# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:49:12 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 3-[[2-[(1-ethylpiperidin-4-yl)-methyl-amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCC(CC1)N(C)c2nc3ccsc3c(n2)N(C)CCC#N
#
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
 HXE  HXE  3-[[2-[(1-ethylpiperidin-4-yl)-methyl-amino]thieno[3,2-d]pyrimidin-4-yl]-methyl-amino]propanenitrile  ligand  51  25  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HXE
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
 HXE  N4   N  NS    0  -0.275  8.0508  45.1566  57.3562
 HXE  C13  C  CSP   0   0.124  8.1663  45.9883  58.1431
 HXE  C12  C  CH2   0  -0.549  8.2880  47.0516  59.1253
 HXE  C11  C  CH2   0  -0.318  7.7994  48.3949  58.5623
 HXE  N3   N  NT    0  -0.489  7.8958  49.4532  59.5414
 HXE  C10  C  CH3   0  -0.560  9.1460  50.1808  59.6309
 HXE  C9   C  CR6   0   0.592  6.8952  49.6130  60.4389
 HXE  N2   N  N     0  -0.545  5.9174  48.7229  60.4046
 HXE  C14  C  CR56  0  -0.371  6.8280  50.6598  61.3920
 HXE  C17  C  CR56  0   0.303  5.7029  50.6708  62.2250
 HXE  C16  C  CR15  0  -0.213  5.7138  51.7866  63.1240
 HXE  C15  C  CR15  0  -0.440  6.8010  52.5723  62.9528
 HXE  S    S  S2    0   0.200  7.8610  52.0200  61.7196
 HXE  N5   N  N     0  -0.536  4.7241  49.7608  62.1732
 HXE  C8   C  CR6   0   0.614  4.8822  48.8172  61.2515
 HXE  N1   N  NT    0  -0.498  3.9235  47.8617  61.1670
 HXE  C7   C  CH3   0  -0.528  2.8854  47.8198  62.1739
 HXE  C4   C  CH1   0  -0.099  3.9567  46.8361  60.1359
 HXE  C3   C  CH2   0  -0.429  2.6129  46.6538  59.4379
 HXE  C2   C  CH2   0  -0.280  2.7279  45.5780  58.3685
 HXE  C5   C  CH2   0  -0.434  4.4538  45.4933  60.6590
 HXE  C6   C  CH2   0  -0.290  4.4708  44.4539  59.5485
 HXE  N    N  NT    0  -0.413  3.1654  44.3120  58.9289
 HXE  C1   C  CH2   0  -0.266  3.1497  43.2676  57.9183
 HXE  C    C  CH3   0  -0.682  3.3289  41.8678  58.4836
 HXE  H1   H  HCH2  0   0.313  9.3330  47.1161  59.4349
 HXE  H2   H  HCH2  0   0.314  7.7009  46.7728  60.0018
 HXE  H3   H  HCH2  0   0.282  8.4024  48.6747  57.6993
 HXE  H4   H  HCH2  0   0.281  6.7702  48.2988  58.2236
 HXE  H5   H  HCH3  0   0.255  9.5744  50.1337  60.6323
 HXE  H6   H  HCH3  0   0.279  9.8664  49.7237  58.9573
 HXE  H7   H  HCH3  0   0.256  9.0417  51.2246  59.3291
 HXE  H8   H  HCR5  0   0.269  4.9345  51.9738  63.8484
 HXE  H9   H  HCR5  0   0.305  7.0509  53.4713  63.4960
 HXE  H10  H  HCH3  0   0.243  3.2980  47.9673  63.1705
 HXE  H11  H  HCH3  0   0.232  2.1157  48.5788  62.0158
 HXE  H12  H  HCH3  0   0.242  2.4051  46.8443  62.1583
 HXE  H13  H  HCH1  0   0.255  4.6640  47.1768  59.3799
 HXE  H14  H  HCH2  0   0.238  2.2980  47.5930  58.9771
 HXE  H15  H  HCH2  0   0.222  1.8340  46.3643  60.1483
 HXE  H16  H  HCH2  0   0.185  3.4157  45.9272  57.5757
 HXE  H17  H  HCH2  0   0.238  1.7542  45.4338  57.8938
 HXE  H18  H  HCH2  0   0.222  3.8120  45.1428  61.4736
 HXE  H19  H  HCH2  0   0.236  5.4620  45.6030  61.0662
 HXE  H20  H  HCH2  0   0.242  4.7815  43.4949  59.9656
