# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:44:47 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 6-[3-methyl-5-(4-methylpiperazin-1-yl)carbonyl-thiophen-2-yl]-8-oxidanyl-3~{H}-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(=O)c2sc(c(C)c2)c3cc(O)c4N=CNC(=O)c4c3
#
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
 7JK  7JK  6-[3-methyl-5-(4-methylpiperazin-1-yl)carbonyl-thiophen-2-yl]-8-oxidanyl-3~{H}-quinazolin-4-one  ligand  47  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_7JK
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
 7JK  C4   C  C     0   0.526  -3.3312   1.1660  -0.4938
 7JK  C5   C  CR5   0   0.173   0.0366   1.4991   1.1477
 7JK  C6   C  CR5   0  -0.275   0.4911   0.5664   0.2481
 7JK  C8   C  CH3   0  -0.755   0.8503   2.1596   2.2150
 7JK  C13  C  CR6   0   0.336   3.2744  -1.8823  -0.3413
 7JK  C15  C  CR66  0  -0.065   4.2221   0.3251  -0.0395
 7JK  C22  C  CH2   0  -0.327  -3.7860  -1.2390  -0.0550
 7JK  C26  C  CH2   0  -0.322  -5.3421   0.0899  -1.3383
 7JK  C1   C  CR5   0  -0.326  -1.9314   1.0271  -0.0141
 7JK  C2   C  CR15  0  -0.196  -1.3488   1.7652   0.9714
 7JK  S3   S  S2    0   0.255  -0.7774   0.0136  -0.7851
 7JK  O7   O  O     0  -0.473  -3.7754   2.2857  -0.7046
 7JK  C9   C  CR6   0   0.112   1.8403   0.0256   0.0748
 7JK  N10  N  NR16  0  -0.665   6.5828   0.4799  -0.1708
 7JK  C12  C  CR16  0  -0.402   2.0156  -1.3496  -0.1607
 7JK  C14  C  CR16  0  -0.384   2.9457   0.8602   0.1274
 7JK  C16  C  CR66  0   0.150   4.4036  -1.0398  -0.2752
 7JK  N17  N  N     0  -0.481   5.6310  -1.6274  -0.4508
 7JK  C18  C  CR16  0   0.165   6.6529  -0.8563  -0.3909
 7JK  C19  C  CR6   0   0.567   5.4080   1.1776   0.0167
 7JK  O20  O  O     0  -0.445   5.4046   2.3783   0.2082
 7JK  N21  N  NT    0  -0.457  -4.0261   0.0311  -0.7236
 7JK  C23  C  CH2   0  -0.269  -4.8980  -1.5233   0.9431
 7JK  N24  N  NT    0  -0.414  -6.1971  -1.4956   0.3045
 7JK  C25  C  CH2   0  -0.280  -6.4306  -0.2097  -0.3227
 7JK  C27  C  CH3   0  -0.519  -7.2525  -1.8338   1.2324
 7JK  H1   H  HCH3  0   0.255   1.2147   3.1368   1.8927
 7JK  H2   H  HCH3  0   0.258   0.2471   2.3204   3.1082
 7JK  H3   H  HCH3  0   0.252   1.7165   1.5643   2.4997
 7JK  H4   H  HCH2  0   0.250  -3.7405  -2.0342  -0.8037
 7JK  H5   H  HCH2  0   0.272  -2.8368  -1.2260   0.4734
 7JK  H6   H  HCH2  0   0.267  -5.4977   1.0669  -1.7872
 7JK  H7   H  HCH2  0   0.251  -5.3725  -0.6573  -2.1367
 7JK  H8   H  HCR5  0   0.271  -1.8983   2.4713   1.5797
 7JK  H9   H  HNR6  0   0.437   7.4476   1.0041  -0.1345
 7JK  H10  H  HOH1  0   0.475   4.3794  -3.3715  -0.6619
 7JK  H11  H  HCR6  0   0.274   1.1580  -2.0114  -0.1859
 7JK  H12  H  HCR6  0   0.269   2.8274   1.9255   0.2680
 7JK  H13  H  HCR6  0   0.307   7.6505  -1.2558  -0.5191
 7JK  H14  H  HCH2  0   0.248  -4.7297  -2.5127   1.3744
 7JK  H15  H  HCH2  0   0.197  -4.8301  -0.7929   1.7695
 7JK  H17  H  HCH2  0   0.200  -6.4762   0.6078   0.4186
