# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 07:11:51 2021
#   Inital geometry file: a 104 line input string
#   Ligand name: 3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1scc2CCc3cnc(SCC(=O)C(C)(C)C)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
 CJA  CJA  3,3-dimethyl-1-{[9-(methylsulfanyl)-5,6-dihydrothieno[3,4-h]quinazolin-2-yl]sulfanyl}butan-2-one  ligand  43  23  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CJA
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
 CJA  C10  C  CR16  0  -0.073  73.7444  -85.7602  -2.4865
 CJA  C15  C  C     0   0.488  75.1091  -90.9127  -1.0402
 CJA  C17  C  CT    0  -0.228  75.0619  -92.3585  -0.5541
 CJA  C20  C  CH3   0  -0.642  76.5260  -92.8237  -0.4682
 CJA  C22  C  CR6   0   0.257  72.2796  -87.4012  -1.6529
 CJA  C01  C  CH3   0  -0.801  70.4886  -91.8337  -0.3627
 CJA  C03  C  CR5   0  -0.431  70.5789  -89.1736  -1.0369
 CJA  C05  C  CR15  0  -0.568  68.6313  -87.7081  -1.5210
 CJA  C06  C  CR5   0   0.172  69.8094  -87.0740  -1.7303
 CJA  C07  C  CH2   0  -0.515  70.0170  -85.6495  -2.1421
 CJA  C08  C  CH2   0  -0.518  71.2676  -85.5297  -3.0104
 CJA  C09  C  CR6   0  -0.013  72.4429  -86.2123  -2.3765
 CJA  C12  C  CR6   0   0.224  74.5105  -87.5319  -1.3270
 CJA  C14  C  CH2   0  -0.733  75.3167  -89.8390   0.0097
 CJA  C18  C  CH3   0  -0.630  74.3067  -93.2252  -1.5593
 CJA  C19  C  CH3   0  -0.653  74.4191  -92.4912   0.8289
 CJA  C23  C  CR5   0   0.200  70.9383  -87.9141  -1.4614
 CJA  N11  N  N     0  -0.423  74.7834  -86.4041  -1.9671
 CJA  N21  N  N     0  -0.433  73.3172  -88.0609  -1.1386
 CJA  O16  O  O     0  -0.379  75.0325  -90.6286  -2.2093
 CJA  S02  S  S2    0   0.095  71.6499  -90.4710  -0.6045
 CJA  S04  S  S2    0   0.255  68.8651  -89.3290  -0.9866
 CJA  S13  S  S2    0   0.081  75.9429  -88.2924  -0.6524
 CJA  H1   H  HCR6  0   0.275  73.9626  -84.8387  -3.0170
 CJA  H2   H  HCH3  0   0.238  77.1010  -92.2444   0.2564
 CJA  H3   H  HCH3  0   0.245  76.5553  -93.8668  -0.1487
 CJA  H4   H  HCH3  0   0.242  77.0285  -92.7551  -1.4339
 CJA  H5   H  HCH3  0   0.292  71.0919  -92.6984  -0.0906
 CJA  H6   H  HCH3  0   0.283  69.7932  -91.6342   0.4515
 CJA  H7   H  HCH3  0   0.285  69.9445  -92.0663  -1.2766
 CJA  H8   H  HCR5  0   0.299  67.6310  -87.3220  -1.6444
 CJA  H9   H  HCH2  0   0.260  70.1337  -85.0301  -1.2473
 CJA  H10  H  HCH2  0   0.266  69.1461  -85.2690  -2.6758
 CJA  H11  H  HCH2  0   0.263  71.0727  -85.9893  -3.9849
 CJA  H12  H  HCH2  0   0.266  71.4993  -84.4809  -3.2006
 CJA  H13  H  HCH2  0   0.325  74.3730  -89.6656   0.5329
 CJA  H14  H  HCH2  0   0.320  76.0351  -90.1554   0.7681
