# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:01:22 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-[(4-amino-6,7-dihydro-5H-cyclopenta[4,5]thieno[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)c2c3CCCc3sc2n1
#
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
 RMV  RMV  2-[(4-amino-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(diethylamino)ethyl]acetamide  ligand  50  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 OK
;

data_comp_RMV
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
 RMV  C12  C  CH2   0  -0.278  18.2222  -12.9869  43.1139
 RMV  C13  C  CH3   0  -0.662  18.9071  -12.4148  44.3458
 RMV  C18  C  CR56  0  -0.030  20.1985  -11.0332  35.4781
 RMV  C20  C  CR56  0  -0.036  21.4195  -11.6319  35.7933
 RMV  C21  C  CR55  0   0.192  21.7559  -12.6693  34.8707
 RMV  C22  C  CR55  0  -0.226  20.8190  -12.8286  33.9112
 RMV  C23  C  CH2   0  -0.479  21.0949  -13.9567  32.9759
 RMV  C10  C  CH2   0  -0.301  19.5248  -12.0190  41.3285
 RMV  C14  C  CH2   0  -0.319  17.1108  -12.2438  41.0773
 RMV  C15  C  CH3   0  -0.683  17.1265  -13.5023  40.2125
 RMV  C24  C  CH2   0  -0.462  22.5673  -14.2818  33.3256
 RMV  C25  C  CH2   0  -0.527  22.8466  -13.6882  34.7280
 RMV  C02  C  CR6   0   0.485  22.0663  -11.1032  36.9364
 RMV  N03  N  N     0  -0.460  21.4935  -10.1087  37.6177
 RMV  C04  C  CR6   0   0.214  20.3253   -9.6527  37.2055
 RMV  S05  S  S2    0   0.059  19.5354   -8.3421  38.0871
 RMV  C06  C  CH2   0  -0.712  20.5398   -8.1345  39.5846
 RMV  C07  C  C     0   0.524  19.6968   -8.3536  40.8281
 RMV  N08  N  NH1   0  -0.595  19.3554   -9.6150  41.1268
 RMV  C09  C  CH2   0  -0.311  19.6612  -10.8252  40.3975
 RMV  N11  N  NT    0  -0.420  18.2337  -12.0639  41.9870
 RMV  O16  O  O     0  -0.495  19.3510   -7.4006  41.5145
 RMV  N17  N  N     0  -0.455  19.6237  -10.0455  36.1599
 RMV  S19  S  S2    0   0.210  19.4796  -11.7442  34.0638
 RMV  H1   H  HCH2  0   0.229  17.1801  -13.1941  43.3668
 RMV  H2   H  HCH2  0   0.198  18.6705  -13.9580  42.8559
 RMV  H3   H  HCH3  0   0.227  18.8483  -13.1234  45.1725
 RMV  H4   H  HCH3  0   0.223  19.9633  -12.2011  44.1783
 RMV  H5   H  HCH3  0   0.222  18.4221  -11.4890  44.6561
 RMV  H6   H  HCH2  0   0.257  20.9693  -13.6935  31.9247
 RMV  H7   H  HCH2  0   0.255  20.4276  -14.7998  33.1758
 RMV  H8   H  HCH2  0   0.222  19.7486  -12.9303  40.7542
 RMV  H9   H  HCH2  0   0.249  20.2994  -11.9409  42.0938
 RMV  H10  H  HCH2  0   0.233  17.0393  -11.3666  40.4282
 RMV  H11  H  HCH2  0   0.237  16.2004  -12.2329  41.6808
 RMV  H12  H  HCH3  0   0.234  16.2083  -13.5597  39.6268
 RMV  H13  H  HCH3  0   0.223  17.9617  -13.5061  39.5107
 RMV  H14  H  HCH3  0   0.227  17.1908  -14.4099  40.8151
 RMV  H15  H  HCH2  0   0.246  22.7691  -15.3511  33.2854
 RMV  H16  H  HCH2  0   0.249  23.2205  -13.8004  32.5974
 RMV  H17  H  HCH2  0   0.255  22.7706  -14.4467  35.5125
 RMV  H18  H  HCH2  0   0.250  23.8521  -13.2658  34.7874
 RMV  H19  H  HNH2  0   0.408  23.6893  -11.1224  38.1561
