# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 00:36:03 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-{[3-(piperidin-1-yl)propyl]sulfanyl}-6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(SCCCN2CCCCC2)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
 RMG  RMG  2-{[3-(piperidin-1-yl)propyl]sulfanyl}-6,7,8,9-tetrahydro-5H-cyclohepta[4,5]thieno[2,3-d]pyrimidin-4-amine  ligand  53  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 PERFECT
;

data_comp_RMG
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
 RMG  C10  C  CH2   0  -0.286  19.7861  -11.2656  42.2211
 RMG  C11  C  CH2   0  -0.466  20.9448  -12.2295  42.4283
 RMG  C12  C  CH2   0  -0.432  21.3162  -12.3262  43.9022
 RMG  C13  C  CH2   0  -0.438  21.5661  -10.9317  44.4603
 RMG  C14  C  CH2   0  -0.272  20.3794  -10.0215  44.1833
 RMG  C02  C  CR6   0   0.451  20.5705  -11.6451  37.9658
 RMG  N03  N  N     0  -0.452  20.4606  -10.4559  38.5599
 RMG  C04  C  CR6   0   0.207  20.0638   -9.4139  37.8515
 RMG  S05  S  S2    0   0.036  19.9787   -7.8279  38.6098
 RMG  C06  C  CH2   0  -0.564  20.1555   -8.1994  40.3744
 RMG  C07  C  CH2   0  -0.446  18.8584   -8.6723  41.0116
 RMG  N09  N  NT    0  -0.412  20.0840   -9.9526  42.7630
 RMG  N15  N  N     0  -0.453  19.7260   -9.4034  36.5767
 RMG  C16  C  CR56  0  -0.037  19.8571  -10.5866  35.9828
 RMG  C17  C  CR56  0  -0.011  20.2964  -11.7752  36.5753
 RMG  C18  C  CR5   0   0.237  20.3557  -12.8702  35.6341
 RMG  C19  C  CR5   0  -0.239  19.9335  -12.4920  34.3996
 RMG  C20  C  CH2   0  -0.512  19.8647  -13.3273  33.1607
 RMG  C21  C  CH2   0  -0.422  21.2279  -13.8481  32.7031
 RMG  C22  C  CH2   0  -0.433  21.7947  -14.9702  33.5649
 RMG  C23  C  CH2   0  -0.435  22.0962  -14.6180  35.0180
 RMG  C24  C  CH2   0  -0.584  20.8705  -14.2644  35.8684
 RMG  S25  S  S2    0   0.208  19.4838  -10.8159  34.3179
 RMG  H1   H  HCH2  0   0.184  18.8735  -11.6894  42.6804
 RMG  H2   H  HCH2  0   0.242  19.5845  -11.1707  41.1528
 RMG  H3   H  HCH2  0   0.230  20.6708  -13.2118  42.0348
 RMG  H4   H  HCH2  0   0.216  21.8106  -11.8775  41.8558
 RMG  H5   H  HCH2  0   0.232  22.1918  -12.9642  44.0399
 RMG  H6   H  HCH2  0   0.212  20.4937  -12.7962  44.4523
 RMG  H7   H  HCH2  0   0.214  22.4605  -10.5048  43.9965
 RMG  H8   H  HCH2  0   0.229  21.7503  -10.9692  45.5362
 RMG  H9   H  HCH2  0   0.230  20.5957   -9.0118  44.5422
 RMG  H10  H  HCH2  0   0.179  19.5064  -10.3802  44.7600
 RMG  H11  H  HNH2  0   0.419  21.0508  -12.4700  39.7409
 RMG  H12  H  HNH2  0   0.418  20.8597  -13.6153  38.4918
 RMG  H13  H  HCH2  0   0.286  20.9515   -8.9295  40.5025
 RMG  H14  H  HCH2  0   0.276  20.4885   -7.2631  40.8266
 RMG  H15  H  HCH2  0   0.244  18.0991   -7.8927  40.9198
 RMG  H16  H  HCH2  0   0.237  18.4731   -9.5371  40.4686
 RMG  H17  H  HCH2  0   0.226  19.2867   -8.0644  43.0164
 RMG  H18  H  HCH2  0   0.202  18.0603   -9.3206  42.9000
 RMG  H20  H  HCH2  0   0.258  19.4144  -12.7459  32.3537
 RMG  H21  H  HCH2  0   0.254  19.1863  -14.1713  33.3277
