# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:25:07 2021
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-[(4-amino-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(diethylamino)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)CCNC(=O)CSc1nc(N)c2c3CCCCc3sc2n1
#
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
 RNV  RNV  2-[(4-amino-5,6,7,8-tetrahydro[1]benzothieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(diethylamino)ethyl]acetamide  ligand  53  26  .  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_RNV
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
 RNV  C10  C  CH2   0  -0.285  20.3447  -11.7665  41.1889
 RNV  C12  C  CH2   0  -0.308  18.0073  -11.7101  41.8350
 RNV  C02  C  CR6   0   0.488  21.4143  -10.6198  37.2324
 RNV  N03  N  N     0  -0.497  20.7487   -9.6711  37.8999
 RNV  C04  C  CR6   0   0.237  19.4698   -9.4776  37.6211
 RNV  S05  S  S2    0   0.078  18.5631   -8.2224  38.4555
 RNV  C06  C  CH2   0  -0.718  19.7338   -7.5817  39.6785
 RNV  C07  C  C     0   0.560  19.7874   -8.4679  40.9120
 RNV  N08  N  NH1   0  -0.605  20.7874   -9.3618  40.8948
 RNV  C09  C  CH2   0  -0.310  20.8810  -10.4763  41.8066
 RNV  N11  N  NT    0  -0.390  18.9724  -11.6540  40.7528
 RNV  C13  C  CH3   0  -0.682  17.7483  -13.0895  42.4420
 RNV  C14  C  CH2   0  -0.267  18.6592  -12.4991  39.6161
 RNV  C15  C  CH3   0  -0.686  17.2871  -12.2204  39.0262
 RNV  O16  O  O     0  -0.496  18.9915   -8.3248  41.8274
 RNV  N17  N  N     0  -0.451  18.7350  -10.1234  36.7385
 RNV  C18  C  CR56  0  -0.027  19.3985  -11.0727  36.0858
 RNV  C19  C  CR56  0   0.001  20.7462  -11.3883  36.2461
 RNV  C20  C  CR5   0   0.221  21.1734  -12.4593  35.3833
 RNV  C21  C  CR5   0  -0.269  20.1489  -12.9410  34.6362
 RNV  C22  C  CH2   0  -0.479  20.2306  -14.0731  33.6653
 RNV  C23  C  CH2   0  -0.449  21.5169  -14.8605  33.8999
 RNV  C24  C  CH2   0  -0.443  22.7041  -13.9169  34.0366
 RNV  C25  C  CH2   0  -0.549  22.5647  -13.0103  35.2587
 RNV  S26  S  S2    0   0.206  18.6493  -12.0992  34.9166
 RNV  H1   H  HCH2  0   0.207  20.5193  -12.5854  41.9050
 RNV  H2   H  HCH2  0   0.223  20.9620  -12.0020  40.3165
 RNV  H3   H  HCH2  0   0.231  18.3398  -11.0284  42.6198
 RNV  H4   H  HCH2  0   0.227  17.0610  -11.2933  41.4821
 RNV  H5   H  HNH2  0   0.410  23.1250  -10.2107  38.2509
 RNV  H6   H  HNH2  0   0.428  23.2653  -11.5124  37.1401
 RNV  H7   H  HCH2  0   0.306  20.7069   -7.4366  39.2108
 RNV  H8   H  HCH2  0   0.319  19.3398   -6.6043  39.9559
 RNV  H9   H  HNH1  0   0.402  21.2530   -9.4657  40.0021
 RNV  H10  H  HCH2  0   0.248  21.9276  -10.6296  42.0779
 RNV  H11  H  HCH2  0   0.244  20.3549  -10.2191  42.7241
 RNV  H13  H  HCH3  0   0.228  17.0655  -13.0012  43.2881
 RNV  H14  H  HCH3  0   0.219  17.2904  -13.7733  41.7252
 RNV  H15  H  HCH3  0   0.222  18.6632  -13.5572  42.8090
 RNV  H16  H  HCH2  0   0.186  18.7399  -13.5750  39.8449
 RNV  H17  H  HCH2  0   0.221  19.4126  -12.3040  38.8480
 RNV  H18  H  HCH3  0   0.225  17.1834  -12.7338  38.0696
 RNV  H19  H  HCH3  0   0.221  16.4778  -12.5683  39.6698
 RNV  H20  H  HCH3  0   0.229  17.1550  -11.1524  38.8529