 RMV  H20  H  HNH2  0   0.421  23.7578  -12.2591  36.8675
 RMV  H21  H  HCH2  0   0.324  21.3904   -8.8142  39.5187
 RMV  H22  H  HCH2  0   0.315  20.9197   -7.1151  39.6008
 RMV  H23  H  HNH1  0   0.389  18.7345   -9.7436  41.9166
 RMV  H24  H  HCH2  0   0.264  20.6838  -10.8044  40.0225
 RMV  H25  H  HCH2  0   0.236  19.0085  -10.9351  39.5258
 RMV  N01  N  NH2   0  -0.828  23.2361  -11.5681  37.3763

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
 RMV  C23  C24  single    1.548  0.020  1.548
 RMV  C23  C22  single    1.491  0.020  1.491
 RMV  C24  C25  single    1.548  0.020  1.548
 RMV  C22  S19  aromatic  1.730  0.020  1.730
 RMV  C22  C21  aromatic  1.350  0.020  1.350
 RMV  S19  C18  aromatic  1.739  0.020  1.739
 RMV  C25  C21  single    1.499  0.020  1.499
 RMV  C21  C20  aromatic  1.428  0.020  1.428
 RMV  C18  C20  aromatic  1.396  0.020  1.396
 RMV  C18  N17  aromatic  1.331  0.020  1.331
 RMV  C20  C02  aromatic  1.416  0.020  1.416
 RMV  N17  C04  aromatic  1.319  0.020  1.319
 RMV  C02  N01  single    1.333  0.020  1.333
 RMV  C02  N03  aromatic  1.335  0.020  1.335
 RMV  C04  N03  aromatic  1.320  0.020  1.320
 RMV  C04  S05  single    1.766  0.020  1.766
 RMV  S05  C06  single    1.815  0.020  1.815
 RMV  C15  C14  single    1.527  0.020  1.527
 RMV  C06  C07  single    1.518  0.020  1.518
 RMV  C14  N11  single    1.456  0.020  1.456
 RMV  C09  C10  single    1.520  0.020  1.520
 RMV  C09  N08  single    1.446  0.020  1.446
 RMV  C07  N08  single    1.340  0.020  1.340
 RMV  C07  O16  double    1.224  0.020  1.224
 RMV  C10  N11  single    1.450  0.020  1.450
 RMV  N11  C12  single    1.457  0.020  1.457
 RMV  C12  C13  single    1.521  0.020  1.521
 RMV  C12  H1   single    0.970  0.020  1.090
 RMV  C12  H2   single    0.970  0.020  1.090
 RMV  C13  H3   single    0.970  0.020  1.090
 RMV  C13  H4   single    0.970  0.020  1.090
 RMV  C13  H5   single    0.970  0.020  1.090
 RMV  C23  H6   single    0.970  0.020  1.090
 RMV  C23  H7   single    0.970  0.020  1.090
 RMV  C10  H8   single    0.970  0.020  1.090
 RMV  C10  H9   single    0.970  0.020  1.090
 RMV  C14  H10  single    0.970  0.020  1.090
 RMV  C14  H11  single    0.970  0.020  1.090
 RMV  C15  H12  single    0.970  0.020  1.090
 RMV  C15  H13  single    0.970  0.020  1.090
 RMV  C15  H14  single    0.970  0.020  1.090
 RMV  C24  H15  single    0.970  0.020  1.090
 RMV  C24  H16  single    0.970  0.020  1.090
 RMV  C25  H17  single    0.970  0.020  1.090
 RMV  C25  H18  single    0.970  0.020  1.090
 RMV  N01  H19  single    0.860  0.020  1.020
 RMV  N01  H20  single    0.860  0.020  1.020
 RMV  C06  H21  single    0.970  0.020  1.090
 RMV  C06  H22  single    0.970  0.020  1.090
 RMV  N08  H23  single    0.860  0.020  1.020
 RMV  C09  H24  single    0.970  0.020  1.090
 RMV  C09  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
 RMV  H2   C12  H1   106.00  3.000
 RMV  H2   C12  N11  112.00  3.000
 RMV  H1   C12  N11  107.87  3.000