 RMG  H22  H  HCH2  0   0.223  21.9349  -13.0144  32.6569
 RMG  H23  H  HCH2  0   0.239  21.1235  -14.2212  31.6812
 RMG  H24  H  HCH2  0   0.217  21.0990  -15.8168  33.5461
 RMG  H25  H  HCH2  0   0.236  22.7165  -15.3279  33.0987
 RMG  H26  H  HCH2  0   0.244  22.5833  -15.4817  35.4774
 RMG  H27  H  HCH2  0   0.227  22.8173  -13.7970  35.0669
 RMG  H28  H  HCH2  0   0.264  20.0738  -14.9903  35.6739
 RMG  H29  H  HCH2  0   0.236  21.1430  -14.4144  36.9091
 RMG  C08  C  CH2   0  -0.270  19.0323   -8.9909  42.4925
 RMG  N01  N  NH2   0  -0.849  20.9673  -12.6541  38.7550

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
 RMG  C21  C22  single    1.524  0.020  1.524
 RMG  C21  C20  single    1.529  0.020  1.529
 RMG  C22  C23  single    1.525  0.020  1.525
 RMG  C20  C19  single    1.496  0.020  1.496
 RMG  C23  C24  single    1.533  0.020  1.533
 RMG  C19  S25  aromatic  1.737  0.020  1.737
 RMG  C19  C18  aromatic  1.358  0.020  1.358
 RMG  S25  C16  aromatic  1.722  0.020  1.722
 RMG  C18  C24  single    1.505  0.020  1.505
 RMG  C18  C17  aromatic  1.445  0.020  1.445
 RMG  C16  C17  aromatic  1.399  0.020  1.399
 RMG  C16  N15  aromatic  1.330  0.020  1.330
 RMG  C17  C02  aromatic  1.423  0.020  1.423
 RMG  N15  C04  aromatic  1.319  0.020  1.319
 RMG  C02  N01  single    1.341  0.020  1.341
 RMG  C02  N03  aromatic  1.334  0.020  1.334
 RMG  C04  N03  aromatic  1.321  0.020  1.321
 RMG  C04  S05  single    1.760  0.020  1.760
 RMG  S05  C06  single    1.812  0.020  1.812
 RMG  C06  C07  single    1.521  0.020  1.521
 RMG  C07  C08  single    1.525  0.020  1.525
 RMG  C08  N09  single    1.451  0.020  1.451
 RMG  N09  C14  single    1.452  0.020  1.452
 RMG  N09  C10  single    1.451  0.020  1.451
 RMG  C14  C13  single    1.521  0.020  1.521
 RMG  C10  C11  single    1.521  0.020  1.521
 RMG  C13  C12  single    1.523  0.020  1.523
 RMG  C11  C12  single    1.523  0.020  1.523
 RMG  C10  H1   single    0.970  0.020  1.090
 RMG  C10  H2   single    0.970  0.020  1.090
 RMG  C11  H3   single    0.970  0.020  1.090
 RMG  C11  H4   single    0.970  0.020  1.090
 RMG  C12  H5   single    0.970  0.020  1.090
 RMG  C12  H6   single    0.970  0.020  1.090
 RMG  C13  H7   single    0.970  0.020  1.090
 RMG  C13  H8   single    0.970  0.020  1.090
 RMG  C14  H9   single    0.970  0.020  1.090
 RMG  C14  H10  single    0.970  0.020  1.090
 RMG  N01  H11  single    0.890  0.020  1.040
 RMG  N01  H12  single    0.890  0.020  1.040
 RMG  C06  H13  single    0.970  0.020  1.090
 RMG  C06  H14  single    0.970  0.020  1.090
 RMG  C07  H15  single    0.970  0.020  1.090
 RMG  C07  H16  single    0.970  0.020  1.090
 RMG  C08  H17  single    0.970  0.020  1.090
 RMG  C08  H18  single    0.970  0.020  1.090
 RMG  C20  H20  single    0.970  0.020  1.090
 RMG  C20  H21  single    0.970  0.020  1.090
 RMG  C21  H22  single    0.970  0.020  1.090
 RMG  C21  H23  single    0.970  0.020  1.090
 RMG  C22  H24  single    0.970  0.020  1.090
