# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:55:21 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-{[(4-chlorophenyl)methyl]sulfanyl}-7-methyl-N-(prop-2-en-1-yl)-7,8-dihydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1Cc2sc3nc(SCc4ccc(Cl)cc4)nc(NCC=C)c3c2C=C1
#
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
 BC0  BC0  2-{[(4-chlorophenyl)methyl]sulfanyl}-7-methyl-N-(prop-2-en-1-yl)-7,8-dihydropyrido[4',3':4,5]thieno[2,3-d]pyrimidin-4-amine  ligand  46  27  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BC0
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
 BC0  N1   N   NT    0  -0.454  -6.1823   1.9459  -0.4460
 BC0  N3   N   N     0  -0.445  -0.1841   0.8783  -0.1081
 BC0  C4   C   CR5   0   0.328  -3.8089   0.5731  -0.0073
 BC0  C5   C   CR5   0  -0.368  -3.8093   1.9321  -0.1109
 BC0  C6   C   CR56  0  -0.019  -1.5065   1.0563  -0.1062
 BC0  C7   C   CR56  0  -0.019  -2.4671   0.0512  -0.0338
 BC0  C8   C   CR6   0   0.511  -1.9356  -1.2694  -0.0205
 BC0  C10  C   CH2   0  -0.623   2.6803   0.8372  -0.0154
 BC0  C13  C   CR16  0  -0.196   6.1824   0.2239   1.2996
 BC0  C15  C   CR16  0  -0.196   6.2607   0.2469  -1.1139
 BC0  C17  C   CH2   0  -0.319  -2.2106  -3.7126  -0.0757
 BC0  C20  C   CH2   0  -0.266  -5.0512   2.7585  -0.0319
 BC0  C1   C   CH3   0  -0.515  -7.4194   2.6708  -0.6020
 BC0  C11  C   CR6   0   0.106   4.1601   0.6029   0.0297
 BC0  C12  C   CR16  0  -0.288   4.8179   0.4643   1.2483
 BC0  C14  C   CR6   0  -0.051   6.8919   0.1175   0.1133
 BC0  C16  C   CR16  0  -0.291   4.8950   0.4861  -1.1458
 BC0  C18  C   C1    0  -0.202  -3.2528  -4.6667   0.4152
 BC0  C19  C   C2    0  -0.516  -3.7403  -5.6664  -0.3080
 BC0  C2   C   C1    0   0.040  -6.1976   0.6175  -0.1592
 BC0  C3   C   C1    0  -0.519  -5.0839  -0.1071   0.0863
 BC0  C9   C   CR6   0   0.219   0.1723  -0.3833  -0.0297
 BC0  N2   N   N     0  -0.489  -0.6190  -1.4509  -0.0003
 BC0  N4   N   NH1   0  -0.675  -2.7215  -2.3558  -0.0230
 BC0  S1   S   S2    0   0.226  -2.2259   2.6248  -0.1987
 BC0  S2   S   S2    0   0.059   1.8775  -0.7976   0.0244
 BC0  CL   CL  CL    0  -0.128   8.5990  -0.1791   0.1665
 BC0  H1   H   HCH2  0   0.298   2.3404   1.4196   0.8395
 BC0  H2   H   HCH2  0   0.297   2.3849   1.3549  -0.9266
 BC0  H4   H   HCR6  0   0.282   6.8224   0.1630  -2.0342
 BC0  H5   H   HCH2  0   0.263  -1.3294  -3.7677   0.5647
 BC0  H6   H   HCH2  0   0.247  -1.8907  -3.9769  -1.0887
 BC0  H7   H   HCH2  0   0.257  -4.9918   3.6287  -0.6921
 BC0  H8   H   HCH2  0   0.232  -5.2017   3.1541   0.9879
 BC0  H9   H   HCH3  0   0.252  -8.2071   2.0007  -0.9397
 BC0  H10  H   HCH3  0   0.228  -7.7406   3.1420   0.3335
 BC0  H11  H   HCH3  0   0.246  -7.2976   3.4557  -1.3494
 BC0  H12  H   HCR6  0   0.268   4.2621   0.5509   2.1741
 BC0  H13  H   HCR6  0   0.267   4.3999   0.5903  -2.1036
 BC0  H14  H   H     0   0.258  -3.6008  -4.5112   1.4320
 BC0  H15  H   H     0   0.244  -3.4154  -5.8447  -1.3263
 BC0  H16  H   H     0   0.246  -4.4778  -6.3475   0.0956
 BC0  H17  H   H     0   0.282  -7.1709   0.1440  -0.1839
 BC0  H18  H   H     0   0.236  -5.1834  -1.1555   0.3167
 BC0  H19  H   HNH1  0   0.407  -3.6853  -2.2329  -0.2835
