# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:03:18 2021
#   Inital geometry file: a 116 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-(piperidin-1-yl)ethyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(SCC(=O)NCCN2CCCCC2)nc3sc4CCCc4c13
#
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
 RMJ  RMJ  2-[(4-amino-6,7-dihydro-5H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(piperidin-1-yl)ethyl]acetamide  ligand  51  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_RMJ
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
 RMJ  C10  C  CH2   0  -0.295  19.5338  -11.0232  41.7238
 RMJ  C12  C  CH2   0  -0.338  17.2045  -11.5604  41.3942
 RMJ  C13  C  CH2   0  -0.464  17.3424  -12.2969  40.0489
 RMJ  C02  C  CR6   0   0.486  20.6411  -11.1528  37.2511
 RMJ  N03  N  N     0  -0.460  20.0783  -10.1090  37.8621
 RMJ  C04  C  CR6   0   0.216  19.6502   -9.1018  37.1193
 RMJ  S05  S  S2    0   0.088  18.8978   -7.7250  37.9123
 RMJ  C06  C  CH2   0  -0.744  18.9617   -8.2266  39.6315
 RMJ  C07  C  C     0   0.563  20.3626   -8.1752  40.2262
 RMJ  N08  N  NH1   0  -0.614  20.5017   -8.7584  41.4295
 RMJ  C09  C  CH2   0  -0.318  19.5130   -9.5479  42.1327
 RMJ  N11  N  NT    0  -0.422  18.3712  -11.7088  42.2466
 RMJ  C14  C  CH2   0  -0.432  18.1902  -13.5657  40.2105
 RMJ  C15  C  CH2   0  -0.471  18.0441  -14.1215  41.6204
 RMJ  C16  C  CH2   0  -0.283  18.5510  -13.1014  42.6533
 RMJ  O17  O  O     0  -0.484  21.2805   -7.5974  39.6681
 RMJ  N18  N  N     0  -0.458  19.7004   -8.9839  35.8052
 RMJ  C19  C  CR56  0  -0.030  20.2523  -10.0310  35.2000
 RMJ  S20  S  S2    0   0.207  20.4345  -10.1346  33.4731
 RMJ  C21  C  CR56  0  -0.031  20.7561  -11.1647  35.8407
 RMJ  C22  C  CR55  0   0.193  21.2964  -12.1042  34.9102
 RMJ  C23  C  CR55  0  -0.227  21.1888  -11.6840  33.6316
 RMJ  C24  C  CH2   0  -0.478  21.6749  -12.6736  32.6271
 RMJ  C25  C  CH2   0  -0.462  22.4384  -13.6673  33.5355
 RMJ  C26  C  CH2   0  -0.527  21.8992  -13.4754  34.9734
 RMJ  H1   H  HCH2  0   0.246  20.4420  -11.4820  42.1185
 RMJ  H2   H  HCH2  0   0.205  19.6181  -11.0824  40.6267
 RMJ  H3   H  HCH2  0   0.237  17.0007  -10.4995  41.2263
 RMJ  H4   H  HCH2  0   0.240  16.3370  -11.9414  41.9401
 RMJ  H5   H  HCH2  0   0.226  17.7848  -11.6453  39.2907
 RMJ  H6   H  HCH2  0   0.233  16.3442  -12.5513  39.6847
 RMJ  H7   H  HNH2  0   0.409  20.9672  -12.1125  39.0108
 RMJ  H8   H  HNH2  0   0.422  21.4770  -12.9936  37.6245
 RMJ  H9   H  HCH2  0   0.335  18.3166   -7.5231  40.1656
 RMJ  H10  H  HCH2  0   0.303  18.5114   -9.2127  39.7320
 RMJ  H11  H  HNH1  0   0.394  21.4332   -8.7391  41.8177
 RMJ  H12  H  HCH2  0   0.250  18.5213   -9.1223  41.9771
 RMJ  H13  H  HCH2  0   0.269  19.7114   -9.4611  43.2007
 RMJ  H15  H  HCH2  0   0.205  19.2453  -13.3442  40.0229
 RMJ  H16  H  HCH2  0   0.237  17.9056  -14.3123  39.4670
 RMJ  H17  H  HCH2  0   0.221  16.9920  -14.3585  41.8058
 RMJ  H18  H  HCH2  0   0.236  18.5924  -15.0588  41.7343
 RMJ  H19  H  HCH2  0   0.222  18.0407  -13.2720  43.6080
 RMJ  H20  H  HCH2  0   0.225  19.6133  -13.2695  42.8403