 CJA  H15  H  HCH3  0   0.233  74.2686  -94.2549  -1.2017
 CJA  H16  H  HCH3  0   0.224  73.2795  -92.8805  -1.6948
 CJA  H17  H  HCH3  0   0.236  74.7877  -93.2308  -2.5364
 CJA  H18  H  HCH3  0   0.240  74.9495  -91.9287   1.5971
 CJA  H19  H  HCH3  0   0.229  73.3800  -92.1599   0.8349
 CJA  H20  H  HCH3  0   0.247  74.4299  -93.5388   1.1328

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
 CJA  C08  C07  single    1.527  0.020  1.527
 CJA  C08  C09  single    1.500  0.020  1.500
 CJA  C07  C06  single    1.497  0.020  1.497
 CJA  C10  C09  aromatic  1.382  0.020  1.382
 CJA  C10  N11  aromatic  1.328  0.020  1.328
 CJA  C09  C22  aromatic  1.401  0.020  1.401
 CJA  O16  C15  double    1.206  0.020  1.206
 CJA  C06  C05  aromatic  1.354  0.020  1.354
 CJA  C06  C23  aromatic  1.433  0.020  1.433
 CJA  C05  S04  aromatic  1.723  0.020  1.723
 CJA  N11  C12  aromatic  1.325  0.020  1.325
 CJA  C22  C23  aromatic  1.449  0.020  1.449
 CJA  C22  N21  aromatic  1.333  0.020  1.333
 CJA  C23  C03  aromatic  1.377  0.020  1.377
 CJA  S04  C03  aromatic  1.722  0.020  1.722
 CJA  C03  S02  single    1.737  0.020  1.737
 CJA  C12  N21  aromatic  1.319  0.020  1.319
 CJA  C12  S13  single    1.756  0.020  1.756
 CJA  C18  C17  single    1.527  0.020  1.527
 CJA  C15  C17  single    1.526  0.020  1.526
 CJA  C15  C14  single    1.516  0.020  1.516
 CJA  C20  C17  single    1.539  0.020  1.539
 CJA  S02  C01  single    1.807  0.020  1.807
 CJA  S13  C14  single    1.795  0.020  1.795
 CJA  C17  C19  single    1.531  0.020  1.531
 CJA  C10  H1   single    0.930  0.020  1.080
 CJA  C20  H2   single    0.970  0.020  1.090
 CJA  C20  H3   single    0.970  0.020  1.090
 CJA  C20  H4   single    0.970  0.020  1.090
 CJA  C01  H5   single    0.970  0.020  1.090
 CJA  C01  H6   single    0.970  0.020  1.090
 CJA  C01  H7   single    0.970  0.020  1.090
 CJA  C05  H8   single    0.930  0.020  1.080
 CJA  C07  H9   single    0.970  0.020  1.090
 CJA  C07  H10  single    0.970  0.020  1.090
 CJA  C08  H11  single    0.970  0.020  1.090
 CJA  C08  H12  single    0.970  0.020  1.090
 CJA  C14  H13  single    0.970  0.020  1.090
 CJA  C14  H14  single    0.970  0.020  1.090
 CJA  C18  H15  single    0.970  0.020  1.090
 CJA  C18  H16  single    0.970  0.020  1.090
 CJA  C18  H17  single    0.970  0.020  1.090
 CJA  C19  H18  single    0.970  0.020  1.090
 CJA  C19  H19  single    0.970  0.020  1.090
 CJA  C19  H20  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
 CJA  H1   C10  N11  116.45  3.000
 CJA  H1   C10  C09  120.39  3.000
 CJA  N11  C10  C09  123.16  3.000
 CJA  O16  C15  C14  120.89  3.000
 CJA  C14  C15  C17  117.04  3.000