 RMV  H2   C12  C13  109.78  3.000
 RMV  H1   C12  C13  108.27  3.000
 RMV  N11  C12  C13  112.62  3.000
 RMV  H5   C13  H4   107.95  3.000
 RMV  H5   C13  H3   108.18  3.000
 RMV  H4   C13  H3   107.22  3.000
 RMV  H5   C13  C12  110.46  3.000
 RMV  H4   C13  C12  112.67  3.000
 RMV  H3   C13  C12  110.20  3.000
 RMV  S19  C18  N17  122.80  3.000
 RMV  N17  C18  C20  125.48  3.000
 RMV  S19  C18  C20  111.71  3.000
 RMV  C02  C20  C21  133.24  3.000
 RMV  C02  C20  C18  114.94  3.000
 RMV  C21  C20  C18  111.81  3.000
 RMV  C25  C21  C22  110.91  3.000
 RMV  C25  C21  C20  136.57  3.000
 RMV  C22  C21  C20  112.41  3.000
 RMV  S19  C22  C23  132.28  3.000
 RMV  S19  C22  C21  113.61  3.000
 RMV  C23  C22  C21  113.99  3.000
 RMV  H7   C23  H6   106.98  3.000
 RMV  H7   C23  C24  112.16  3.000
 RMV  H6   C23  C24  112.20  3.000
 RMV  H7   C23  C22  110.83  3.000
 RMV  H6   C23  C22  113.61  3.000
 RMV  C24  C23  C22  101.13  3.000
 RMV  H9   C10  H8   106.31  3.000
 RMV  H9   C10  N11  108.40  3.000
 RMV  H8   C10  N11  113.12  3.000
 RMV  H9   C10  C09  108.02  3.000
 RMV  H8   C10  C09  108.21  3.000
 RMV  N11  C10  C09  112.48  3.000
 RMV  H11  C14  H10  105.39  3.000
 RMV  H11  C14  N11  107.24  3.000
 RMV  H10  C14  N11  108.79  3.000
 RMV  H11  C14  C15  109.25  3.000
 RMV  H10  C14  C15  109.00  3.000
 RMV  N11  C14  C15  116.59  3.000
 RMV  H14  C15  H13  107.89  3.000
 RMV  H14  C15  H12  107.60  3.000
 RMV  H13  C15  H12  107.39  3.000
 RMV  H14  C15  C14  111.92  3.000
 RMV  H13  C15  C14  112.03  3.000
 RMV  H12  C15  C14  109.81  3.000
 RMV  H16  C24  H15  107.32  3.000
 RMV  H16  C24  C25  109.13  3.000
 RMV  H15  C24  C25  112.12  3.000
 RMV  H16  C24  C23  109.04  3.000
 RMV  H15  C24  C23  111.97  3.000
 RMV  C25  C24  C23  107.20  3.000
 RMV  H18  C25  H17  107.04  3.000
 RMV  H18  C25  C24  111.32  3.000
 RMV  H17  C25  C24  111.79  3.000
 RMV  H18  C25  C21  113.69  3.000
 RMV  H17  C25  C21  110.64  3.000
 RMV  C24  C25  C21  102.44  3.000
 RMV  N03  C02  N01  117.90  3.000
 RMV  N03  C02  C20  119.62  3.000
 RMV  N01  C02  C20  122.48  3.000
 RMV  C04  N03  C02  118.54  3.000
 RMV  N17  C04  S05  112.26  3.000
 RMV  S05  C04  N03  119.76  3.000
 RMV  N17  C04  N03  127.97  3.000
 RMV  C06  S05  C04  104.43  3.000
 RMV  H22  C06  H21  108.21  3.000
 RMV  H22  C06  C07  108.48  3.000
 RMV  H21  C06  C07  113.11  3.000
 RMV  H22  C06  S05  108.22  3.000
 RMV  H21  C06  S05  108.08  3.000
 RMV  C07  C06  S05  110.60  3.000
 RMV  O16  C07  N08  122.38  3.000
 RMV  O16  C07  C06  120.24  3.000
 RMV  N08  C07  C06  117.37  3.000
 RMV  H23  N08  C09  114.63  3.000
 RMV  H23  N08  C07  116.71  3.000
 RMV  C09  N08  C07  128.42  3.000
 RMV  H25  C09  H24  106.71  3.000
 RMV  H25  C09  N08  111.08  3.000
 RMV  H24  C09  N08  110.87  3.000
 RMV  H25  C09  C10  110.82  3.000
 RMV  H24  C09  C10  108.07  3.000
 RMV  N08  C09  C10  109.24  3.000
 RMV  C14  N11  C10  114.00  3.000
 RMV  C10  N11  C12  112.20  3.000
 RMV  C14  N11  C12  113.51  3.000
