# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:48:26 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-({[(3S)-1-methylpiperidin-3-yl]methyl}sulfanyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@H](CSc2nc(N)c3c(sc4CCCCc34)n2)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
 ROG  ROG  2-({[(3S)-1-methylpiperidin-3-yl]methyl}sulfanyl)-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-4-amine  ligand  47  23  .  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_ROG
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
 ROG  C10  C  CH2   0  -0.276  18.8851  -10.0414  43.0422
 ROG  C12  C  CH3   0  -0.518  16.7111  -10.9162  42.5577
 ROG  C13  C  CH2   0  -0.242  17.8673   -9.6299  40.9092
 ROG  C15  C  CR56  0  -0.030  19.3500  -11.4324  35.1684
 ROG  C16  C  CR56  0  -0.024  20.6898  -11.6840  35.4597
 ROG  C17  C  CR56  0   0.224  21.2981  -12.6042  34.5337
 ROG  C18  C  CR56  0  -0.269  20.4131  -13.0410  33.6035
 ROG  C20  C  C     0  -0.448  22.0067  -14.7548  32.8103
 ROG  C21  C  C     0  -0.442  23.0909  -13.7706  33.2279
 ROG  C22  C  C     0  -0.549  22.7301  -13.0562  34.5292
 ROG  C02  C  CR6   0   0.470  21.1762  -11.0026  36.6044
 ROG  N03  N  N     0  -0.449  20.3754  -10.1700  37.2726
 ROG  C04  C  CR6   0   0.212  19.1289  -10.0196  36.8616
 ROG  S05  S  S2    0   0.043  18.0704   -8.9051  37.7174
 ROG  C06  C  CH2   0  -0.580  19.0950   -8.3517  39.1065
 ROG  C07  C  CH1   0  -0.228  19.2132   -9.3462  40.2528
 ROG  C08  C  CH2   0  -0.427  20.1969   -8.8191  41.2952
 ROG  C09  C  CH2   0  -0.439  20.2723   -9.7689  42.4836
 ROG  N11  N  NT    0  -0.409  18.0008  -10.5573  42.0153
 ROG  N14  N  N     0  -0.458  18.5419  -10.6160  35.8392
 ROG  C19  C  C     0  -0.478  20.6992  -14.0241  32.5156
 ROG  S23  S  S2    0   0.199  18.8298  -12.3381  33.7908
 ROG  H1   H  HCH2  0   0.180  18.4846   -9.1111  43.4872
 ROG  H2   H  HCH2  0   0.231  18.9446  -10.7741  43.8512
 ROG  H3   H  HCH3  0   0.231  16.8313  -11.6558  43.3508
 ROG  H4   H  HCH3  0   0.188  16.1609  -10.0601  42.9800
 ROG  H5   H  HCH3  0   0.230  16.0873  -11.3584  41.7793
 ROG  H6   H  HCH2  0   0.176  17.4149   -8.6727  41.2357
 ROG  H7   H  HCH2  0   0.231  17.1822  -10.0651  40.1765
 ROG  H9   H  H     0   0.243  22.3183  -15.3140  31.9268
 ROG  H10  H  H     0   0.243  24.0472  -14.2816  33.3491
 ROG  H11  H  H     0   0.229  23.2284  -13.0294  32.4350
 ROG  H12  H  H     0   0.251  22.9081  -13.7236  35.3800
 ROG  H13  H  H     0   0.251  23.3975  -12.2000  34.6568
 ROG  H14  H  HNH2  0   0.404  22.6737  -10.6824  37.9285
 ROG  H15  H  HNH2  0   0.424  23.0527  -11.8357  36.7156
 ROG  H16  H  HCH2  0   0.287  20.0800   -8.0944  38.7179
 ROG  H17  H  HCH2  0   0.279  18.6221   -7.4252  39.4426
 ROG  H18  H  HCH1  0   0.236  19.6068  -10.2876  39.8561
 ROG  H19  H  HCH2  0   0.234  21.1842   -8.6822  40.8459