 7JK  H18  H  HCH2  0   0.245  -7.3953  -0.2317  -0.8354
 7JK  H19  H  HCH3  0   0.195  -7.3413  -1.1186   2.0648
 7JK  H20  H  HCH3  0   0.235  -8.2114  -1.8618   0.7129
 7JK  H21  H  HCH3  0   0.235  -7.0729  -2.8216   1.6590
 7JK  O11  O  OH1   0  -0.619   3.4310  -3.1908  -0.5658

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
 7JK  O7   C4   double    1.223  0.020  1.223
 7JK  C26  C25  single    1.519  0.020  1.519
 7JK  C26  N21  single    1.454  0.020  1.454
 7JK  C4   N21  single    1.350  0.020  1.350
 7JK  C4   C1   single    1.486  0.020  1.486
 7JK  C25  N24  single    1.450  0.020  1.450
 7JK  N21  C22  single    1.455  0.020  1.455
 7JK  C1   S3   aromatic  1.718  0.020  1.718
 7JK  C1   C2   aromatic  1.362  0.020  1.362
 7JK  S3   C6   aromatic  1.727  0.020  1.727
 7JK  N24  C27  single    1.445  0.020  1.445
 7JK  N24  C23  single    1.448  0.020  1.448
 7JK  C22  C23  single    1.521  0.020  1.521
 7JK  C2   C5   aromatic  1.422  0.020  1.422
 7JK  C6   C5   aromatic  1.373  0.020  1.373
 7JK  C6   C9   single    1.464  0.020  1.464
 7JK  C5   C8   single    1.496  0.020  1.496
 7JK  C9   C12  aromatic  1.406  0.020  1.406
 7JK  C9   C14  aromatic  1.386  0.020  1.386
 7JK  C12  C13  aromatic  1.379  0.020  1.379
 7JK  C14  C15  aromatic  1.394  0.020  1.394
 7JK  C13  O11  single    1.337  0.020  1.337
 7JK  C13  C16  aromatic  1.410  0.020  1.410
 7JK  C15  C16  aromatic  1.397  0.020  1.397
 7JK  C15  C19  single    1.462  0.020  1.462
 7JK  C16  N17  single    1.372  0.020  1.372
 7JK  O20  C19  double    1.216  0.020  1.216
 7JK  C19  N10  single    1.379  0.020  1.379
 7JK  N17  C18  double    1.282  0.020  1.282
 7JK  N10  C18  single    1.356  0.020  1.356
 7JK  C8   H1   single    0.970  0.020  1.090
 7JK  C8   H2   single    0.970  0.020  1.090
 7JK  C8   H3   single    0.970  0.020  1.090
 7JK  C22  H4   single    0.970  0.020  1.090
 7JK  C22  H5   single    0.970  0.020  1.090
 7JK  C26  H6   single    0.970  0.020  1.090
 7JK  C26  H7   single    0.970  0.020  1.090
 7JK  C2   H8   single    0.930  0.020  1.080
 7JK  N10  H9   single    0.860  0.020  1.020
 7JK  O11  H10  single    0.850  0.020  0.980
 7JK  C12  H11  single    0.930  0.020  1.080
 7JK  C14  H12  single    0.930  0.020  1.080
 7JK  C18  H13  single    0.930  0.020  1.080
 7JK  C23  H14  single    0.970  0.020  1.090
 7JK  C23  H15  single    0.970  0.020  1.090
 7JK  C25  H17  single    0.970  0.020  1.090
 7JK  C25  H18  single    0.970  0.020  1.090
 7JK  C27  H19  single    0.970  0.020  1.090
 7JK  C27  H20  single    0.970  0.020  1.090
 7JK  C27  H21  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
 7JK  N21  C4   O7   123.59  3.000
 7JK  N21  C4   C1   117.45  3.000
 7JK  O7   C4   C1   118.90  3.000
 7JK  C2   C5   C8   122.41  3.000
 7JK  C8   C5   C6   125.97  3.000
 7JK  C2   C5   C6   111.62  3.000
 7JK  C9   C6   S3   119.21  3.000
 7JK  C9   C6   C5   129.31  3.000
