# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:59:14 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: 2-[(4-amino-6,7,8,9-tetrahydro-5H-cyclohepta[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)nc3sc4CCCCCc4c13
#
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
 RM7  RM7  2-[(4-amino-6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidin-2-yl)sulfanyl]-N-[2-(piperidin-1-yl)ethyl]acetamide  ligand  57  28  .  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_RM7
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
 RM7  C10  C  CH2   0  -0.274  18.7163   -9.9097  42.1716
 RM7  C12  C  CH2   0  -0.256  17.2088  -10.7932  40.5364
 RM7  C13  C  CH2   0  -0.482  16.8602  -12.0437  39.7250
 RM7  C15  C  CH2   0  -0.430  19.1109  -13.0491  40.1680
 RM7  C16  C  CH2   0  -0.296  18.9311  -12.2082  41.4339
 RM7  C02  C  CR6   0   0.493  21.3996  -10.8343  37.9266
 RM7  N03  N  N     0  -0.506  21.1350   -9.6191  38.4113
 RM7  C04  C  CR6   0   0.239  20.1687   -8.9047  37.8581
 RM7  S05  S  S2    0   0.069  19.8288   -7.2854  38.4660
 RM7  C06  C  CH2   0  -0.709  21.1015   -7.0322  39.7330
 RM7  C07  C  C     0   0.537  20.6325   -7.5126  41.0951
 RM7  N08  N  NH1   0  -0.611  20.7511   -8.8332  41.2889
 RM7  C09  C  CH2   0  -0.323  20.1658   -9.5133  42.4205
 RM7  N11  N  NT    0  -0.407  18.5603  -10.8509  41.0838
 RM7  C14  C  CH2   0  -0.430  18.1014  -12.6445  39.0855
 RM7  O17  O  O     0  -0.496  20.1868   -6.7308  41.9235
 RM7  N18  N  N     0  -0.448  19.4007   -9.2452  36.8462
 RM7  C19  C  CR56  0  -0.033  19.6503  -10.4678  36.3792
 RM7  C20  C  CR56  0  -0.025  20.6189  -11.3519  36.8607
 RM7  C21  C  CR5   0   0.230  20.5980  -12.6144  36.1775
 RM7  C22  C  CR5   0  -0.223  19.6627  -12.6384  35.1924
 RM7  C23  C  CH2   0  -0.526  19.4678  -13.7813  34.2512
 RM7  C24  C  CH2   0  -0.417  20.7133  -14.0696  33.3723
 RM7  C25  C  CH2   0  -0.458  22.0345  -13.4722  33.8582
 RM7  C26  C  CH2   0  -0.412  22.5250  -13.9334  35.2304
 RM7  C27  C  CH2   0  -0.569  21.4722  -13.8218  36.3461
 RM7  S28  S  S2    0   0.206  18.7609  -11.1618  35.0748
 RM7  H1   H  HCH2  0   0.234  18.1629   -9.0011  41.9202
 RM7  H2   H  HCH2  0   0.197  18.2791  -10.2849  43.1130
 RM7  H3   H  HCH2  0   0.218  17.1398   -9.9029  39.9033
 RM7  H4   H  HCH2  0   0.191  16.4573  -10.6730  41.3343
 RM7  H5   H  HCH2  0   0.236  16.1141  -11.7890  38.9698
 RM7  H6   H  HCH2  0   0.219  16.3906  -12.7901  40.3723
 RM7  H7   H  HCH2  0   0.215  18.9935  -14.1037  40.4289
 RM7  H8   H  HCH2  0   0.221  20.1275  -12.9307  39.7868
 RM7  H9   H  HCH2  0   0.190  18.1860  -12.6730  42.1033