 CJA  O16  C15  C17  122.02  3.000
 CJA  C19  C17  C18  109.75  3.000
 CJA  C19  C17  C20  108.84  3.000
 CJA  C18  C17  C20  109.62  3.000
 CJA  C19  C17  C15  112.51  3.000
 CJA  C20  C17  C15  105.95  3.000
 CJA  C18  C17  C15  110.08  3.000
 CJA  H4   C20  H3   107.87  3.000
 CJA  H4   C20  H2   108.16  3.000
 CJA  H3   C20  H2   107.39  3.000
 CJA  H4   C20  C17  111.71  3.000
 CJA  H3   C20  C17  109.32  3.000
 CJA  H2   C20  C17  112.20  3.000
 CJA  N21  C22  C23  119.64  3.000
 CJA  N21  C22  C09  121.90  3.000
 CJA  C23  C22  C09  118.46  3.000
 CJA  H7   C01  H6   110.34  3.000
 CJA  H7   C01  H5   108.48  3.000
 CJA  H6   C01  H5   108.21  3.000
 CJA  H7   C01  S02  111.72  3.000
 CJA  H6   C01  S02  111.85  3.000
 CJA  H5   C01  S02  106.03  3.000
 CJA  S04  C03  S02  122.62  3.000
 CJA  S02  C03  C23  126.80  3.000
 CJA  S04  C03  C23  110.57  3.000
 CJA  H8   C05  S04  119.86  3.000
 CJA  H8   C05  C06  128.40  3.000
 CJA  S04  C05  C06  111.74  3.000
 CJA  C23  C06  C07  120.02  3.000
 CJA  C23  C06  C05  112.45  3.000
 CJA  C07  C06  C05  127.49  3.000
 CJA  H10  C07  H9   106.73  3.000
 CJA  H10  C07  C08  110.40  3.000
 CJA  H9   C07  C08  109.46  3.000
 CJA  H10  C07  C06  110.85  3.000
 CJA  H9   C07  C06  109.17  3.000
 CJA  C08  C07  C06  110.15  3.000
 CJA  H12  C08  H11  106.63  3.000
 CJA  H12  C08  C09  110.17  3.000
 CJA  H11  C08  C09  108.94  3.000
 CJA  H12  C08  C07  110.40  3.000
 CJA  H11  C08  C07  109.11  3.000
 CJA  C09  C08  C07  111.45  3.000
 CJA  C08  C09  C22  120.87  3.000
 CJA  C22  C09  C10  115.36  3.000
 CJA  C08  C09  C10  123.74  3.000
 CJA  S13  C12  N21  120.62  3.000
 CJA  S13  C12  N11  112.71  3.000
 CJA  N21  C12  N11  126.64  3.000
 CJA  H14  C14  H13  106.36  3.000
 CJA  H14  C14  S13  106.04  3.000
 CJA  H13  C14  S13  109.94  3.000
 CJA  H14  C14  C15  111.47  3.000
 CJA  H13  C14  C15  109.01  3.000
 CJA  S13  C14  C15  113.74  3.000
 CJA  H17  C18  H16  107.81  3.000
 CJA  H17  C18  H15  107.74  3.000
 CJA  H16  C18  H15  107.81  3.000
 CJA  H17  C18  C17  112.03  3.000
 CJA  H16  C18  C17  111.57  3.000
 CJA  H15  C18  C17  109.71  3.000
 CJA  H20  C19  H19  107.43  3.000
 CJA  H20  C19  H18  107.12  3.000
 CJA  H19  C19  H18  107.64  3.000
 CJA  H20  C19  C17  109.32  3.000
 CJA  H19  C19  C17  112.25  3.000
 CJA  H18  C19  C17  112.81  3.000
 CJA  C06  C23  C03  112.87  3.000
 CJA  C03  C23  C22  127.32  3.000
 CJA  C06  C23  C22  119.81  3.000
 CJA  C12  N11  C10  116.12  3.000
 CJA  C12  N21  C22  116.79  3.000
 CJA  C03  S02  C01  101.56  3.000
 CJA  C05  S04  C03   92.36  3.000
 CJA  C14  S13  C12  103.31  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