 BC0  H3   H   HCR6  0   0.281   6.6835   0.1211   2.2525

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
 BC0  C1   N1   single    1.442  0.020  1.442
 BC0  C20  N1   single    1.453  0.020  1.453
 BC0  C20  C5   single    1.494  0.020  1.494
 BC0  N1   C2   single    1.359  0.020  1.359
 BC0  C2   C3   double    1.351  0.020  1.351
 BC0  C5   S1   aromatic  1.730  0.020  1.730
 BC0  C5   C4   aromatic  1.363  0.020  1.363
 BC0  S1   C6   aromatic  1.728  0.020  1.728
 BC0  C3   C4   single    1.448  0.020  1.448
 BC0  C4   C7   aromatic  1.440  0.020  1.440
 BC0  C6   C7   aromatic  1.392  0.020  1.392
 BC0  C6   N3   aromatic  1.334  0.020  1.334
 BC0  C7   C8   aromatic  1.424  0.020  1.424
 BC0  N3   C9   aromatic  1.313  0.020  1.313
 BC0  C8   N4   single    1.341  0.020  1.341
 BC0  C8   N2   aromatic  1.329  0.020  1.329
 BC0  N4   C17  single    1.451  0.020  1.451
 BC0  C9   N2   aromatic  1.329  0.020  1.329
 BC0  C9   S2   single    1.756  0.020  1.756
 BC0  C10  S2   single    1.822  0.020  1.822
 BC0  C10  C11  single    1.499  0.020  1.499
 BC0  C18  C17  single    1.496  0.020  1.496
 BC0  C18  C19  double    1.327  0.020  1.327
 BC0  C11  C16  aromatic  1.391  0.020  1.391
 BC0  C11  C12  aromatic  1.392  0.020  1.392
 BC0  C16  C15  aromatic  1.387  0.020  1.387
 BC0  C12  C13  aromatic  1.386  0.020  1.386
 BC0  C15  C14  aromatic  1.386  0.020  1.386
 BC0  C13  C14  aromatic  1.386  0.020  1.386
 BC0  C14  CL   single    1.733  0.020  1.733
 BC0  C10  H1   single    0.970  0.020  1.090
 BC0  C10  H2   single    0.970  0.020  1.090
 BC0  C13  H3   single    0.930  0.020  1.080
 BC0  C15  H4   single    0.930  0.020  1.080
 BC0  C17  H5   single    0.970  0.020  1.090
 BC0  C17  H6   single    0.970  0.020  1.090
 BC0  C20  H7   single    0.970  0.020  1.090
 BC0  C20  H8   single    0.970  0.020  1.090
 BC0  C1   H9   single    0.970  0.020  1.090
 BC0  C1   H10  single    0.970  0.020  1.090
 BC0  C1   H11  single    0.970  0.020  1.090
 BC0  C12  H12  single    0.930  0.020  1.080
 BC0  C16  H13  single    0.930  0.020  1.080
 BC0  C18  H14  single    0.930  0.020  1.080
 BC0  C19  H15  single    0.930  0.020  1.080
 BC0  C19  H16  single    0.930  0.020  1.080
 BC0  C2   H17  single    0.930  0.020  1.080
 BC0  C3   H18  single    0.930  0.020  1.080
 BC0  N4   H19  single    0.860  0.020  1.020

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
 BC0  C2   N1   C1   120.29  3.000
 BC0  C2   N1   C20  119.69  3.000
 BC0  C1   N1   C20  114.67  3.000
 BC0  C9   N3   C6   113.39  3.000
 BC0  C3   C4   C7   130.64  3.000
 BC0  C7   C4   C5   111.12  3.000
 BC0  C3   C4   C5   118.23  3.000
 BC0  S1   C5   C20  122.82  3.000
 BC0  S1   C5   C4   113.75  3.000
 BC0  C20  C5   C4   123.22  3.000
 BC0  S1   C6   C7   111.76  3.000
 BC0  C7   C6   N3   125.99  3.000
 BC0  S1   C6   N3   122.25  3.000
 BC0  C8   C7   C6   114.37  3.000
 BC0  C8   C7   C4   133.16  3.000
 BC0  C6   C7   C4   112.47  3.000
 BC0  N4   C8   N2   118.03  3.000
 BC0  N2   C8   C7   119.78  3.000
 BC0  N4   C8   C7   122.19  3.000
 BC0  H2   C10  H1   108.54  3.000
 BC0  H2   C10  S2   108.99  3.000