 7JK  S3   C6   C5   111.49  3.000
 7JK  H3   C8   H2   107.86  3.000
 7JK  H3   C8   H1   107.52  3.000
 7JK  H2   C8   H1   107.15  3.000
 7JK  H3   C8   C5   112.20  3.000
 7JK  H2   C8   C5   110.42  3.000
 7JK  H1   C8   C5   111.48  3.000
 7JK  C16  C13  C12  119.61  3.000
 7JK  C16  C13  O11  119.92  3.000
 7JK  C12  C13  O11  120.47  3.000
 7JK  C19  C15  C16  118.10  3.000
 7JK  C19  C15  C14  120.96  3.000
 7JK  C16  C15  C14  120.94  3.000
 7JK  H5   C22  H4   107.78  3.000
 7JK  H5   C22  C23  108.77  3.000
 7JK  H4   C22  C23  110.11  3.000
 7JK  H5   C22  N21  110.93  3.000
 7JK  H4   C22  N21  109.09  3.000
 7JK  C23  C22  N21  110.12  3.000
 7JK  H7   C26  H6   107.99  3.000
 7JK  H7   C26  C25  109.48  3.000
 7JK  H6   C26  C25  110.55  3.000
 7JK  H7   C26  N21  107.83  3.000
 7JK  H6   C26  N21  109.92  3.000
 7JK  C25  C26  N21  110.99  3.000
 7JK  S3   C1   C2   110.91  3.000
 7JK  C2   C1   C4   125.85  3.000
 7JK  S3   C1   C4   122.87  3.000
 7JK  H8   C2   C1   122.90  3.000
 7JK  H8   C2   C5   123.19  3.000
 7JK  C1   C2   C5   113.90  3.000
 7JK  C1   S3   C6    92.07  3.000
 7JK  C14  C9   C12  119.72  3.000
 7JK  C14  C9   C6   120.54  3.000
 7JK  C12  C9   C6   119.74  3.000
 7JK  H9   N10  C19  117.45  3.000
 7JK  H9   N10  C18  118.17  3.000
 7JK  C19  N10  C18  124.37  3.000
 7JK  H11  C12  C9   120.16  3.000
 7JK  H11  C12  C13  118.92  3.000
 7JK  C9   C12  C13  120.90  3.000
 7JK  H12  C14  C9   120.74  3.000
 7JK  H12  C14  C15  119.60  3.000
 7JK  C9   C14  C15  119.64  3.000
 7JK  N17  C16  C15  123.79  3.000
 7JK  N17  C16  C13  117.03  3.000
 7JK  C15  C16  C13  119.18  3.000
 7JK  C18  N17  C16  116.72  3.000
 7JK  H13  C18  N17  120.49  3.000
 7JK  H13  C18  N10  115.50  3.000
 7JK  N17  C18  N10  124.01  3.000
 7JK  O20  C19  N10  121.56  3.000
 7JK  N10  C19  C15  113.00  3.000
 7JK  O20  C19  C15  125.44  3.000
 7JK  C26  N21  C22  112.27  3.000
 7JK  C22  N21  C4   124.78  3.000
 7JK  C26  N21  C4   120.25  3.000
 7JK  H15  C23  H14  107.10  3.000
 7JK  H15  C23  N24  111.86  3.000
 7JK  H14  C23  N24  109.25  3.000
 7JK  H15  C23  C22  108.80  3.000
 7JK  H14  C23  C22  108.41  3.000
 7JK  N24  C23  C22  111.28  3.000
 7JK  C27  N24  C25  111.57  3.000
 7JK  C27  N24  C23  111.56  3.000
 7JK  C25  N24  C23  110.63  3.000
 7JK  H18  C25  H17  107.06  3.000
 7JK  H18  C25  N24  109.11  3.000
 7JK  H17  C25  N24  111.89  3.000
 7JK  H18  C25  C26  108.84  3.000
 7JK  H17  C25  C26  109.42  3.000
 7JK  N24  C25  C26  110.42  3.000
 7JK  H21  C27  H20  107.92  3.000
 7JK  H21  C27  H19  107.81  3.000
 7JK  H20  C27  H19  107.81  3.000
 7JK  H21  C27  N24  110.04  3.000
 7JK  H20  C27  N24  110.00  3.000
 7JK  H19  C27  N24  113.10  3.000
 7JK  H10  O11  C13  108.27  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
 7JK  CONST_01  S3   C1   C2   C5      0.00   0.0  0
 7JK  CONST_02  C1   S3   C6   C5      0.00   0.0  0
 7JK  CONST_05  C2   C1   S3   C6      0.00   0.0  0