 ROG  H20  H  HCH2  0   0.211  19.8673   -7.8311  41.6392
 ROG  H21  H  HCH2  0   0.216  20.7293  -10.7133  42.1731
 ROG  H22  H  HCH2  0   0.231  20.9044   -9.3508  43.2701
 ROG  H24  H  H     0   0.253  20.7652  -13.5070  31.5528
 ROG  H25  H  H     0   0.257  19.8783  -14.7392  32.4218
 ROG  H8   H  H     0   0.229  21.8461  -15.4849  33.6090
 ROG  N01  N  NH2   0  -0.832  22.4234  -11.1373  37.0667

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
 ROG  C20  C19  single    1.526  0.020  1.526
 ROG  C20  C21  single    1.523  0.020  1.523
 ROG  C19  C18  single    1.494  0.020  1.494
 ROG  C21  C22  single    1.528  0.020  1.528
 ROG  C18  S23  aromatic  1.742  0.020  1.742
 ROG  C18  C17  aromatic  1.356  0.020  1.356
 ROG  S23  C15  aromatic  1.729  0.020  1.729
 ROG  C17  C22  single    1.502  0.020  1.502
 ROG  C17  C16  aromatic  1.440  0.020  1.440
 ROG  C15  C16  aromatic  1.394  0.020  1.394
 ROG  C15  N14  aromatic  1.330  0.020  1.330
 ROG  C16  C02  aromatic  1.418  0.020  1.418
 ROG  N14  C04  aromatic  1.321  0.020  1.321
 ROG  C02  N01  single    1.337  0.020  1.337
 ROG  C02  N03  aromatic  1.335  0.020  1.335
 ROG  C04  N03  aromatic  1.321  0.020  1.321
 ROG  C04  S05  single    1.759  0.020  1.759
 ROG  S05  C06  single    1.813  0.020  1.813
 ROG  C06  C07  single    1.522  0.020  1.522
 ROG  C13  C07  single    1.524  0.020  1.524
 ROG  C13  N11  single    1.450  0.020  1.450
 ROG  C07  C08  single    1.527  0.020  1.527
 ROG  C12  N11  single    1.444  0.020  1.444
 ROG  N11  C10  single    1.450  0.020  1.450
 ROG  C08  C09  single    1.523  0.020  1.523
 ROG  C10  C09  single    1.520  0.020  1.520
 ROG  C10  H1   single    0.970  0.020  1.090
 ROG  C10  H2   single    0.970  0.020  1.090
 ROG  C12  H3   single    0.970  0.020  1.090
 ROG  C12  H4   single    0.970  0.020  1.090
 ROG  C12  H5   single    0.970  0.020  1.090
 ROG  C13  H6   single    0.970  0.020  1.090
 ROG  C13  H7   single    0.970  0.020  1.090
 ROG  C20  H8   single    0.970  0.020  1.090
 ROG  C20  H9   single    0.970  0.020  1.090
 ROG  C21  H10  single    0.970  0.020  1.090
 ROG  C21  H11  single    0.970  0.020  1.090
 ROG  C22  H12  single    0.970  0.020  1.090
 ROG  C22  H13  single    0.970  0.020  1.090
 ROG  N01  H14  single    0.860  0.020  1.020
 ROG  N01  H15  single    0.860  0.020  1.020
 ROG  C06  H16  single    0.970  0.020  1.090
 ROG  C06  H17  single    0.970  0.020  1.090
 ROG  C07  H18  single    0.970  0.020  1.090
 ROG  C08  H19  single    0.970  0.020  1.090
 ROG  C08  H20  single    0.970  0.020  1.090
 ROG  C09  H21  single    0.970  0.020  1.090
 ROG  C09  H22  single    0.970  0.020  1.090
 ROG  C19  H24  single    0.970  0.020  1.090
 ROG  C19  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
 ROG  H2   C10  H1   106.59  3.000
 ROG  H2   C10  N11  108.59  3.000