 RMV  C04  N17  C18  113.42  3.000
 RMV  C22  S19  C18   90.46  3.000
 RMV  H20  N01  H19  117.62  3.000
 RMV  H20  N01  C02  121.90  3.000
 RMV  H19  N01  C02  119.77  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
 RMV  CONST_01  C21  C22  S19  C18     0.00   0.0  0
 RMV  CONST_02  C22  C21  C20  C18     0.00   0.0  0
 RMV  CONST_03  N03  C02  C20  C18     0.00   0.0  0
 RMV  CONST_04  N03  C04  N17  C18     0.00   0.0  0
 RMV  CONST_05  S19  C22  C21  C20     0.00   0.0  0
 RMV  CONST_06  C22  S19  C18  C20     0.00   0.0  0
 RMV  CONST_07  C04  N17  C18  C20     0.00   0.0  0
 RMV  CONST_08  C04  N03  C02  C20     0.00   0.0  0
 RMV  CONST_09  S19  C18  C20  C21     0.00   0.0  0
 RMV  CONST_10  N17  C18  C20  C21   180.00   0.0  0
 RMV  CONST_11  N03  C02  C20  C21   180.00   0.0  0
 RMV  CONST_12  N17  C18  S19  C22   180.00   0.0  0
 RMV  CONST_13  C02  C20  C21  C22   180.00   0.0  0
 RMV  CONST_14  S19  C18  C20  C02   180.00   0.0  0
 RMV  CONST_15  N17  C18  C20  C02     0.00   0.0  0
 RMV  CONST_16  N17  C04  N03  C02     0.00   0.0  0
 RMV  CONST_17  S19  C18  N17  C04   180.00   0.0  0
 RMV  CONST_18  N01  C02  C20  C18   180.00   0.0  0
 RMV  CONST_19  S05  C04  N17  C18   180.00   0.0  0
 RMV  CONST_20  N01  C02  C20  C21     0.00   0.0  0
 RMV  CONST_21  C04  N03  C02  N01   180.00   0.0  0
 RMV  CONST_22  S05  C04  N03  C02   180.00   0.0  0
 RMV  CONST_23  H19  N01  C02  C20   180.00   0.0  0
 RMV  CONST_24  H20  N01  C02  C20     0.00   0.0  0
 RMV  CONST_25  C09  N08  C07  C06     0.00   0.0  0
 RMV  CONST_26  O16  C07  N08  C09   180.00   0.0  0
 RMV  CONST_27  H23  N08  C07  C06   180.00   0.0  0
 RMV  Var_01    C24  C25  C21  C20  -171.84  30.0  1
 RMV  Var_02    C24  C23  C22  C21   -12.79  30.0  1
 RMV  Var_03    C23  C24  C25  C21   -19.94  30.0  1
 RMV  Var_04    C25  C24  C23  C22    19.79  30.0  1
 RMV  Var_05    N17  C04  S05  C06   172.22  30.0  2
 RMV  Var_06    C07  C06  S05  C04  -120.67  30.0  3
 RMV  Var_07    C15  C14  N11  C12   -71.33  30.0  2
 RMV  Var_08    C09  C10  N11  C12  -165.34  30.0  1
 RMV  Var_09    C14  N11  C12  C13  -151.81  30.0  1
 RMV  Var_10    C07  N08  C09  C10   159.67  30.0  3
 RMV  Var_11    N08  C07  C06  S05    74.19  30.0  3
 RMV  Var_12    N11  C10  C09  N08    53.62  30.0  3
 RMV  Var_13    H12  C15  C14  N11   176.19  30.0  3
 RMV  Var_14    H3   C13  C12  N11   178.22  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
 RMV  plan-1  C06  0.020
 RMV  plan-1  C07  0.020
 RMV  plan-1  N08  0.020
 RMV  plan-1  C09  0.020
 RMV  plan-1  O16  0.020
 RMV  plan-1  H23  0.020
 RMV  plan-2  C18  0.020
 RMV  plan-2  C20  0.020
 RMV  plan-2  C21  0.020
 RMV  plan-2  C22  0.020
 RMV  plan-2  C23  0.020
 RMV  plan-2  C25  0.020
 RMV  plan-2  C02  0.020
 RMV  plan-2  N03  0.020
 RMV  plan-2  C04  0.020
 RMV  plan-2  S05  0.020
 RMV  plan-2  N17  0.020
 RMV  plan-2  S19  0.020
 RMV  plan-2  N01  0.020
 RMV  plan-3  C02  0.020
 RMV  plan-3  H19  0.020
 RMV  plan-3  H20  0.020
 RMV  plan-3  N01  0.020

