# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:04:21 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: (7S)-7-methyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-7,8-dihydro[1]benzothieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1Cc2sc3nc(SCCCN4CCCCC4)nc(N)c3c2C=C1
#
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
 RNJ  RNJ  (7S)-7-methyl-2-{[3-(piperidin-1-yl)propyl]sulfanyl}-7,8-dihydro[1]benzothieno[2,3-d]pyrimidin-4-amine  ligand  51  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RNJ
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
 RNJ  C11  C  CH2   0  -0.458  20.1198  -12.1398  42.2372
 RNJ  C12  C  CH2   0  -0.433  19.9760  -12.3001  43.7444
 RNJ  C13  C  CH2   0  -0.438  19.0567  -11.2174  44.2929
 RNJ  C14  C  CH2   0  -0.273  19.5261   -9.8380  43.8567
 RNJ  C16  C  CR56  0  -0.034  19.7809  -10.5828  35.5842
 RNJ  C17  C  CR56  0  -0.003  20.1626  -11.7517  36.2426
 RNJ  C02  C  CR6   0   0.465  19.9810  -11.7134  37.6485
 RNJ  N03  N  N     0  -0.452  19.4340  -10.6398  38.2184
 RNJ  C04  C  CR6   0   0.209  19.0953   -9.6136  37.4563
 RNJ  S05  S  S2    0   0.040  18.3230   -8.2120  38.1866
 RNJ  C06  C  CH2   0  -0.565  18.4889   -8.5212  39.9645
 RNJ  C07  C  CH2   0  -0.448  19.8571   -8.1425  40.5074
 RNJ  N09  N  NT    0  -0.413  19.6277   -9.7386  42.4109
 RNJ  C10  C  CH2   0  -0.288  20.5498  -10.7251  41.8781
 RNJ  N15  N  N     0  -0.455  19.2523   -9.5023  36.1494
 RNJ  C18  C  CR5   0   0.254  20.6878  -12.7401  35.3392
 RNJ  C19  C  CR5   0  -0.295  20.7231  -12.2859  34.0562
 RNJ  C20  C  CH2   0  -0.467  21.1677  -13.1359  32.9124
 RNJ  C21  C  CH1   0  -0.287  22.2355  -14.1286  33.3810
 RNJ  C22  C  CH3   0  -0.668  22.5361  -15.1563  32.2977
 RNJ  C23  C  C1    0  -0.204  21.8210  -14.7744  34.6770
 RNJ  C24  C  C1    0  -0.334  21.1144  -14.1127  35.5974
 RNJ  S25  S  S2    0   0.224  20.0956  -10.6827  33.8842
 RNJ  H1   H  HCH2  0   0.216  19.1636  -12.3590  41.7498
 RNJ  H2   H  HCH2  0   0.229  20.8533  -12.8485  41.8432
 RNJ  H3   H  HCH2  0   0.210  20.9624  -12.2094  44.2115
 RNJ  H4   H  HCH2  0   0.231  19.6000  -13.2942  43.9953
 RNJ  H5   H  HCH2  0   0.229  19.0189  -11.2561  45.3839
 RNJ  H6   H  HCH2  0   0.214  18.0365  -11.3810  43.9326
 RNJ  H7   H  HCH2  0   0.179  20.4935   -9.6129  44.3429
 RNJ  H8   H  HCH2  0   0.230  18.8196   -9.0808  44.2070
 RNJ  H9   H  HNH2  0   0.417  20.2213  -12.5964  39.4526
 RNJ  H10  H  HNH2  0   0.415  20.9089  -13.4768  38.1584
 RNJ  H11  H  HCH2  0   0.276  17.7073   -7.9146  40.4269
 RNJ  H12  H  HCH2  0   0.287  18.2532   -9.5643  40.1622
 RNJ  H13  H  HCH2  0   0.237  20.6346   -8.6848  39.9659
 RNJ  H14  H  HCH2  0   0.245  20.0443   -7.0819  40.3261
 RNJ  H15  H  HCH2  0   0.201  20.9873   -8.1102  42.3353
 RNJ  H16  H  HCH2  0   0.226  19.2868   -7.7047  42.5228
 RNJ  H18  H  HCH2  0   0.241  20.5857  -10.6275  40.7920
 RNJ  H19  H  HCH2  0   0.184  21.5785  -10.5517  42.2461
 RNJ  H20  H  HCH2  0   0.265  21.5609  -12.5325  32.0926
 RNJ  H21  H  HCH2  0   0.253  20.3034  -13.6826  32.5129