 HXE  H21  H  HCH2  0   0.184  5.2357  44.7273  58.7964
 HXE  H23  H  HCH2  0   0.185  3.9140  43.4502  57.1432
 HXE  H24  H  HCH2  0   0.226  2.1830  43.3156  57.4101
 HXE  H25  H  HCH3  0   0.233  3.1678  41.1290  57.6982
 HXE  H26  H  HCH3  0   0.226  4.3290  41.6996  58.8834
 HXE  H27  H  HCH3  0   0.222  2.6087  41.6750  59.2799

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
 HXE  C    C1   single    1.520  0.020  1.520
 HXE  C1   N    single    1.453  0.020  1.453
 HXE  C2   N    single    1.452  0.020  1.452
 HXE  C2   C3   single    1.521  0.020  1.521
 HXE  N4   C13  triple    1.151  0.020  1.151
 HXE  N    C6   single    1.452  0.020  1.452
 HXE  C11  C12  single    1.536  0.020  1.536
 HXE  C11  N3   single    1.445  0.020  1.445
 HXE  C13  C12  single    1.453  0.020  1.453
 HXE  C6   C5   single    1.521  0.020  1.521
 HXE  C3   C4   single    1.525  0.020  1.525
 HXE  C10  N3   single    1.449  0.020  1.449
 HXE  N3   C9   single    1.354  0.020  1.354
 HXE  C4   C5   single    1.524  0.020  1.524
 HXE  C4   N1   single    1.455  0.020  1.455
 HXE  N2   C9   aromatic  1.323  0.020  1.323
 HXE  N2   C8   aromatic  1.341  0.020  1.341
 HXE  C9   C14  aromatic  1.417  0.020  1.417
 HXE  N1   C8   single    1.356  0.020  1.356
 HXE  N1   C7   single    1.447  0.020  1.447
 HXE  C8   N5   aromatic  1.328  0.020  1.328
 HXE  C14  S    aromatic  1.739  0.020  1.739
 HXE  C14  C17  aromatic  1.400  0.020  1.400
 HXE  S    C15  aromatic  1.717  0.020  1.717
 HXE  C17  N5   aromatic  1.337  0.020  1.337
 HXE  C17  C16  aromatic  1.433  0.020  1.433
 HXE  C15  C16  aromatic  1.352  0.020  1.352
 HXE  C12  H1   single    0.970  0.020  1.090
 HXE  C12  H2   single    0.970  0.020  1.090
 HXE  C11  H3   single    0.970  0.020  1.090
 HXE  C11  H4   single    0.970  0.020  1.090
 HXE  C10  H5   single    0.970  0.020  1.090
 HXE  C10  H6   single    0.970  0.020  1.090
 HXE  C10  H7   single    0.970  0.020  1.090
 HXE  C16  H8   single    0.930  0.020  1.080
 HXE  C15  H9   single    0.930  0.020  1.080
 HXE  C7   H10  single    0.970  0.020  1.090
 HXE  C7   H11  single    0.970  0.020  1.090
 HXE  C7   H12  single    0.970  0.020  1.090
 HXE  C4   H13  single    0.970  0.020  1.090
 HXE  C3   H14  single    0.970  0.020  1.090
 HXE  C3   H15  single    0.970  0.020  1.090
 HXE  C2   H16  single    0.970  0.020  1.090
 HXE  C2   H17  single    0.970  0.020  1.090
 HXE  C5   H18  single    0.970  0.020  1.090
 HXE  C5   H19  single    0.970  0.020  1.090
 HXE  C6   H20  single    0.970  0.020  1.090
 HXE  C6   H21  single    0.970  0.020  1.090
 HXE  C1   H23  single    0.970  0.020  1.090
 HXE  C1   H24  single    0.970  0.020  1.090
 HXE  C    H25  single    0.970  0.020  1.090
 HXE  C    H26  single    0.970  0.020  1.090
 HXE  C    H27  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
 HXE  C12  C13  N4   180.00  3.000
 HXE  H2   C12  H1   107.60  3.000
 HXE  H2   C12  C11  110.28  3.000
 HXE  H1   C12  C11  110.90  3.000
 HXE  H2   C12  C13  108.12  3.000
 HXE  H1   C12  C13  108.37  3.000
 HXE  C11  C12  C13  111.44  3.000