 RNV  H21  H  HCH2  0   0.254  20.2085  -13.6878  32.6408
 RNV  H22  H  HCH2  0   0.258  19.3602  -14.7257  33.7651
 RNV  H23  H  HCH2  0   0.230  21.4198  -15.4649  34.8064
 RNV  H24  H  HCH2  0   0.244  21.6732  -15.5547  33.0727
 RNV  H25  H  HCH2  0   0.244  23.6368  -14.4784  34.1072
 RNV  H26  H  HCH2  0   0.230  22.7758  -13.3000  33.1359
 RNV  H27  H  HCH2  0   0.253  22.8278  -13.5631  36.1675
 RNV  H28  H  HCH2  0   0.251  23.2866  -12.1933  35.1713
 RNV  N01  N  NH2   0  -0.841  22.6966  -10.7983  37.5561

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
 RNV  C22  C23  single    1.526  0.020  1.526
 RNV  C22  C21  single    1.494  0.020  1.494
 RNV  C23  C24  single    1.523  0.020  1.523
 RNV  C24  C25  single    1.528  0.020  1.528
 RNV  C21  S26  aromatic  1.742  0.020  1.742
 RNV  C21  C20  aromatic  1.356  0.020  1.356
 RNV  S26  C18  aromatic  1.727  0.020  1.727
 RNV  C20  C25  single    1.502  0.020  1.502
 RNV  C20  C19  aromatic  1.440  0.020  1.440
 RNV  C18  C19  aromatic  1.393  0.020  1.393
 RNV  C18  N17  aromatic  1.329  0.020  1.329
 RNV  C19  C02  aromatic  1.418  0.020  1.418
 RNV  N17  C04  aromatic  1.318  0.020  1.318
 RNV  C02  N01  single    1.335  0.020  1.335
 RNV  C02  N03  aromatic  1.337  0.020  1.337
 RNV  C04  N03  aromatic  1.323  0.020  1.323
 RNV  C04  S05  single    1.759  0.020  1.759
 RNV  S05  C06  single    1.810  0.020  1.810
 RNV  C06  C07  single    1.520  0.020  1.520
 RNV  C15  C14  single    1.519  0.020  1.519
 RNV  C14  N11  single    1.451  0.020  1.451
 RNV  C07  N08  single    1.341  0.020  1.341
 RNV  C07  O16  double    1.221  0.020  1.221
 RNV  N08  C09  single    1.443  0.020  1.443
 RNV  N11  C10  single    1.444  0.020  1.444
 RNV  N11  C12  single    1.451  0.020  1.451
 RNV  C10  C09  single    1.528  0.020  1.528
 RNV  C12  C13  single    1.529  0.020  1.529
 RNV  C10  H1   single    0.970  0.020  1.090
 RNV  C10  H2   single    0.970  0.020  1.090
 RNV  C12  H3   single    0.970  0.020  1.090
 RNV  C12  H4   single    0.970  0.020  1.090
 RNV  N01  H5   single    0.860  0.020  1.020
 RNV  N01  H6   single    0.860  0.020  1.020
 RNV  C06  H7   single    0.970  0.020  1.090
 RNV  C06  H8   single    0.970  0.020  1.090
 RNV  N08  H9   single    0.890  0.020  1.040
 RNV  C09  H10  single    0.970  0.020  1.090
 RNV  C09  H11  single    0.970  0.020  1.090
 RNV  C13  H13  single    0.970  0.020  1.090
 RNV  C13  H14  single    0.970  0.020  1.090
 RNV  C13  H15  single    0.970  0.020  1.090
 RNV  C14  H16  single    0.970  0.020  1.090
 RNV  C14  H17  single    0.970  0.020  1.090
 RNV  C15  H18  single    0.970  0.020  1.090
 RNV  C15  H19  single    0.970  0.020  1.090
 RNV  C15  H20  single    0.970  0.020  1.090
 RNV  C22  H21  single    0.970  0.020  1.090
 RNV  C22  H22  single    0.970  0.020  1.090
 RNV  C23  H23  single    0.970  0.020  1.090
 RNV  C23  H24  single    0.970  0.020  1.090
 RNV  C24  H25  single    0.970  0.020  1.090
 RNV  C24  H26  single    0.970  0.020  1.090
 RNV  C25  H27  single    0.970  0.020  1.090
 RNV  C25  H28  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
 RNV  H2   C10  H1   105.59  3.000
 RNV  H2   C10  N11  108.18  3.000