 RM7  H10  H  HCH2  0   0.233  19.8653  -12.1978  41.9978
 RM7  H11  H  HNH2  0   0.407  22.9704  -11.0343  39.1896
 RM7  H12  H  HNH2  0   0.417  22.7710  -12.3508  38.1136
 RM7  H13  H  HCH2  0   0.312  22.0222   -7.5185  39.4128
 RM7  H14  H  HCH2  0   0.318  21.2695   -5.9571  39.7675
 RM7  H15  H  HNH1  0   0.419  20.9968   -9.3888  40.4781
 RM7  H16  H  HCH2  0   0.246  20.7818  -10.3837  42.6516
 RM7  H17  H  HCH2  0   0.250  20.2145   -8.8612  43.2920
 RM7  H19  H  HCH2  0   0.221  17.8361  -13.5057  38.4693
 RM7  H20  H  HCH2  0   0.238  18.5528  -11.9143  38.4127
 RM7  H21  H  HCH2  0   0.263  18.6014  -13.6118  33.6107
 RM7  H22  H  HCH2  0   0.258  19.2215  -14.6678  34.8427
 RM7  H23  H  HCH2  0   0.236  20.5287  -13.6835  32.3681
 RM7  H24  H  HCH2  0   0.228  20.8164  -15.1519  33.2651
 RM7  H25  H  HCH2  0   0.239  22.8048  -13.7092  33.1201
 RM7  H26  H  HCH2  0   0.224  21.9510  -12.3825  33.8552
 RM7  H27  H  HCH2  0   0.228  22.8614  -14.9719  35.1787
 RM7  H28  H  HCH2  0   0.230  23.4031  -13.3394  35.4973
 RM7  H29  H  HCH2  0   0.261  20.8333  -14.7082  36.3212
 RM7  H30  H  HCH2  0   0.244  21.9503  -13.8659  37.3247
 RM7  N01  N  NH2   0  -0.834  22.4038  -11.5021  38.5017

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
 RM7  C24  C25  single    1.529  0.020  1.529
 RM7  C24  C23  single    1.551  0.020  1.551
 RM7  C25  C26  single    1.529  0.020  1.529
 RM7  C23  C22  single    1.493  0.020  1.493
 RM7  C22  S28  aromatic  1.734  0.020  1.734
 RM7  C22  C21  aromatic  1.359  0.020  1.359
 RM7  C26  C27  single    1.538  0.020  1.538
 RM7  S28  C19  aromatic  1.725  0.020  1.725
 RM7  C21  C27  single    1.500  0.020  1.500
 RM7  C21  C20  aromatic  1.436  0.020  1.436
 RM7  C19  C20  aromatic  1.397  0.020  1.397
 RM7  C19  N18  aromatic  1.332  0.020  1.332
 RM7  C20  C02  aromatic  1.419  0.020  1.419
 RM7  N18  C04  aromatic  1.315  0.020  1.315
 RM7  C02  N03  aromatic  1.335  0.020  1.335
 RM7  C02  N01  single    1.336  0.020  1.336
 RM7  C04  N03  aromatic  1.323  0.020  1.323
 RM7  C04  S05  single    1.763  0.020  1.763
 RM7  S05  C06  single    1.814  0.020  1.814
 RM7  C14  C13  single    1.520  0.020  1.520
 RM7  C14  C15  single    1.535  0.020  1.535
 RM7  C06  C07  single    1.519  0.020  1.519
 RM7  C13  C12  single    1.531  0.020  1.531
 RM7  C12  N11  single    1.459  0.020  1.459
 RM7  C15  C16  single    1.530  0.020  1.530
 RM7  C07  N08  single    1.340  0.020  1.340
 RM7  C07  O17  double    1.223  0.020  1.223
 RM7  N08  C09  single    1.444  0.020  1.444
 RM7  N11  C16  single    1.450  0.020  1.450