 ROG  H1   C10  N11  111.30  3.000
 ROG  H2   C10  C09  110.03  3.000
 ROG  H1   C10  C09  109.12  3.000
 ROG  N11  C10  C09  111.10  3.000
 ROG  H5   C12  H4   107.63  3.000
 ROG  H5   C12  H3   107.86  3.000
 ROG  H4   C12  H3   107.64  3.000
 ROG  H5   C12  N11  110.08  3.000
 ROG  H4   C12  N11  113.38  3.000
 ROG  H3   C12  N11  110.07  3.000
 ROG  H7   C13  H6   106.59  3.000
 ROG  H7   C13  N11  108.32  3.000
 ROG  H6   C13  N11  111.44  3.000
 ROG  H7   C13  C07  109.81  3.000
 ROG  H6   C13  C07  109.07  3.000
 ROG  N11  C13  C07  111.49  3.000
 ROG  S23  C15  N14  122.72  3.000
 ROG  N14  C15  C16  126.11  3.000
 ROG  S23  C15  C16  111.17  3.000
 ROG  C02  C16  C17  132.93  3.000
 ROG  C02  C16  C15  114.30  3.000
 ROG  C17  C16  C15  112.76  3.000
 ROG  C22  C17  C18  121.55  3.000
 ROG  C22  C17  C16  126.66  3.000
 ROG  C18  C17  C16  111.79  3.000
 ROG  S23  C18  C19  121.18  3.000
 ROG  S23  C18  C17  112.91  3.000
 ROG  C19  C18  C17  125.91  3.000
 ROG  H9   C20  H8   106.92  3.000
 ROG  H9   C20  C19  109.49  3.000
 ROG  H8   C20  C19  109.55  3.000
 ROG  H9   C20  C21  110.49  3.000
 ROG  H8   C20  C21  109.61  3.000
 ROG  C19  C20  C21  110.70  3.000
 ROG  H11  C21  H10  106.72  3.000
 ROG  H11  C21  C22  109.28  3.000
 ROG  H10  C21  C22  109.36  3.000
 ROG  H11  C21  C20  109.18  3.000
 ROG  H10  C21  C20  110.61  3.000
 ROG  C22  C21  C20  111.57  3.000
 ROG  H13  C22  H12  106.69  3.000
 ROG  H13  C22  C21  108.76  3.000
 ROG  H12  C22  C21  109.77  3.000
 ROG  H13  C22  C17  110.25  3.000
 ROG  H12  C22  C17  109.62  3.000
 ROG  C21  C22  C17  111.63  3.000
 ROG  N03  C02  N01  116.71  3.000
 ROG  N03  C02  C16  119.87  3.000
 ROG  N01  C02  C16  123.41  3.000
 ROG  C04  N03  C02  118.78  3.000
 ROG  N14  C04  S05  113.27  3.000
 ROG  S05  C04  N03  119.24  3.000
 ROG  N14  C04  N03  127.48  3.000
 ROG  C06  S05  C04  103.07  3.000
 ROG  H17  C06  H16  107.49  3.000
 ROG  H17  C06  C07  110.85  3.000
 ROG  H16  C06  C07  110.65  3.000
 ROG  H17  C06  S05  104.47  3.000
 ROG  H16  C06  S05  108.04  3.000
 ROG  C07  C06  S05  114.93  3.000
 ROG  H18  C07  C08  108.21  3.000
 ROG  H18  C07  C06  108.47  3.000
 ROG  C08  C07  C06  109.79  3.000
 ROG  H18  C07  C13  108.27  3.000
 ROG  C08  C07  C13  109.82  3.000
 ROG  C06  C07  C13  112.17  3.000
 ROG  H20  C08  H19  106.70  3.000
 ROG  H20  C08  C09  109.38  3.000
 ROG  H19  C08  C09  110.73  3.000
 ROG  H20  C08  C07  109.36  3.000
 ROG  H19  C08  C07  110.15  3.000
 ROG  C09  C08  C07  110.44  3.000
 ROG  H22  C09  H21  107.04  3.000
 ROG  H22  C09  C08  110.60  3.000
 ROG  H21  C09  C08  109.72  3.000
 ROG  H22  C09  C10  109.40  3.000
 ROG  H21  C09  C10  109.31  3.000
 ROG  C08  C09  C10  110.69  3.000
 ROG  C13  N11  C12  111.30  3.000
 ROG  C12  N11  C10  111.53  3.000
 ROG  C13  N11  C10  111.65  3.000
 ROG  C04  N14  C15  113.41  3.000