 RNJ  H22  H  HCH1  0   0.255  23.1563  -13.5618  33.5809
 RNJ  H23  H  HCH3  0   0.236  23.3092  -15.8551  32.6196
 RNJ  H24  H  HCH3  0   0.225  21.6436  -15.7339  32.0494
 RNJ  H25  H  HCH3  0   0.235  22.8859  -14.6712  31.3860
 RNJ  H26  H  H     0   0.254  22.1412  -15.7914  34.8716
 RNJ  H27  H  H     0   0.242  20.8313  -14.6080  36.5173
 RNJ  C08  C  CH2   0  -0.269  19.9698   -8.3877  42.0085
 RNJ  N01  N  NH2   0  -0.843  20.3170  -12.7242  38.4592

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
 RNJ  C22  C21  single    1.523  0.020  1.523
 RNJ  C21  C20  single    1.531  0.020  1.531
 RNJ  C21  C23  single    1.506  0.020  1.506
 RNJ  C20  C19  single    1.493  0.020  1.493
 RNJ  C23  C24  double    1.336  0.020  1.336
 RNJ  C19  S25  aromatic  1.730  0.020  1.730
 RNJ  C19  C18  aromatic  1.361  0.020  1.361
 RNJ  S25  C16  aromatic  1.732  0.020  1.732
 RNJ  C24  C18  single    1.460  0.020  1.460
 RNJ  C18  C17  aromatic  1.438  0.020  1.438
 RNJ  C16  C17  aromatic  1.395  0.020  1.395
 RNJ  C16  N15  aromatic  1.329  0.020  1.329
 RNJ  C17  C02  aromatic  1.418  0.020  1.418
 RNJ  N15  C04  aromatic  1.321  0.020  1.321
 RNJ  C02  N01  single    1.339  0.020  1.339
 RNJ  C02  N03  aromatic  1.333  0.020  1.333
 RNJ  C04  N03  aromatic  1.322  0.020  1.322
 RNJ  C04  S05  single    1.759  0.020  1.759
 RNJ  S05  C06  single    1.812  0.020  1.812
 RNJ  C06  C07  single    1.520  0.020  1.520
 RNJ  C07  C08  single    1.525  0.020  1.525
 RNJ  C08  N09  single    1.450  0.020  1.450
 RNJ  N09  C14  single    1.453  0.020  1.453
 RNJ  N09  C10  single    1.452  0.020  1.452
 RNJ  C14  C13  single    1.521  0.020  1.521
 RNJ  C10  C11  single    1.522  0.020  1.522
 RNJ  C13  C12  single    1.523  0.020  1.523
 RNJ  C11  C12  single    1.522  0.020  1.522
 RNJ  C11  H1   single    0.970  0.020  1.090
 RNJ  C11  H2   single    0.970  0.020  1.090
 RNJ  C12  H3   single    0.970  0.020  1.090
 RNJ  C12  H4   single    0.970  0.020  1.090
 RNJ  C13  H5   single    0.970  0.020  1.090
 RNJ  C13  H6   single    0.970  0.020  1.090
 RNJ  C14  H7   single    0.970  0.020  1.090
 RNJ  C14  H8   single    0.970  0.020  1.090
 RNJ  N01  H9   single    0.860  0.020  1.020
 RNJ  N01  H10  single    0.860  0.020  1.020
 RNJ  C06  H11  single    0.970  0.020  1.090
 RNJ  C06  H12  single    0.970  0.020  1.090
 RNJ  C07  H13  single    0.970  0.020  1.090
 RNJ  C07  H14  single    0.970  0.020  1.090
 RNJ  C08  H15  single    0.970  0.020  1.090
 RNJ  C08  H16  single    0.970  0.020  1.090
 RNJ  C10  H18  single    0.970  0.020  1.090
 RNJ  C10  H19  single    0.970  0.020  1.090
 RNJ  C20  H20  single    0.970  0.020  1.090
 RNJ  C20  H21  single    0.970  0.020  1.090
 RNJ  C21  H22  single    0.970  0.020  1.090
 RNJ  C22  H23  single    0.970  0.020  1.090
 RNJ  C22  H24  single    0.970  0.020  1.090
 RNJ  C22  H25  single    0.970  0.020  1.090
 RNJ  C23  H26  single    0.930  0.020  1.080
 RNJ  C24  H27  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