 RMJ  H21  H  HCH2  0   0.256  22.3164  -12.2385  31.8597
 RMJ  H22  H  HCH2  0   0.255  20.8359  -13.1501  32.1117
 RMJ  H23  H  HCH2  0   0.246  22.3385  -14.6961  33.1928
 RMJ  H24  H  HCH2  0   0.249  23.5005  -13.4206  33.5176
 RMJ  H25  H  HCH2  0   0.254  21.1391  -14.2213  35.2254
 RMJ  H26  H  HCH2  0   0.251  22.6967  -13.5678  35.7136
 RMJ  N01  N  NH2   0  -0.839  21.0880  -12.1534  38.0134

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
 RMJ  C24  C25  single    1.548  0.020  1.548
 RMJ  C24  C23  single    1.492  0.020  1.492
 RMJ  C25  C26  single    1.548  0.020  1.548
 RMJ  C23  S20  aromatic  1.731  0.020  1.731
 RMJ  C23  C22  aromatic  1.350  0.020  1.350
 RMJ  S20  C19  aromatic  1.740  0.020  1.740
 RMJ  C26  C22  single    1.499  0.020  1.499
 RMJ  C22  C21  aromatic  1.428  0.020  1.428
 RMJ  C19  C21  aromatic  1.396  0.020  1.396
 RMJ  C19  N18  aromatic  1.329  0.020  1.329
 RMJ  C21  C02  aromatic  1.415  0.020  1.415
 RMJ  N18  C04  aromatic  1.320  0.020  1.320
 RMJ  C02  N01  single    1.335  0.020  1.335
 RMJ  C02  N03  aromatic  1.334  0.020  1.334
 RMJ  C04  N03  aromatic  1.323  0.020  1.323
 RMJ  C04  S05  single    1.758  0.020  1.758
 RMJ  S05  C06  single    1.792  0.020  1.792
 RMJ  C14  C15  single    1.523  0.020  1.523
 RMJ  C14  C13  single    1.534  0.020  1.534
 RMJ  C15  C16  single    1.538  0.020  1.538
 RMJ  C13  C12  single    1.540  0.020  1.540
 RMJ  C06  C07  single    1.523  0.020  1.523
 RMJ  O17  C07  double    1.220  0.020  1.220
 RMJ  C07  N08  single    1.344  0.020  1.344
 RMJ  C16  N11  single    1.462  0.020  1.462
 RMJ  C12  N11  single    1.453  0.020  1.453
 RMJ  N11  C10  single    1.447  0.020  1.447
 RMJ  C10  C09  single    1.531  0.020  1.531
 RMJ  N08  C09  single    1.447  0.020  1.447
 RMJ  C10  H1   single    0.970  0.020  1.090
 RMJ  C10  H2   single    0.970  0.020  1.090
 RMJ  C12  H3   single    0.970  0.020  1.090
 RMJ  C12  H4   single    0.970  0.020  1.090
 RMJ  C13  H5   single    0.970  0.020  1.090
 RMJ  C13  H6   single    0.970  0.020  1.090
 RMJ  N01  H7   single    0.860  0.020  1.020
 RMJ  N01  H8   single    0.860  0.020  1.020
 RMJ  C06  H9   single    0.970  0.020  1.090
 RMJ  C06  H10  single    0.970  0.020  1.090
 RMJ  N08  H11  single    0.860  0.020  1.020
 RMJ  C09  H12  single    0.970  0.020  1.090
 RMJ  C09  H13  single    0.970  0.020  1.090
 RMJ  C14  H15  single    0.970  0.020  1.090
 RMJ  C14  H16  single    0.970  0.020  1.090
 RMJ  C15  H17  single    0.970  0.020  1.090
 RMJ  C15  H18  single    0.970  0.020  1.090
 RMJ  C16  H19  single    0.970  0.020  1.090
 RMJ  C16  H20  single    0.970  0.020  1.090
 RMJ  C24  H21  single    0.970  0.020  1.090
 RMJ  C24  H22  single    0.970  0.020  1.090
 RMJ  C25  H23  single    0.970  0.020  1.090
 RMJ  C25  H24  single    0.970  0.020  1.090
 RMJ  C26  H25  single    0.970  0.020  1.090
 RMJ  C26  H26  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
 RMJ  H2   C10  H1   105.90  3.000
 RMJ  H2   C10  N11  113.31  3.000
 RMJ  H1   C10  N11  109.79  3.000
 RMJ  H2   C10  C09  108.59  3.000
 RMJ  H1   C10  C09  108.65  3.000