 CJA  CONST_01  C23  C22  C09  C10   180.00   0.0  0
 CJA  CONST_02  N21  C22  C09  C10     0.00   0.0  0
 CJA  CONST_03  N21  C12  N11  C10     0.00   0.0  0
 CJA  CONST_04  N11  C10  C09  C22     0.00   0.0  0
 CJA  CONST_05  C05  C06  C23  C22   180.00   0.0  0
 CJA  CONST_06  S04  C03  C23  C22   180.00   0.0  0
 CJA  CONST_07  N11  C12  N21  C22     0.00   0.0  0
 CJA  CONST_08  C05  C06  C23  C03     0.00   0.0  0
 CJA  CONST_09  C09  C22  C23  C03   180.00   0.0  0
 CJA  CONST_10  N21  C22  C23  C03     0.00   0.0  0
 CJA  CONST_11  C06  C05  S04  C03     0.00   0.0  0
 CJA  CONST_12  C23  C03  S04  C05     0.00   0.0  0
 CJA  CONST_13  C09  C22  C23  C06     0.00   0.0  0
 CJA  CONST_14  N21  C22  C23  C06   180.00   0.0  0
 CJA  CONST_15  S04  C03  C23  C06     0.00   0.0  0
 CJA  CONST_16  C12  N11  C10  C09     0.00   0.0  0
 CJA  CONST_17  C12  N21  C22  C09     0.00   0.0  0
 CJA  CONST_18  C23  C22  N21  C12   180.00   0.0  0
 CJA  CONST_19  S04  C05  C06  C23     0.00   0.0  0
 CJA  CONST_20  S13  C12  N11  C10   180.00   0.0  0
 CJA  CONST_21  S02  C03  C23  C22     0.00   0.0  0
 CJA  CONST_22  S13  C12  N21  C22   180.00   0.0  0
 CJA  CONST_23  S02  C03  S04  C05   180.00   0.0  0
 CJA  CONST_24  S02  C03  C23  C06   180.00   0.0  0
 CJA  CONST_25  H1   C10  C09  C22   180.00   0.0  0
 CJA  CONST_26  H8   C05  S04  C03   180.00   0.0  0
 CJA  Var_01    C07  C08  C09  C10  -145.64  30.0  1
 CJA  Var_02    C08  C07  C06  C05  -147.37  30.0  1
 CJA  Var_03    C09  C08  C07  C06   -49.57  30.0  1
 CJA  Var_04    C23  C03  S02  C01  -173.23  30.0  1
 CJA  Var_05    N11  C12  S13  C14  -175.04  30.0  2
 CJA  Var_06    H5   C01  S02  C03   179.69  30.0  3
 CJA  Var_07    H13  C14  S13  C12   -43.14  30.0  3
 CJA  Var_08    S13  C14  C15  C17   159.07  30.0  3
 CJA  Var_09    O16  C15  C17  C20    92.82  30.0  3
 CJA  Var_10    H15  C18  C17  C15  -179.48  30.0  3
 CJA  Var_11    H2   C20  C17  C15    62.47  30.0  3
 CJA  Var_12    H18  C19  C17  C15   -59.83  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
 CJA  plan-1  C15  0.020
 CJA  plan-1  C17  0.020
 CJA  plan-1  C14  0.020
 CJA  plan-1  O16  0.020
 CJA  plan-2  C22  0.020
 CJA  plan-2  C03  0.020
 CJA  plan-2  C05  0.020
 CJA  plan-2  C06  0.020
 CJA  plan-2  C07  0.020
 CJA  plan-2  C23  0.020
 CJA  plan-2  S02  0.020
 CJA  plan-2  S04  0.020
 CJA  plan-2  H8   0.020
 CJA  plan-3  C10  0.020
 CJA  plan-3  C22  0.020
 CJA  plan-3  C08  0.020
 CJA  plan-3  C09  0.020
 CJA  plan-3  C12  0.020
 CJA  plan-3  C23  0.020
 CJA  plan-3  N11  0.020
 CJA  plan-3  N21  0.020
 CJA  plan-3  S13  0.020
 CJA  plan-3  H1   0.020