 RNV  H1   C10  N11  113.87  3.000
 RNV  H2   C10  C09  107.82  3.000
 RNV  H1   C10  C09  108.02  3.000
 RNV  N11  C10  C09  112.94  3.000
 RNV  H4   C12  H3   104.94  3.000
 RNV  H4   C12  C13  109.00  3.000
 RNV  H3   C12  C13  109.24  3.000
 RNV  H4   C12  N11  108.69  3.000
 RNV  H3   C12  N11  108.03  3.000
 RNV  C13  C12  N11  116.33  3.000
 RNV  C19  C02  N03  119.82  3.000
 RNV  N03  C02  N01  116.87  3.000
 RNV  C19  C02  N01  123.31  3.000
 RNV  C04  N03  C02  118.66  3.000
 RNV  N17  C04  S05  112.34  3.000
 RNV  S05  C04  N03  120.18  3.000
 RNV  N17  C04  N03  127.48  3.000
 RNV  C06  S05  C04  103.87  3.000
 RNV  H8   C06  H7   108.22  3.000
 RNV  H8   C06  C07  109.22  3.000
 RNV  H7   C06  C07  113.24  3.000
 RNV  H8   C06  S05  104.81  3.000
 RNV  H7   C06  S05  109.57  3.000
 RNV  C07  C06  S05  111.39  3.000
 RNV  O16  C07  N08  124.99  3.000
 RNV  O16  C07  C06  121.12  3.000
 RNV  N08  C07  C06  113.86  3.000
 RNV  H9   N08  C09  116.63  3.000
 RNV  H9   N08  C07  115.00  3.000
 RNV  C09  N08  C07  123.71  3.000
 RNV  H11  C09  H10  106.68  3.000
 RNV  H11  C09  N08  108.59  3.000
 RNV  H10  C09  N08  109.12  3.000
 RNV  H11  C09  C10  111.76  3.000
 RNV  H10  C09  C10  108.56  3.000
 RNV  N08  C09  C10  111.96  3.000
 RNV  C14  N11  C12  114.72  3.000
 RNV  C12  N11  C10  113.81  3.000
 RNV  C14  N11  C10  113.35  3.000
 RNV  H15  C13  H14  107.70  3.000
 RNV  H15  C13  H13  107.37  3.000
 RNV  H14  C13  H13  107.31  3.000
 RNV  H15  C13  C12  112.22  3.000
 RNV  H14  C13  C12  112.06  3.000
 RNV  H13  C13  C12  109.93  3.000
 RNV  H17  C14  H16  105.63  3.000
 RNV  H17  C14  C15  108.47  3.000
 RNV  H16  C14  C15  109.00  3.000
 RNV  H17  C14  N11  107.32  3.000
 RNV  H16  C14  N11  112.95  3.000
 RNV  C15  C14  N11  113.10  3.000
 RNV  H20  C15  H19  108.44  3.000
 RNV  H20  C15  H18  108.07  3.000
 RNV  H19  C15  H18  107.26  3.000
 RNV  H20  C15  C14  110.55  3.000
 RNV  H19  C15  C14  112.48  3.000
 RNV  H18  C15  C14  109.88  3.000
 RNV  C18  N17  C04  113.61  3.000
 RNV  S26  C18  C19  111.28  3.000
 RNV  C19  C18  N17  126.01  3.000
 RNV  S26  C18  N17  122.71  3.000
 RNV  C20  C19  C18  112.73  3.000
 RNV  C18  C19  C02  114.40  3.000
 RNV  C20  C19  C02  132.85  3.000
 RNV  C25  C20  C21  121.59  3.000
 RNV  C25  C20  C19  126.69  3.000
 RNV  C21  C20  C19  111.72  3.000
 RNV  S26  C21  C22  121.19  3.000
 RNV  S26  C21  C20  112.95  3.000
 RNV  C22  C21  C20  125.86  3.000
 RNV  H22  C22  H21  106.23  3.000
 RNV  H22  C22  C23  110.44  3.000
 RNV  H21  C22  C23  110.03  3.000
 RNV  H22  C22  C21  110.48  3.000
 RNV  H21  C22  C21  109.90  3.000
 RNV  C23  C22  C21  109.71  3.000
 RNV  H24  C23  H23  106.83  3.000
 RNV  H24  C23  C24  110.53  3.000
 RNV  H23  C23  C24  109.71  3.000
 RNV  H24  C23  C22  109.42  3.000
 RNV  H23  C23  C22  109.73  3.000
 RNV  C24  C23  C22  110.56  3.000
 RNV  H26  C24  H25  106.71  3.000
 RNV  H26  C24  C25  109.26  3.000
 RNV  H25  C24  C25  109.37  3.000
 RNV  H26  C24  C23  109.06  3.000
 RNV  H25  C24  C23  110.69  3.000
 RNV  C25  C24  C23  111.61  3.000
 RNV  H28  C25  H27  106.54  3.000
 RNV  H28  C25  C24  108.60  3.000