 HXE  H4   C11  H3   107.45  3.000
 HXE  H4   C11  N3   109.81  3.000
 HXE  H3   C11  N3   108.16  3.000
 HXE  H4   C11  C12  109.74  3.000
 HXE  H3   C11  C12  109.80  3.000
 HXE  N3   C11  C12  111.77  3.000
 HXE  C9   N3   C10  122.51  3.000
 HXE  C9   N3   C11  119.11  3.000
 HXE  C10  N3   C11  117.85  3.000
 HXE  H7   C10  H6   107.10  3.000
 HXE  H7   C10  H5   109.44  3.000
 HXE  H6   C10  H5   106.90  3.000
 HXE  H7   C10  N3   112.37  3.000
 HXE  H6   C10  N3   108.80  3.000
 HXE  H5   C10  N3   111.97  3.000
 HXE  C14  C9   N2   118.65  3.000
 HXE  C14  C9   N3   124.62  3.000
 HXE  N2   C9   N3   116.73  3.000
 HXE  C8   N2   C9   120.46  3.000
 HXE  S    C14  C17  111.05  3.000
 HXE  C17  C14  C9   116.36  3.000
 HXE  S    C14  C9   132.55  3.000
 HXE  N5   C17  C16  124.04  3.000
 HXE  C16  C17  C14  111.91  3.000
 HXE  N5   C17  C14  124.04  3.000
 HXE  H8   C16  C15  124.35  3.000
 HXE  H8   C16  C17  123.37  3.000
 HXE  C15  C16  C17  112.28  3.000
 HXE  H9   C15  S    119.09  3.000
 HXE  H9   C15  C16  127.32  3.000
 HXE  S    C15  C16  113.60  3.000
 HXE  C15  S    C14   91.15  3.000
 HXE  C8   N5   C17  115.03  3.000
 HXE  N1   C8   N5   117.36  3.000
 HXE  N5   C8   N2   125.45  3.000
 HXE  N1   C8   N2   117.18  3.000
 HXE  C4   N1   C7   119.29  3.000
 HXE  C7   N1   C8   118.96  3.000
 HXE  C4   N1   C8   121.65  3.000
 HXE  H12  C7   H11  108.05  3.000
 HXE  H12  C7   H10  107.58  3.000
 HXE  H11  C7   H10  107.78  3.000
 HXE  H12  C7   N1   109.45  3.000
 HXE  H11  C7   N1   112.62  3.000
 HXE  H10  C7   N1   111.18  3.000
 HXE  H13  C4   C5   107.56  3.000
 HXE  H13  C4   C3   106.96  3.000
 HXE  C5   C4   C3   109.82  3.000
 HXE  H13  C4   N1   106.62  3.000
 HXE  C5   C4   N1   112.66  3.000
 HXE  C3   C4   N1   112.86  3.000
 HXE  H15  C3   H14  107.24  3.000
 HXE  H15  C3   C2   108.87  3.000
 HXE  H14  C3   C2   109.46  3.000
 HXE  H15  C3   C4   111.23  3.000
 HXE  H14  C3   C4   110.13  3.000
 HXE  C2   C3   C4   109.85  3.000
 HXE  H17  C2   H16  106.52  3.000
 HXE  H17  C2   N    108.73  3.000
 HXE  H16  C2   N    111.38  3.000
 HXE  H17  C2   C3   109.35  3.000
 HXE  H16  C2   C3   109.12  3.000
 HXE  N    C2   C3   111.59  3.000
 HXE  H19  C5   H18  107.20  3.000
 HXE  H19  C5   C6   109.29  3.000
 HXE  H18  C5   C6   109.33  3.000
 HXE  H19  C5   C4   109.89  3.000
 HXE  H18  C5   C4   110.26  3.000
 HXE  C6   C5   C4   110.79  3.000
 HXE  H21  C6   H20  106.26  3.000
 HXE  H21  C6   N    110.82  3.000
 HXE  H20  C6   N    109.46  3.000
 HXE  H21  C6   C5   109.57  3.000
 HXE  H20  C6   C5   108.95  3.000
 HXE  N    C6   C5   111.61  3.000
 HXE  C1   N    C6   112.13  3.000
 HXE  C6   N    C2   110.51  3.000
 HXE  C1   N    C2   110.79  3.000
 HXE  H24  C1   H23  106.18  3.000
 HXE  H24  C1   C    108.51  3.000
 HXE  H23  C1   C    109.38  3.000
 HXE  H24  C1   N    107.53  3.000
 HXE  H23  C1   N    111.22  3.000
 HXE  C    C1   N    113.69  3.000
 HXE  H27  C    H26  108.10  3.000
 HXE  H27  C    H25  107.97  3.000
 HXE  H26  C    H25  107.17  3.000
 HXE  H27  C    C1   110.88  3.000