 RMG  C22  H25  single    0.970  0.020  1.090
 RMG  C23  H26  single    0.970  0.020  1.090
 RMG  C23  H27  single    0.970  0.020  1.090
 RMG  C24  H28  single    0.970  0.020  1.090
 RMG  C24  H29  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
 RMG  H2   C10  H1   106.70  3.000
 RMG  H2   C10  N09  108.95  3.000
 RMG  H1   C10  N09  111.16  3.000
 RMG  H2   C10  C11  109.22  3.000
 RMG  H1   C10  C11  109.22  3.000
 RMG  N09  C10  C11  111.47  3.000
 RMG  H4   C11  H3   107.37  3.000
 RMG  H4   C11  C12  109.47  3.000
 RMG  H3   C11  C12  110.64  3.000
 RMG  H4   C11  C10  109.09  3.000
 RMG  H3   C11  C10  109.23  3.000
 RMG  C12  C11  C10  110.97  3.000
 RMG  H6   C12  H5   106.74  3.000
 RMG  H6   C12  C13  109.40  3.000
 RMG  H5   C12  C13  110.93  3.000
 RMG  H6   C12  C11  109.28  3.000
 RMG  H5   C12  C11  110.77  3.000
 RMG  C13  C12  C11  109.66  3.000
 RMG  H8   C13  H7   107.04  3.000
 RMG  H8   C13  C14  109.36  3.000
 RMG  H7   C13  C14  109.09  3.000
 RMG  H8   C13  C12  110.93  3.000
 RMG  H7   C13  C12  109.65  3.000
 RMG  C14  C13  C12  110.69  3.000
 RMG  H10  C14  H9   106.52  3.000
 RMG  H10  C14  N09  111.39  3.000
 RMG  H9   C14  N09  108.51  3.000
 RMG  H10  C14  C13  109.08  3.000
 RMG  H9   C14  C13  109.79  3.000
 RMG  N09  C14  C13  111.42  3.000
 RMG  C17  C02  N03  120.05  3.000
 RMG  N03  C02  N01  115.66  3.000
 RMG  C17  C02  N01  124.28  3.000
 RMG  C04  N03  C02  119.28  3.000
 RMG  N15  C04  S05  113.39  3.000
 RMG  S05  C04  N03  119.62  3.000
 RMG  N15  C04  N03  126.98  3.000
 RMG  C06  S05  C04  103.31  3.000
 RMG  H14  C06  H13  107.67  3.000
 RMG  H14  C06  C07  110.69  3.000
 RMG  H13  C06  C07  111.48  3.000
 RMG  H14  C06  S05  104.91  3.000
 RMG  H13  C06  S05  108.89  3.000
 RMG  C07  C06  S05  112.87  3.000
 RMG  H16  C07  H15  106.16  3.000
 RMG  H16  C07  C08  110.97  3.000
 RMG  H15  C07  C08  108.06  3.000
 RMG  H16  C07  C06  109.82  3.000
 RMG  H15  C07  C06  109.62  3.000
 RMG  C08  C07  C06  112.01  3.000
 RMG  C08  N09  C14  111.18  3.000
 RMG  C14  N09  C10  111.34  3.000
 RMG  C08  N09  C10  112.42  3.000
 RMG  C16  N15  C04  113.53  3.000
 RMG  S25  C16  C17  111.38  3.000
 RMG  C17  C16  N15  126.69  3.000
 RMG  S25  C16  N15  121.93  3.000
 RMG  C18  C17  C16  112.39  3.000
 RMG  C16  C17  C02  113.37  3.000
 RMG  C18  C17  C02  134.24  3.000
 RMG  C24  C18  C19  120.39  3.000
 RMG  C24  C18  C17  127.94  3.000
 RMG  C19  C18  C17  111.60  3.000
 RMG  S25  C19  C20  119.21  3.000
 RMG  S25  C19  C18  113.06  3.000
 RMG  C20  C19  C18  127.70  3.000
 RMG  H21  C20  H20  105.52  3.000
 RMG  H21  C20  C21  109.59  3.000
 RMG  H20  C20  C21  109.13  3.000
 RMG  H21  C20  C19  109.41  3.000
 RMG  H20  C20  C19  109.50  3.000
 RMG  C21  C20  C19  113.39  3.000
 RMG  H23  C21  H22  106.40  3.000
 RMG  H23  C21  C22  108.23  3.000
 RMG  H22  C21  C22  110.15  3.000
 RMG  H23  C21  C20  108.11  3.000
 RMG  H22  C21  C20  109.22  3.000
 RMG  C22  C21  C20  114.40  3.000
 RMG  H25  C22  H24  105.97  3.000