 ROG  H25  C19  H24  106.19  3.000
 ROG  H25  C19  C20  110.29  3.000
 ROG  H24  C19  C20  110.13  3.000
 ROG  H25  C19  C18  110.45  3.000
 ROG  H24  C19  C18  109.94  3.000
 ROG  C20  C19  C18  109.78  3.000
 ROG  C18  S23  C15   91.35  3.000
 ROG  H15  N01  H14  117.28  3.000
 ROG  H15  N01  C02  122.29  3.000
 ROG  H14  N01  C02  118.86  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
 ROG  CONST_01  C17  C18  S23  C15     0.00   0.0  0
 ROG  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 ROG  CONST_03  N03  C02  C16  C15     0.00   0.0  0
 ROG  CONST_04  N03  C04  N14  C15     0.00   0.0  0
 ROG  CONST_05  S23  C18  C17  C16     0.00   0.0  0
 ROG  CONST_06  C18  S23  C15  C16     0.00   0.0  0
 ROG  CONST_07  C04  N14  C15  C16     0.00   0.0  0
 ROG  CONST_08  C04  N03  C02  C16     0.00   0.0  0
 ROG  CONST_09  S23  C15  C16  C17     0.00   0.0  0
 ROG  CONST_10  N14  C15  C16  C17   180.00   0.0  0
 ROG  CONST_11  N03  C02  C16  C17   180.00   0.0  0
 ROG  CONST_12  N14  C15  S23  C18   180.00   0.0  0
 ROG  CONST_13  C02  C16  C17  C18   180.00   0.0  0
 ROG  CONST_14  S23  C15  C16  C02   180.00   0.0  0
 ROG  CONST_15  N14  C15  C16  C02     0.00   0.0  0
 ROG  CONST_16  N14  C04  N03  C02     0.00   0.0  0
 ROG  CONST_17  S23  C15  N14  C04   180.00   0.0  0
 ROG  CONST_18  N01  C02  C16  C15   180.00   0.0  0
 ROG  CONST_19  S05  C04  N14  C15   180.00   0.0  0
 ROG  CONST_20  N01  C02  C16  C17     0.00   0.0  0
 ROG  CONST_21  C04  N03  C02  N01   180.00   0.0  0
 ROG  CONST_22  S05  C04  N03  C02   180.00   0.0  0
 ROG  CONST_23  H14  N01  C02  C16   180.00   0.0  0
 ROG  CONST_24  H15  N01  C02  C16     0.00   0.0  0
 ROG  Var_01    C07  C13  N11  C10    59.81  30.0  1
 ROG  Var_02    C07  C08  C09  C10   -53.43  30.0  1
 ROG  Var_03    C09  C10  N11  C13   -59.21  30.0  1
 ROG  Var_04    C21  C22  C17  C16  -166.84  30.0  1
 ROG  Var_05    C20  C19  C18  C17    15.16  30.0  1
 ROG  Var_06    C20  C21  C22  C17   -44.25  30.0  1
 ROG  Var_07    C21  C20  C19  C18   -46.29  30.0  1
 ROG  Var_08    C19  C20  C21  C22    63.24  30.0  1
 ROG  Var_09    N11  C10  C09  C08    56.00  30.0  1
 ROG  Var_10    C07  C06  S05  C04   -77.60  30.0  3
 ROG  Var_11    N14  C04  S05  C06   175.98  30.0  1
 ROG  Var_12    H3   C12  N11  C10   -57.73  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
 ROG  chir_01  C07  C06  C13  C08  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
 ROG  plan-1  C15  0.020
 ROG  plan-1  C16  0.020
 ROG  plan-1  C17  0.020
 ROG  plan-1  C18  0.020
 ROG  plan-1  C22  0.020
 ROG  plan-1  C02  0.020
 ROG  plan-1  N03  0.020
 ROG  plan-1  C04  0.020
 ROG  plan-1  S05  0.020
 ROG  plan-1  N14  0.020
 ROG  plan-1  C19  0.020
 ROG  plan-1  S23  0.020
 ROG  plan-1  N01  0.020
 ROG  plan-2  C02  0.020
 ROG  plan-2  H14  0.020
 ROG  plan-2  H15  0.020
 ROG  plan-2  N01  0.020