 RM7  N11  C10  single    1.447  0.020  1.447
 RM7  C10  C09  single    1.523  0.020  1.523
 RM7  C10  H1   single    0.970  0.020  1.090
 RM7  C10  H2   single    0.970  0.020  1.090
 RM7  C12  H3   single    0.970  0.020  1.090
 RM7  C12  H4   single    0.970  0.020  1.090
 RM7  C13  H5   single    0.970  0.020  1.090
 RM7  C13  H6   single    0.970  0.020  1.090
 RM7  C15  H7   single    0.970  0.020  1.090
 RM7  C15  H8   single    0.970  0.020  1.090
 RM7  C16  H9   single    0.970  0.020  1.090
 RM7  C16  H10  single    0.970  0.020  1.090
 RM7  N01  H11  single    0.860  0.020  1.020
 RM7  N01  H12  single    0.860  0.020  1.020
 RM7  C06  H13  single    0.970  0.020  1.090
 RM7  C06  H14  single    0.970  0.020  1.090
 RM7  N08  H15  single    0.890  0.020  1.040
 RM7  C09  H16  single    0.970  0.020  1.090
 RM7  C09  H17  single    0.970  0.020  1.090
 RM7  C14  H19  single    0.970  0.020  1.090
 RM7  C14  H20  single    0.970  0.020  1.090
 RM7  C23  H21  single    0.970  0.020  1.090
 RM7  C23  H22  single    0.970  0.020  1.090
 RM7  C24  H23  single    0.970  0.020  1.090
 RM7  C24  H24  single    0.970  0.020  1.090
 RM7  C25  H25  single    0.970  0.020  1.090
 RM7  C25  H26  single    0.970  0.020  1.090
 RM7  C26  H27  single    0.970  0.020  1.090
 RM7  C26  H28  single    0.970  0.020  1.090
 RM7  C27  H29  single    0.970  0.020  1.090
 RM7  C27  H30  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
 RM7  H2   C10  H1   106.15  3.000
 RM7  H2   C10  N11  112.18  3.000
 RM7  H1   C10  N11  108.26  3.000
 RM7  H2   C10  C09  109.03  3.000
 RM7  H1   C10  C09  107.63  3.000
 RM7  N11  C10  C09  113.25  3.000
 RM7  H4   C12  H3   106.68  3.000
 RM7  H4   C12  N11  111.34  3.000
 RM7  H3   C12  N11  107.91  3.000
 RM7  H4   C12  C13  108.50  3.000
 RM7  H3   C12  C13  110.09  3.000
 RM7  N11  C12  C13  112.17  3.000
 RM7  H6   C13  H5   105.97  3.000
 RM7  H6   C13  C14  109.26  3.000
 RM7  H5   C13  C14  111.05  3.000
 RM7  H6   C13  C12  109.97  3.000
 RM7  H5   C13  C12  109.37  3.000
 RM7  C14  C13  C12  111.10  3.000
 RM7  H8   C15  H7   106.74  3.000
 RM7  H8   C15  C14  109.73  3.000
 RM7  H7   C15  C14  110.62  3.000
 RM7  H8   C15  C16  109.78  3.000
 RM7  H7   C15  C16  108.67  3.000
 RM7  C14  C15  C16  111.19  3.000
 RM7  H10  C16  H9   105.57  3.000
 RM7  H10  C16  N11  109.56  3.000
 RM7  H9   C16  N11  111.58  3.000
 RM7  H10  C16  C15  109.40  3.000
 RM7  H9   C16  C15  110.45  3.000
 RM7  N11  C16  C15  110.16  3.000
 RM7  C20  C02  N03  119.73  3.000
 RM7  N03  C02  N01  116.59  3.000
 RM7  C20  C02  N01  123.68  3.000
 RM7  C04  N03  C02  118.98  3.000