 RMG  H25  C22  C23  108.37  3.000
 RMG  H24  C22  C23  108.67  3.000
 RMG  H25  C22  C21  108.26  3.000
 RMG  H24  C22  C21  108.84  3.000
 RMG  C23  C22  C21  116.24  3.000
 RMG  H27  C23  H26  106.29  3.000
 RMG  H27  C23  C24  109.21  3.000
 RMG  H26  C23  C24  107.79  3.000
 RMG  H27  C23  C22  110.26  3.000
 RMG  H26  C23  C22  107.82  3.000
 RMG  C24  C23  C22  115.07  3.000
 RMG  H29  C24  H28  105.14  3.000
 RMG  H29  C24  C23  107.40  3.000
 RMG  H28  C24  C23  109.28  3.000
 RMG  H29  C24  C18  111.29  3.000
 RMG  H28  C24  C18  109.74  3.000
 RMG  C23  C24  C18  113.63  3.000
 RMG  C19  S25  C16   91.54  3.000
 RMG  H18  C08  H17  106.31  3.000
 RMG  H18  C08  N09  111.80  3.000
 RMG  H17  C08  N09  107.67  3.000
 RMG  H18  C08  C07  108.69  3.000
 RMG  H17  C08  C07  108.33  3.000
 RMG  N09  C08  C07  113.72  3.000
 RMG  H12  N01  H11  116.20  3.000
 RMG  H12  N01  C02  122.36  3.000
 RMG  H11  N01  C02  117.61  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
 RMG  CONST_01  S25  C16  C17  C02  180.00   0.0  0
 RMG  CONST_02  N15  C16  C17  C02    0.00   0.0  0
 RMG  CONST_03  N15  C04  N03  C02    0.00   0.0  0
 RMG  CONST_04  C18  C17  C02  N03  180.00   0.0  0
 RMG  CONST_05  C16  C17  C02  N03    0.00   0.0  0
 RMG  CONST_06  C16  N15  C04  N03    0.00   0.0  0
 RMG  CONST_07  S25  C16  N15  C04  180.00   0.0  0
 RMG  CONST_08  C17  C16  N15  C04    0.00   0.0  0
 RMG  CONST_09  C17  C02  N03  C04    0.00   0.0  0
 RMG  CONST_10  C19  S25  C16  N15  180.00   0.0  0
 RMG  CONST_11  C18  C17  C16  N15  180.00   0.0  0
 RMG  CONST_12  C19  S25  C16  C17    0.00   0.0  0
 RMG  CONST_13  S25  C16  C17  C18    0.00   0.0  0
 RMG  CONST_14  C18  C17  C02  N01    0.00   0.0  0
 RMG  CONST_15  C16  C17  C02  N01  180.00   0.0  0
 RMG  CONST_16  C04  N03  C02  N01  180.00   0.0  0
 RMG  CONST_17  S05  C04  N03  C02  180.00   0.0  0
 RMG  CONST_18  C16  N15  C04  S05  180.00   0.0  0
 RMG  CONST_19  H11  N01  C02  N03    0.00   0.0  0
 RMG  Var_01    C13  C14  N09  C10   59.03  30.0  1
 RMG  Var_02    C13  C12  C11  C10  -53.29  30.0  1
 RMG  Var_03    C14  N09  C10  C11  -58.62  30.0  1
 RMG  Var_04    C14  C13  C12  C11   53.55  30.0  1
 RMG  Var_05    N09  C14  C13  C12  -56.76  30.0  1
 RMG  Var_06    N09  C10  C11  C12   56.09  30.0  1
 RMG  Var_07    C07  C08  N09  C10  -65.54  30.0  1
 RMG  Var_08    N15  C04  S05  C06  168.94  30.0  1
 RMG  Var_09    C07  C06  S05  C04  -80.51  30.0  3
 RMG  Var_10    N09  C08  C07  C06  -55.16  30.0  3
 RMG  Var_11    C08  C07  C06  S05  179.50  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
 RMG  plan-1  C02  0.020
 RMG  plan-1  N03  0.020
 RMG  plan-1  C04  0.020
 RMG  plan-1  S05  0.020
 RMG  plan-1  N15  0.020
 RMG  plan-1  C16  0.020
 RMG  plan-1  C17  0.020
 RMG  plan-1  C18  0.020
 RMG  plan-1  C19  0.020
 RMG  plan-1  C20  0.020
 RMG  plan-1  C24  0.020
 RMG  plan-1  S25  0.020
 RMG  plan-1  N01  0.020
 RMG  plan-2  C02  0.020
 RMG  plan-2  H11  0.020
 RMG  plan-2  H12  0.020
 RMG  plan-2  N01  0.020