 RMJ  N11  C10  C09  110.43  3.000
 RMJ  H4   C12  H3   105.48  3.000
 RMJ  H4   C12  N11  107.98  3.000
 RMJ  H3   C12  N11  109.82  3.000
 RMJ  H4   C12  C13  109.91  3.000
 RMJ  H3   C12  C13  110.29  3.000
 RMJ  N11  C12  C13  113.07  3.000
 RMJ  H6   C13  H5   106.09  3.000
 RMJ  H6   C13  C14  110.33  3.000
 RMJ  H5   C13  C14  110.02  3.000
 RMJ  H6   C13  C12  108.71  3.000
 RMJ  H5   C13  C12  110.92  3.000
 RMJ  C14  C13  C12  110.67  3.000
 RMJ  C21  C02  N03  119.82  3.000
 RMJ  N03  C02  N01  117.79  3.000
 RMJ  C21  C02  N01  122.39  3.000
 RMJ  C04  N03  C02  118.37  3.000
 RMJ  N18  C04  S05  113.28  3.000
 RMJ  S05  C04  N03  118.79  3.000
 RMJ  N18  C04  N03  127.93  3.000
 RMJ  C06  S05  C04  101.43  3.000
 RMJ  H10  C06  H9   107.07  3.000
 RMJ  H10  C06  C07  112.03  3.000
 RMJ  H9   C06  C07  109.28  3.000
 RMJ  H10  C06  S05  109.11  3.000
 RMJ  H9   C06  S05  105.50  3.000
 RMJ  C07  C06  S05  113.45  3.000
 RMJ  O17  C07  N08  122.49  3.000
 RMJ  N08  C07  C06  115.47  3.000
 RMJ  O17  C07  C06  121.98  3.000
 RMJ  H11  N08  C09  117.00  3.000
 RMJ  H11  N08  C07  115.56  3.000
 RMJ  C09  N08  C07  126.92  3.000
 RMJ  H13  C09  H12  105.92  3.000
 RMJ  H13  C09  N08  107.96  3.000
 RMJ  H12  C09  N08  109.81  3.000
 RMJ  H13  C09  C10  109.64  3.000
 RMJ  H12  C09  C10  110.51  3.000
 RMJ  N08  C09  C10  112.74  3.000
 RMJ  C16  N11  C12  111.06  3.000
 RMJ  C12  N11  C10  112.63  3.000
 RMJ  C16  N11  C10  116.94  3.000
 RMJ  H16  C14  H15  105.85  3.000
 RMJ  H16  C14  C15  110.86  3.000
 RMJ  H15  C14  C15  108.97  3.000
 RMJ  H16  C14  C13  110.48  3.000
 RMJ  H15  C14  C13  110.32  3.000
 RMJ  C15  C14  C13  110.26  3.000
 RMJ  H18  C15  H17  106.21  3.000
 RMJ  H18  C15  C16  109.51  3.000
 RMJ  H17  C15  C16  110.29  3.000
 RMJ  H18  C15  C14  111.21  3.000
 RMJ  H17  C15  C14  109.16  3.000
 RMJ  C16  C15  C14  110.38  3.000
 RMJ  H20  C16  H19  106.26  3.000
 RMJ  H20  C16  C15  109.49  3.000
 RMJ  H19  C16  C15  109.18  3.000
 RMJ  H20  C16  N11  108.30  3.000
 RMJ  H19  C16  N11  109.47  3.000
 RMJ  C15  C16  N11  113.86  3.000
 RMJ  C19  N18  C04  113.49  3.000
 RMJ  C21  C19  S20  111.68  3.000
 RMJ  C21  C19  N18  125.48  3.000
 RMJ  S20  C19  N18  122.84  3.000
 RMJ  C23  S20  C19   90.46  3.000
 RMJ  C22  C21  C19  111.81  3.000
 RMJ  C19  C21  C02  114.91  3.000
 RMJ  C22  C21  C02  133.28  3.000
 RMJ  C26  C22  C23  110.89  3.000
 RMJ  C26  C22  C21  136.57  3.000
 RMJ  C23  C22  C21  112.46  3.000
 RMJ  C24  C23  C22  113.91  3.000
 RMJ  C22  C23  S20  113.58  3.000
 RMJ  C24  C23  S20  132.41  3.000
 RMJ  H22  C24  H21  107.06  3.000
 RMJ  H22  C24  C25  112.04  3.000
 RMJ  H21  C24  C25  112.27  3.000
 RMJ  H22  C24  C23  110.87  3.000
 RMJ  H21  C24  C23  113.63  3.000
 RMJ  C25  C24  C23  101.04  3.000
 RMJ  H24  C25  H23  107.34  3.000
 RMJ  H24  C25  C26  109.06  3.000
 RMJ  H23  C25  C26  112.18  3.000
 RMJ  H24  C25  C24  109.00  3.000
 RMJ  H23  C25  C24  112.12  3.000
 RMJ  C26  C25  C24  107.09  3.000
 RMJ  H26  C26  H25  107.07  3.000
 RMJ  H26  C26  C25  111.40  3.000
 RMJ  H25  C26  C25  111.80  3.000
 RMJ  H26  C26  C22  113.55  3.000