 RNV  H27  C25  C24  110.01  3.000
 RNV  H28  C25  C20  110.12  3.000
 RNV  H27  C25  C20  109.80  3.000
 RNV  C24  C25  C20  111.63  3.000
 RNV  C21  S26  C18   91.30  3.000
 RNV  H6   N01  H5   117.45  3.000
 RNV  H6   N01  C02  122.63  3.000
 RNV  H5   N01  C02  119.92  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
 RNV  CONST_01  C21  C20  C19  C02   180.00   0.0  0
 RNV  CONST_02  S26  C18  C19  C02   180.00   0.0  0
 RNV  CONST_03  N17  C18  C19  C02     0.00   0.0  0
 RNV  CONST_04  N17  C04  N03  C02     0.00   0.0  0
 RNV  CONST_05  C20  C19  C02  N03   180.00   0.0  0
 RNV  CONST_06  C18  C19  C02  N03     0.00   0.0  0
 RNV  CONST_07  C18  N17  C04  N03     0.00   0.0  0
 RNV  CONST_08  S26  C18  N17  C04   180.00   0.0  0
 RNV  CONST_09  C19  C18  N17  C04     0.00   0.0  0
 RNV  CONST_10  C19  C02  N03  C04     0.00   0.0  0
 RNV  CONST_11  C21  S26  C18  N17   180.00   0.0  0
 RNV  CONST_12  C20  C19  C18  N17   180.00   0.0  0
 RNV  CONST_13  C20  C21  S26  C18     0.00   0.0  0
 RNV  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 RNV  CONST_15  S26  C21  C20  C19     0.00   0.0  0
 RNV  CONST_16  C21  S26  C18  C19     0.00   0.0  0
 RNV  CONST_17  S26  C18  C19  C20     0.00   0.0  0
 RNV  CONST_18  C20  C19  C02  N01     0.00   0.0  0
 RNV  CONST_19  C18  C19  C02  N01   180.00   0.0  0
 RNV  CONST_20  C04  N03  C02  N01   180.00   0.0  0
 RNV  CONST_21  S05  C04  N03  C02   180.00   0.0  0
 RNV  CONST_22  C18  N17  C04  S05   180.00   0.0  0
 RNV  CONST_23  H5   N01  C02  N03     0.00   0.0  0
 RNV  CONST_24  H6   N01  C02  N03   180.00   0.0  0
 RNV  CONST_25  C09  N08  C07  C06   180.00   0.0  0
 RNV  CONST_26  O16  C07  N08  C09     0.00   0.0  0
 RNV  CONST_27  H9   N08  C07  C06     0.00   0.0  0
 RNV  Var_01    C24  C25  C20  C19  -167.31  30.0  1
 RNV  Var_02    C23  C22  C21  C20    15.39  30.0  1
 RNV  Var_03    C23  C24  C25  C20   -43.84  30.0  1
 RNV  Var_04    C24  C23  C22  C21   -46.76  30.0  1
 RNV  Var_05    C25  C24  C23  C22    63.42  30.0  1
 RNV  Var_06    N17  C04  S05  C06   175.85  30.0  2
 RNV  Var_07    C07  C06  S05  C04   -81.30  30.0  3
 RNV  Var_08    C15  C14  N11  C10  -171.00  30.0  2
 RNV  Var_09    C13  C12  N11  C10   -75.28  30.0  3
 RNV  Var_10    C07  N08  C09  C10    97.35  30.0  1
 RNV  Var_11    C09  C10  N11  C12   -76.77  30.0  3
 RNV  Var_12    N08  C07  C06  S05    96.07  30.0  3
 RNV  Var_13    N11  C10  C09  N08   -57.54  30.0  1
 RNV  Var_14    H18  C15  C14  N11   168.84  30.0  3
 RNV  Var_15    H13  C13  C12  N11   175.92  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
 RNV  plan-1  C06  0.020
 RNV  plan-1  C07  0.020
 RNV  plan-1  N08  0.020
 RNV  plan-1  C09  0.020
 RNV  plan-1  O16  0.020
 RNV  plan-1  H9   0.020
 RNV  plan-2  C02  0.020
 RNV  plan-2  N03  0.020
 RNV  plan-2  C04  0.020
 RNV  plan-2  S05  0.020
 RNV  plan-2  N17  0.020
 RNV  plan-2  C18  0.020
 RNV  plan-2  C19  0.020
 RNV  plan-2  C20  0.020
 RNV  plan-2  C21  0.020
 RNV  plan-2  C22  0.020
 RNV  plan-2  C25  0.020
 RNV  plan-2  S26  0.020
 RNV  plan-2  N01  0.020
 RNV  plan-3  C02  0.020
 RNV  plan-3  H5   0.020
 RNV  plan-3  H6   0.020
 RNV  plan-3  N01  0.020

