17  C18  C14  C15    0.00   0.0  0
 6QX  CONST_11  N19  C18  C14  C15  180.00   0.0  0
 6QX  CONST_12  N21  C13  C14  C15  180.00   0.0  0
 6QX  CONST_13  N19  C18  S17  C16  180.00   0.0  0
 6QX  CONST_14  C18  C14  C15  C16    0.00   0.0  0
 6QX  CONST_15  S17  C18  N19  C20  180.00   0.0  0
 6QX  CONST_16  N21  C13  C14  C18    0.00   0.0  0
 6QX  CONST_17  N21  C20  N19  C18    0.00   0.0  0
 6QX  CONST_18  N12  C13  C14  C15    0.00   0.0  0
 6QX  CONST_19  N12  C13  N21  C20  180.00   0.0  0
 6QX  CONST_20  N12  C13  C14  C18  180.00   0.0  0
 6QX  CONST_21  C14  C13  N12  C8   180.00   0.0  0
 6QX  CONST_22  N21  C13  N12  C8     0.00   0.0  0
 6QX  CONST_23  H14  C20  N21  C13  180.00   0.0  0
 6QX  CONST_24  H20  N12  C13  C14    0.00   0.0  0
 6QX  Var_01    C4   C11  C10  C8    56.89  30.0  1
 6QX  Var_02    C4   C6   C7   C8   -56.30  30.0  1
 6QX  Var_03    C23  C24  C15  C14  169.96  30.0  1
 6QX  Var_04    C23  C22  C16  C15   13.23  30.0  1
 6QX  Var_05    C22  C23  C24  C15   20.48  30.0  1
 6QX  Var_06    C24  C23  C22  C16  -20.38  30.0  1
 6QX  Var_07    H1   C1   N2   C4   177.75  30.0  3
 6QX  Var_08    H4   C3   N2   C4   -56.58  30.0  3

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
 6QX  chir_01  C8  N12  C10  C7  positiv
 6QX  chir_02  C4  N2   C11  C6  positiv

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
 6QX  plan-1  C13  0.020
 6QX  plan-1  C14  0.020
 6QX  plan-1  C15  0.020
 6QX  plan-1  C16  0.020
 6QX  plan-1  C20  0.020
 6QX  plan-1  C22  0.020
 6QX  plan-1  C24  0.020
 6QX  plan-1  N19  0.020
 6QX  plan-1  C18  0.020
 6QX  plan-1  N12  0.020
 6QX  plan-1  S17  0.020
 6QX  plan-1  N21  0.020
 6QX  plan-1  H14  0.020
 6QX  plan-2  C8   0.020
 6QX  plan-2  C13  0.020
 6QX  plan-2  N12  0.020
 6QX  plan-2  H20  0.020