 RNJ  H2   C11  H1   107.19  3.000
 RNJ  H2   C11  C10  109.15  3.000
 RNJ  H1   C11  C10  109.14  3.000
 RNJ  H2   C11  C12  110.60  3.000
 RNJ  H1   C11  C12  109.69  3.000
 RNJ  C10  C11  C12  110.99  3.000
 RNJ  H4   C12  H3   106.71  3.000
 RNJ  H4   C12  C13  110.89  3.000
 RNJ  H3   C12  C13  109.34  3.000
 RNJ  H4   C12  C11  110.85  3.000
 RNJ  H3   C12  C11  109.18  3.000
 RNJ  C13  C12  C11  109.80  3.000
 RNJ  H6   C13  H5   106.94  3.000
 RNJ  H6   C13  C14  109.20  3.000
 RNJ  H5   C13  C14  109.22  3.000
 RNJ  H6   C13  C12  109.76  3.000
 RNJ  H5   C13  C12  110.82  3.000
 RNJ  C14  C13  C12  110.81  3.000
 RNJ  H8   C14  H7   106.46  3.000
 RNJ  H8   C14  N09  108.46  3.000
 RNJ  H7   C14  N09  111.25  3.000
 RNJ  H8   C14  C13  109.68  3.000
 RNJ  H7   C14  C13  109.18  3.000
 RNJ  N09  C14  C13  111.66  3.000
 RNJ  S25  C16  N15  122.46  3.000
 RNJ  N15  C16  C17  126.12  3.000
 RNJ  S25  C16  C17  111.43  3.000
 RNJ  C18  C17  C02  133.48  3.000
 RNJ  C02  C17  C16  114.22  3.000
 RNJ  C18  C17  C16  112.29  3.000
 RNJ  N03  C02  N01  116.89  3.000
 RNJ  N03  C02  C17  119.88  3.000
 RNJ  N01  C02  C17  123.22  3.000
 RNJ  C04  N03  C02  118.93  3.000
 RNJ  N15  C04  S05  113.32  3.000
 RNJ  S05  C04  N03  119.44  3.000
 RNJ  N15  C04  N03  127.24  3.000
 RNJ  C06  S05  C04  103.37  3.000
 RNJ  H12  C06  H11  107.51  3.000
 RNJ  H12  C06  C07  111.66  3.000
 RNJ  H11  C06  C07  110.77  3.000
 RNJ  H12  C06  S05  108.79  3.000
 RNJ  H11  C06  S05  104.78  3.000
 RNJ  C07  C06  S05  112.97  3.000
 RNJ  H14  C07  H13  106.14  3.000
 RNJ  H14  C07  C08  107.87  3.000
 RNJ  H13  C07  C08  110.83  3.000
 RNJ  H14  C07  C06  109.69  3.000
 RNJ  H13  C07  C06  109.89  3.000
 RNJ  C08  C07  C06  112.21  3.000
 RNJ  C10  N09  C08  112.42  3.000
 RNJ  C10  N09  C14  111.29  3.000
 RNJ  C08  N09  C14  110.88  3.000
 RNJ  H19  C10  H18  106.65  3.000
 RNJ  H19  C10  N09  111.22  3.000
 RNJ  H18  C10  N09  108.99  3.000
 RNJ  H19  C10  C11  109.27  3.000
 RNJ  H18  C10  C11  109.11  3.000
 RNJ  N09  C10  C11  111.45  3.000
 RNJ  C04  N15  C16  113.55  3.000
 RNJ  C24  C18  C19  118.21  3.000
 RNJ  C24  C18  C17  129.90  3.000
 RNJ  C19  C18  C17  111.85  3.000
 RNJ  S25  C19  C20  124.02  3.000
 RNJ  S25  C19  C18  113.17  3.000
 RNJ  C20  C19  C18  122.67  3.000
 RNJ  H21  C20  H20  106.60  3.000
 RNJ  H21  C20  C21  109.72  3.000
 RNJ  H20  C20  C21  109.70  3.000
 RNJ  H21  C20  C19  109.14  3.000
 RNJ  H20  C20  C19  111.60  3.000
 RNJ  C21  C20  C19  110.02  3.000
 RNJ  H22  C21  C23  107.16  3.000
 RNJ  H22  C21  C22  108.16  3.000
 RNJ  C23  C21  C22  112.15  3.000
 RNJ  H22  C21  C20  107.78  3.000
 RNJ  C23  C21  C20  110.45  3.000
 RNJ  C22  C21  C20  110.94  3.000
 RNJ  H25  C22  H24  107.91  3.000
 RNJ  H25  C22  H23  107.73  3.000
 RNJ  H24  C22  H23  107.92  3.000
 RNJ  H25  C22  C21  110.97  3.000
 RNJ  H24  C22  C21  110.93  3.000
 RNJ  H23  C22  C21  111.24  3.000
 RNJ  H26  C23  C24  119.83  3.000
 RNJ  H26  C23  C21  118.39  3.000
 RNJ  C24  C23  C21  121.74  3.000
 RNJ  H27  C24  C23  119.82  3.000