 7JK  CONST_06  C1   C2   C5   C6      0.00   0.0  0
 7JK  CONST_07  C13  C12  C9   C6    180.00   0.0  0
 7JK  CONST_08  C15  C14  C9   C6    180.00   0.0  0
 7JK  CONST_09  C14  C9   C12  C13     0.00   0.0  0
 7JK  CONST_10  C14  C15  C16  C13     0.00   0.0  0
 7JK  CONST_11  C12  C9   C14  C15     0.00   0.0  0
 7JK  CONST_12  C12  C13  C16  C15     0.00   0.0  0
 7JK  CONST_13  C9   C6   S3   C1    180.00   0.0  0
 7JK  CONST_14  S3   C6   C5   C2      0.00   0.0  0
 7JK  CONST_15  C9   C6   C5   C2    180.00   0.0  0
 7JK  CONST_18  C16  C13  C12  C9      0.00   0.0  0
 7JK  CONST_19  C16  C15  C14  C9      0.00   0.0  0
 7JK  CONST_20  C18  N10  C19  C15     0.00   0.0  0
 7JK  CONST_21  C16  N17  C18  N10     0.00   0.0  0
 7JK  CONST_22  C19  N10  C18  N17     0.00   0.0  0
 7JK  CONST_23  C6   S3   C1   C4    180.00   0.0  0
 7JK  CONST_24  C5   C2   C1   C4    180.00   0.0  0
 7JK  CONST_25  C1   C2   C5   C8    180.00   0.0  0
 7JK  CONST_26  S3   C6   C5   C8    180.00   0.0  0
 7JK  CONST_27  C9   C6   C5   C8      0.00   0.0  0
 7JK  CONST_28  O11  C13  C16  C15   180.00   0.0  0
 7JK  CONST_29  O11  C13  C12  C9    180.00   0.0  0
 7JK  CONST_30  N17  C16  C13  O11     0.00   0.0  0
 7JK  CONST_32  C1   C4   N21  C26   180.00   0.0  0
 7JK  CONST_33  O20  C19  N10  C18   180.00   0.0  0
 7JK  CONST_34  H8   C2   C5   C6    180.00   0.0  0
 7JK  CONST_35  H11  C12  C9   C6      0.00   0.0  0
 7JK  CONST_36  H12  C14  C9   C6      0.00   0.0  0
 7JK  CONST_37  H9   N10  C19  C15   180.00   0.0  0
 7JK  CONST_38  H13  C18  N17  C16   180.00   0.0  0
 7JK  CONST_40  O7   C4   N21  C26     0.00   0.0  0
 7JK  Var_01    C25  C26  N21  C22    54.89  30.0  1
 7JK  Var_02    C25  N24  C23  C22   -58.18  30.0  1
 7JK  Var_03    C23  N24  C25  C26    57.81  30.0  1
 7JK  Var_04    C23  C22  N21  C26   -54.29  30.0  1
 7JK  Var_05    N24  C25  C26  N21   -55.98  30.0  1
 7JK  Var_06    N24  C23  C22  N21    55.76  30.0  1
 7JK  Var_07    N21  C4   C1   C2   -137.30  30.0  2
 7JK  Var_08    H1   C8   C5   C6     96.79  30.0  2
 7JK  Var_09    H19  C27  N24  C23    62.66  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
 7JK  plan-1  C4   0.020
 7JK  plan-1  C5   0.020
 7JK  plan-1  C6   0.020
 7JK  plan-1  C8   0.020
 7JK  plan-1  C1   0.020
 7JK  plan-1  C2   0.020
 7JK  plan-1  S3   0.020
 7JK  plan-1  C9   0.020
 7JK  plan-1  H8   0.020
 7JK  plan-2  C6   0.020
 7JK  plan-2  C13  0.020
 7JK  plan-2  C15  0.020
 7JK  plan-2  C9   0.020
 7JK  plan-2  N10  0.020
 7JK  plan-2  C12  0.020
 7JK  plan-2  C14  0.020
 7JK  plan-2  C16  0.020
 7JK  plan-2  N17  0.020
 7JK  plan-2  C18  0.020
 7JK  plan-2  C19  0.020
 7JK  plan-2  O20  0.020
 7JK  plan-2  H9   0.020
 7JK  plan-2  H11  0.020
 7JK  plan-2  H12  0.020
 7JK  plan-2  H13  0.020
 7JK  plan-2  O11  0.020
 7JK  plan-3  C4   0.020
 7JK  plan-3  C22  0.020
 7JK  plan-3  C26  0.020
 7JK  plan-3  C1   0.020
 7JK  plan-3  O7   0.020
 7JK  plan-3  N21  0.020