 RMJ  H25  C26  C22  110.73  3.000
 RMJ  C25  C26  C22  102.37  3.000
 RMJ  H8   N01  H7   117.69  3.000
 RMJ  H8   N01  C02  122.39  3.000
 RMJ  H7   N01  C02  119.72  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
 RMJ  CONST_01  C23  C22  C21  C02   180.00   0.0  0
 RMJ  CONST_02  S20  C19  C21  C02   180.00   0.0  0
 RMJ  CONST_03  N18  C19  C21  C02     0.00   0.0  0
 RMJ  CONST_04  N18  C04  N03  C02     0.00   0.0  0
 RMJ  CONST_05  C22  C21  C02  N03   180.00   0.0  0
 RMJ  CONST_06  C19  C21  C02  N03     0.00   0.0  0
 RMJ  CONST_07  C19  N18  C04  N03     0.00   0.0  0
 RMJ  CONST_08  S20  C19  N18  C04   180.00   0.0  0
 RMJ  CONST_09  C21  C19  N18  C04     0.00   0.0  0
 RMJ  CONST_10  C21  C02  N03  C04     0.00   0.0  0
 RMJ  CONST_11  C23  S20  C19  N18   180.00   0.0  0
 RMJ  CONST_12  C22  C21  C19  N18   180.00   0.0  0
 RMJ  CONST_13  C22  C23  S20  C19     0.00   0.0  0
 RMJ  CONST_14  C23  C22  C21  C19     0.00   0.0  0
 RMJ  CONST_15  C21  C22  C23  S20     0.00   0.0  0
 RMJ  CONST_16  C22  C21  C19  S20     0.00   0.0  0
 RMJ  CONST_17  C23  S20  C19  C21     0.00   0.0  0
 RMJ  CONST_18  C22  C21  C02  N01     0.00   0.0  0
 RMJ  CONST_19  C19  C21  C02  N01   180.00   0.0  0
 RMJ  CONST_20  C04  N03  C02  N01   180.00   0.0  0
 RMJ  CONST_21  S05  C04  N03  C02   180.00   0.0  0
 RMJ  CONST_22  C19  N18  C04  S05   180.00   0.0  0
 RMJ  CONST_23  H7   N01  C02  N03     0.00   0.0  0
 RMJ  CONST_24  H8   N01  C02  N03   180.00   0.0  0
 RMJ  CONST_25  C09  N08  C07  C06     0.00   0.0  0
 RMJ  CONST_26  O17  C07  N08  C09   180.00   0.0  0
 RMJ  CONST_27  H11  N08  C07  C06   180.00   0.0  0
 RMJ  Var_01    C15  C14  C13  C12    29.33  30.0  1
 RMJ  Var_02    C15  C16  N11  C12    30.34  30.0  1
 RMJ  Var_03    C16  C15  C14  C13   -61.74  30.0  1
 RMJ  Var_04    C16  N11  C12  C13   -64.88  30.0  1
 RMJ  Var_05    C14  C15  C16  N11    31.05  30.0  1
 RMJ  Var_06    C14  C13  C12  N11    32.20  30.0  1
 RMJ  Var_07    C25  C24  C23  S20   170.36  30.0  1
 RMJ  Var_08    C25  C26  C22  C21  -170.83  30.0  1
 RMJ  Var_09    C24  C25  C26  C22   -20.72  30.0  1
 RMJ  Var_10    C26  C25  C24  C23    20.67  30.0  1
 RMJ  Var_11    C09  C10  N11  C12    84.23  30.0  3
 RMJ  Var_12    N18  C04  S05  C06   178.73  30.0  1
 RMJ  Var_13    C07  C06  S05  C04    72.53  30.0  3
 RMJ  Var_14    N11  C10  C09  N08  -168.71  30.0  2
 RMJ  Var_15    C07  N08  C09  C10    85.97  30.0  1
 RMJ  Var_16    O17  C07  C06  S05    13.86  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
 RMJ  plan-1  C06  0.020
 RMJ  plan-1  C07  0.020
 RMJ  plan-1  N08  0.020
 RMJ  plan-1  C09  0.020
 RMJ  plan-1  O17  0.020
 RMJ  plan-1  H11  0.020
 RMJ  plan-2  C02  0.020
 RMJ  plan-2  N03  0.020
 RMJ  plan-2  C04  0.020
 RMJ  plan-2  S05  0.020
 RMJ  plan-2  N18  0.020
 RMJ  plan-2  C19  0.020
 RMJ  plan-2  S20  0.020
 RMJ  plan-2  C21  0.020
 RMJ  plan-2  C22  0.020
 RMJ  plan-2  C23  0.020
 RMJ  plan-2  C24  0.020
 RMJ  plan-2  C26  0.020
 RMJ  plan-2  N01  0.020
 RMJ  plan-3  C02  0.020
 RMJ  plan-3  H7   0.020
 RMJ  plan-3  H8   0.020
 RMJ  plan-3  N01  0.020