 RM7  N18  C04  S05  112.99  3.000
 RM7  S05  C04  N03  119.52  3.000
 RM7  N18  C04  N03  127.48  3.000
 RM7  C06  S05  C04  103.52  3.000
 RM7  H14  C06  H13  108.65  3.000
 RM7  H14  C06  C07  109.36  3.000
 RM7  H13  C06  C07  112.55  3.000
 RM7  H14  C06  S05  105.56  3.000
 RM7  H13  C06  S05  109.00  3.000
 RM7  C07  C06  S05  111.45  3.000
 RM7  O17  C07  N08  124.35  3.000
 RM7  O17  C07  C06  121.19  3.000
 RM7  N08  C07  C06  114.47  3.000
 RM7  H15  N08  C09  117.84  3.000
 RM7  H15  N08  C07  116.50  3.000
 RM7  C09  N08  C07  122.79  3.000
 RM7  H17  C09  H16  106.42  3.000
 RM7  H17  C09  N08  109.07  3.000
 RM7  H16  C09  N08  108.23  3.000
 RM7  H17  C09  C10  109.21  3.000
 RM7  H16  C09  C10  111.36  3.000
 RM7  N08  C09  C10  112.35  3.000
 RM7  C16  N11  C12  111.37  3.000
 RM7  C16  N11  C10  113.57  3.000
 RM7  C12  N11  C10  110.87  3.000
 RM7  H20  C14  H19  106.29  3.000
 RM7  H20  C14  C15  109.84  3.000
 RM7  H19  C14  C15  110.49  3.000
 RM7  H20  C14  C13  109.45  3.000
 RM7  H19  C14  C13  110.54  3.000
 RM7  C15  C14  C13  110.16  3.000
 RM7  C19  N18  C04  113.44  3.000
 RM7  S28  C19  C20  111.33  3.000
 RM7  C20  C19  N18  126.14  3.000
 RM7  S28  C19  N18  122.53  3.000
 RM7  C21  C20  C19  112.48  3.000
 RM7  C19  C20  C02  114.17  3.000
 RM7  C21  C20  C02  133.34  3.000
 RM7  C27  C21  C22  117.93  3.000
 RM7  C27  C21  C20  130.22  3.000
 RM7  C22  C21  C20  111.76  3.000
 RM7  S28  C22  C23  122.75  3.000
 RM7  S28  C22  C21  113.09  3.000
 RM7  C23  C22  C21  124.08  3.000
 RM7  H22  C23  H21  105.34  3.000
 RM7  H22  C23  C24  109.67  3.000
 RM7  H21  C23  C24  109.51  3.000
 RM7  H22  C23  C22  107.99  3.000
 RM7  H21  C23  C22  110.78  3.000
 RM7  C24  C23  C22  113.24  3.000
 RM7  H24  C24  H23  106.03  3.000
 RM7  H24  C24  C25  109.67  3.000
 RM7  H23  C24  C25  107.47  3.000
 RM7  H24  C24  C23  108.39  3.000
 RM7  H23  C24  C23  108.65  3.000
 RM7  C25  C24  C23  116.17  3.000
 RM7  H26  C25  H25  105.56  3.000
 RM7  H26  C25  C26  109.13  3.000
 RM7  H25  C25  C26  108.34  3.000
 RM7  H26  C25  C24  108.82  3.000
 RM7  H25  C25  C24  108.04  3.000
 RM7  C26  C25  C24  116.40  3.000
 RM7  H28  C26  H27  106.31  3.000
 RM7  H28  C26  C27  109.47  3.000
 RM7  H27  C26  C27  108.30  3.000
 RM7  H28  C26  C25  108.24  3.000
 RM7  H27  C26  C25  110.06  3.000
 RM7  C27  C26  C25  114.18  3.000
 RM7  H30  C27  H29  104.12  3.000
 RM7  H30  C27  C26  110.37  3.000
 RM7  H29  C27  C26  108.96  3.000
 RM7  H30  C27  C21  112.90  3.000
 RM7  H29  C27  C21  108.03  3.000
 RM7  C26  C27  C21  112.07  3.000
 RM7  C22  S28  C19   91.33  3.000