 HXE  H26  C    C1   112.74  3.000
 HXE  H25  C    C1   109.80  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
 HXE  CONST_01  N5   C8   N2   C9      0.00   0.0  0
 HXE  CONST_02  C15  S    C14  C9    180.00   0.0  0
 HXE  CONST_03  N5   C17  C14  C9      0.00   0.0  0
 HXE  CONST_04  C16  C17  C14  C9    180.00   0.0  0
 HXE  CONST_05  S    C14  C9   N2    180.00   0.0  0
 HXE  CONST_06  C17  C14  C9   N2      0.00   0.0  0
 HXE  CONST_07  C17  N5   C8   N2      0.00   0.0  0
 HXE  CONST_08  C8   N2   C9   C14     0.00   0.0  0
 HXE  CONST_09  C16  C15  S    C14     0.00   0.0  0
 HXE  CONST_10  C8   N5   C17  C14     0.00   0.0  0
 HXE  CONST_11  C15  C16  C17  C14     0.00   0.0  0
 HXE  CONST_12  C15  S    C14  C17     0.00   0.0  0
 HXE  CONST_13  S    C15  C16  C17     0.00   0.0  0
 HXE  CONST_14  S    C14  C17  C16     0.00   0.0  0
 HXE  CONST_15  C8   N5   C17  C16   180.00   0.0  0
 HXE  CONST_16  N5   C17  C16  C15   180.00   0.0  0
 HXE  CONST_17  N5   C17  C14  S     180.00   0.0  0
 HXE  CONST_18  C8   N2   C9   N3    180.00   0.0  0
 HXE  CONST_19  S    C14  C9   N3      0.00   0.0  0
 HXE  CONST_20  C17  C14  C9   N3    180.00   0.0  0
 HXE  CONST_21  N1   C8   N2   C9    180.00   0.0  0
 HXE  CONST_22  N1   C8   N5   C17   180.00   0.0  0
 HXE  CONST_23  C4   N1   C8   N2      0.00   0.0  0
 HXE  CONST_24  C4   N1   C8   N5    180.00   0.0  0
 HXE  CONST_25  H9   C15  S    C14   180.00   0.0  0
 HXE  CONST_26  H8   C16  C17  C14   180.00   0.0  0
 HXE  CONST_27  N2   C9   N3   C11     0.00   0.0  0
 HXE  CONST_28  C14  C9   N3   C11   180.00   0.0  0
 HXE  CONST_29  N2   C9   N3   C10   180.00   0.0  0
 HXE  CONST_30  C14  C9   N3   C10     0.00   0.0  0
 HXE  CONST_31  C7   N1   C8   N2    180.00   0.0  0
 HXE  CONST_32  C7   N1   C8   N5      0.00   0.0  0
 HXE  Var_01    N    C2   C3   C4     58.05  30.0  1
 HXE  Var_02    N    C6   C5   C4    -56.14  30.0  1
 HXE  Var_03    C6   N    C2   C3    -60.40  30.0  1
 HXE  Var_04    C5   C6   N    C2     59.16  30.0  1
 HXE  Var_05    C    C1   N    C2   -168.62  30.0  2
 HXE  Var_06    C9   N3   C11  C12   -83.99  30.0  3
 HXE  Var_07    H5   C10  N3   C9     48.86  30.0  3
 HXE  Var_08    H10  C7   N1   C8    -43.14  30.0  3
 HXE  Var_09    H25  C    C1   N     172.08  30.0  3
 HXE  Var_10    C11  C12  C13  N4    -32.25  30.0  3
 HXE  Var_11    N3   C11  C12  C13   179.00  30.0  2

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
 HXE  chir_01  C4  C3  C5  N1  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
 HXE  plan-1  N3   0.020
 HXE  plan-1  C9   0.020
 HXE  plan-1  N2   0.020
 HXE  plan-1  C14  0.020
 HXE  plan-1  C17  0.020
 HXE  plan-1  C16  0.020
 HXE  plan-1  C15  0.020
 HXE  plan-1  S    0.020
 HXE  plan-1  N5   0.020
 HXE  plan-1  C8   0.020
 HXE  plan-1  N1   0.020
 HXE  plan-1  H8   0.020
 HXE  plan-1  H9   0.020
 HXE  plan-2  C11  0.020
 HXE  plan-2  N3   0.020
 HXE  plan-2  C10  0.020
 HXE  plan-2  C9   0.020
 HXE  plan-3  C8   0.020
 HXE  plan-3  N1   0.020
 HXE  plan-3  C7   0.020
 HXE  plan-3  C4   0.020