 RNJ  H27  C24  C18  120.26  3.000
 RNJ  C23  C24  C18  119.89  3.000
 RNJ  C19  S25  C16   91.25  3.000
 RNJ  H16  C08  H15  106.21  3.000
 RNJ  H16  C08  N09  107.68  3.000
 RNJ  H15  C08  N09  111.67  3.000
 RNJ  H16  C08  C07  108.43  3.000
 RNJ  H15  C08  C07  108.60  3.000
 RNJ  N09  C08  C07  113.91  3.000
 RNJ  H10  N01  H9   116.57  3.000
 RNJ  H10  N01  C02  122.19  3.000
 RNJ  H9   N01  C02  118.57  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
 RNJ  CONST_01  C18  C19  S25  C16     0.00   0.0  0
 RNJ  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 RNJ  CONST_03  N03  C02  C17  C16     0.00   0.0  0
 RNJ  CONST_04  N03  C04  N15  C16     0.00   0.0  0
 RNJ  CONST_05  S25  C19  C18  C17     0.00   0.0  0
 RNJ  CONST_06  C19  S25  C16  C17     0.00   0.0  0
 RNJ  CONST_07  C04  N15  C16  C17     0.00   0.0  0
 RNJ  CONST_08  C04  N03  C02  C17     0.00   0.0  0
 RNJ  CONST_09  C19  C18  C17  C02   180.00   0.0  0
 RNJ  CONST_10  S25  C16  C17  C02   180.00   0.0  0
 RNJ  CONST_11  N15  C16  C17  C02     0.00   0.0  0
 RNJ  CONST_12  N15  C04  N03  C02     0.00   0.0  0
 RNJ  CONST_13  C18  C17  C02  N03   180.00   0.0  0
 RNJ  CONST_14  S25  C16  N15  C04   180.00   0.0  0
 RNJ  CONST_15  C19  S25  C16  N15   180.00   0.0  0
 RNJ  CONST_16  C18  C17  C16  N15   180.00   0.0  0
 RNJ  CONST_17  S25  C16  C17  C18     0.00   0.0  0
 RNJ  CONST_18  N01  C02  C17  C16   180.00   0.0  0
 RNJ  CONST_19  S05  C04  N15  C16   180.00   0.0  0
 RNJ  CONST_20  C18  C17  C02  N01     0.00   0.0  0
 RNJ  CONST_21  C04  N03  C02  N01   180.00   0.0  0
 RNJ  CONST_22  S05  C04  N03  C02   180.00   0.0  0
 RNJ  CONST_23  H9   N01  C02  C17   180.00   0.0  0
 RNJ  CONST_24  H10  N01  C02  C17     0.00   0.0  0
 RNJ  Var_01    C14  N09  C10  C11    58.65  30.0  1
 RNJ  Var_02    C14  C13  C12  C11   -53.03  30.0  1
 RNJ  Var_03    N09  C14  C13  C12    56.21  30.0  1
 RNJ  Var_04    N09  C10  C11  C12   -56.25  30.0  1
 RNJ  Var_05    C10  N09  C14  C13   -58.76  30.0  1
 RNJ  Var_06    C10  C11  C12  C13    53.15  30.0  1
 RNJ  Var_07    C23  C24  C18  C17  -166.47  30.0  1
 RNJ  Var_08    C21  C20  C19  C18   -31.92  30.0  1
 RNJ  Var_09    C21  C23  C24  C18     1.98  30.0  1
 RNJ  Var_10    C07  C08  N09  C14  -169.89  30.0  1
 RNJ  Var_11    N15  C04  S05  C06  -171.06  30.0  1
 RNJ  Var_12    C07  C06  S05  C04    81.10  30.0  3
 RNJ  Var_13    N09  C08  C07  C06    53.92  30.0  3
 RNJ  Var_14    C08  C07  C06  S05   179.04  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
 RNJ  chir_01  C21  C22  C20  C23  negativ

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
 RNJ  plan-1  C16  0.020
 RNJ  plan-1  C17  0.020
 RNJ  plan-1  C02  0.020
 RNJ  plan-1  N03  0.020
 RNJ  plan-1  C04  0.020
 RNJ  plan-1  S05  0.020
 RNJ  plan-1  N15  0.020
 RNJ  plan-1  C18  0.020
 RNJ  plan-1  C19  0.020
 RNJ  plan-1  C20  0.020
 RNJ  plan-1  C24  0.020
 RNJ  plan-1  S25  0.020
 RNJ  plan-1  N01  0.020
 RNJ  plan-2  C02  0.020
 RNJ  plan-2  H9   0.020
 RNJ  plan-2  H10  0.020
 RNJ  plan-2  N01  0.020