 RM7  H12  N01  H11  116.86  3.000
 RM7  H12  N01  C02  122.11  3.000
 RM7  H11  N01  C02  119.01  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
 RM7  CONST_01  S28  C19  C20  C02   180.00   0.0  0
 RM7  CONST_02  N18  C19  C20  C02     0.00   0.0  0
 RM7  CONST_03  N18  C04  N03  C02     0.00   0.0  0
 RM7  CONST_04  C21  C20  C02  N03   180.00   0.0  0
 RM7  CONST_05  C19  C20  C02  N03     0.00   0.0  0
 RM7  CONST_06  C19  N18  C04  N03     0.00   0.0  0
 RM7  CONST_07  S28  C19  N18  C04   180.00   0.0  0
 RM7  CONST_08  C20  C19  N18  C04     0.00   0.0  0
 RM7  CONST_09  C20  C02  N03  C04     0.00   0.0  0
 RM7  CONST_10  C22  S28  C19  N18   180.00   0.0  0
 RM7  CONST_11  C21  C20  C19  N18   180.00   0.0  0
 RM7  CONST_12  C22  S28  C19  C20     0.00   0.0  0
 RM7  CONST_13  S28  C19  C20  C21     0.00   0.0  0
 RM7  CONST_14  C21  C20  C02  N01     0.00   0.0  0
 RM7  CONST_15  C19  C20  C02  N01   180.00   0.0  0
 RM7  CONST_16  C04  N03  C02  N01   180.00   0.0  0
 RM7  CONST_17  S05  C04  N03  C02   180.00   0.0  0
 RM7  CONST_18  C19  N18  C04  S05   180.00   0.0  0
 RM7  CONST_19  H11  N01  C02  N03     0.00   0.0  0
 RM7  CONST_20  H12  N01  C02  N03   180.00   0.0  0
 RM7  CONST_21  C09  N08  C07  C06   180.00   0.0  0
 RM7  CONST_22  O17  C07  N08  C09     0.00   0.0  0
 RM7  CONST_23  H15  N08  C07  C06     0.00   0.0  0
 RM7  Var_01    C15  C14  C13  C12    60.42  30.0  1
 RM7  Var_02    C15  C16  N11  C12    69.55  30.0  1
 RM7  Var_03    C16  C15  C14  C13   -26.16  30.0  1
 RM7  Var_04    C16  N11  C12  C13   -33.87  30.0  1
 RM7  Var_05    C14  C13  C12  N11   -29.79  30.0  1
 RM7  Var_06    C14  C15  C16  N11   -35.79  30.0  1
 RM7  Var_07    C09  C10  N11  C12  -157.25  30.0  3
 RM7  Var_08    N18  C04  S05  C06  -175.35  30.0  2
 RM7  Var_09    C07  C06  S05  C04   -89.54  30.0  3
 RM7  Var_10    N11  C10  C09  N08    62.75  30.0  2
 RM7  Var_11    C07  N08  C09  C10    85.77  30.0  2
 RM7  Var_12    N08  C07  C06  S05    81.45  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
 RM7  plan-1  C06  0.020
 RM7  plan-1  C07  0.020
 RM7  plan-1  N08  0.020
 RM7  plan-1  C09  0.020
 RM7  plan-1  O17  0.020
 RM7  plan-1  H15  0.020
 RM7  plan-2  C02  0.020
 RM7  plan-2  N03  0.020
 RM7  plan-2  C04  0.020
 RM7  plan-2  S05  0.020
 RM7  plan-2  N18  0.020
 RM7  plan-2  C19  0.020
 RM7  plan-2  C20  0.020
 RM7  plan-2  C21  0.020
 RM7  plan-2  C22  0.020
 RM7  plan-2  C23  0.020
 RM7  plan-2  C27  0.020
 RM7  plan-2  S28  0.020
 RM7  plan-2  N01  0.020
 RM7  plan-3  C02  0.020
 RM7  plan-3  H11  0.020
 RM7  plan-3  H12  0.020
 RM7  plan-3  N01  0.020