 BC0  H1   C10  S2   108.98  3.000
 BC0  H2   C10  C11  111.56  3.000
 BC0  H1   C10  C11  111.60  3.000
 BC0  S2   C10  C11  107.11  3.000
 BC0  H3   C13  C14  120.63  3.000
 BC0  H3   C13  C12  120.33  3.000
 BC0  C14  C13  C12  119.03  3.000
 BC0  H4   C15  C16  120.35  3.000
 BC0  H4   C15  C14  120.64  3.000
 BC0  C16  C15  C14  119.01  3.000
 BC0  H6   C17  H5   107.16  3.000
 BC0  H6   C17  N4   111.24  3.000
 BC0  H5   C17  N4   108.08  3.000
 BC0  H6   C17  C18  110.69  3.000
 BC0  H5   C17  C18  109.76  3.000
 BC0  N4   C17  C18  109.83  3.000
 BC0  H8   C20  H7   106.25  3.000
 BC0  H8   C20  C5   111.12  3.000
 BC0  H7   C20  C5   111.28  3.000
 BC0  H8   C20  N1   110.95  3.000
 BC0  H7   C20  N1   108.38  3.000
 BC0  C5   C20  N1   108.83  3.000
 BC0  H11  C1   H10  107.96  3.000
 BC0  H11  C1   H9   108.14  3.000
 BC0  H10  C1   H9   108.52  3.000
 BC0  H11  C1   N1   109.88  3.000
 BC0  H10  C1   N1   112.04  3.000
 BC0  H9   C1   N1   110.18  3.000
 BC0  C16  C11  C12  118.80  3.000
 BC0  C12  C11  C10  120.57  3.000
 BC0  C16  C11  C10  120.61  3.000
 BC0  H12  C12  C11  119.85  3.000
 BC0  H12  C12  C13  119.16  3.000
 BC0  C11  C12  C13  120.99  3.000
 BC0  CL   C14  C15  119.45  3.000
 BC0  CL   C14  C13  119.40  3.000
 BC0  C15  C14  C13  121.16  3.000
 BC0  H13  C16  C11  119.84  3.000
 BC0  H13  C16  C15  119.14  3.000
 BC0  C11  C16  C15  121.01  3.000
 BC0  H14  C18  C19  120.04  3.000
 BC0  H14  C18  C17  116.05  3.000
 BC0  C19  C18  C17  123.91  3.000
 BC0  H16  C19  H15  116.83  3.000
 BC0  H16  C19  C18  121.44  3.000
 BC0  H15  C19  C18  121.73  3.000
 BC0  H17  C2   C3   120.71  3.000
 BC0  H17  C2   N1   115.64  3.000
 BC0  C3   C2   N1   123.59  3.000
 BC0  H18  C3   C2   118.96  3.000
 BC0  H18  C3   C4   123.50  3.000
 BC0  C2   C3   C4   117.52  3.000
 BC0  S2   C9   N2   112.83  3.000
 BC0  S2   C9   N3   119.48  3.000
 BC0  N2   C9   N3   127.69  3.000
 BC0  C9   N2   C8   118.66  3.000
 BC0  H19  N4   C17  116.25  3.000
 BC0  H19  N4   C8   117.58  3.000
 BC0  C17  N4   C8   123.47  3.000
 BC0  C6   S1   C5    90.86  3.000
 BC0  C9   S2   C10  102.45  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
 BC0  CONST_01  C5   S1   C6   N3    180.00   0.0  0
 BC0  CONST_02  C4   C7   C6   N3    180.00   0.0  0
 BC0  CONST_03  C8   C7   C6   N3      0.00   0.0  0
 BC0  CONST_04  C8   N2   C9   N3      0.00   0.0  0
 BC0  CONST_05  C6   S1   C5   C4      0.00   0.0  0
 BC0  CONST_06  S1   C6   C7   C4      0.00   0.0  0
 BC0  CONST_07  N2   C8   C7   C4    180.00   0.0  0
 BC0  CONST_08  C7   C6   S1   C5      0.00   0.0  0
 BC0  CONST_09  C6   C7   C4   C5      0.00   0.0  0
 BC0  CONST_10  C8   C7   C4   C5    180.00   0.0  0
 BC0  CONST_11  N2   C8   C7   C6      0.00   0.0  0
 BC0  CONST_12  N2   C9   N3   C6      0.00   0.0  0
 BC0  CONST_13  S1   C5   C4   C7      0.00   0.0  0
 BC0  CONST_14  C9   N3   C6   C7      0.00   0.0  0
 BC0  CONST_15  C9   N2   C8   C7      0.00   0.0  0
 BC0  CONST_16  S1   C6   C7   C8    180.00   0.0  0
 BC0  CONST_17  C16  C11  C12  C13     0.00   0.0  0
 BC0  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 BC0  CONST_19  C12  C11  C16  C15     0.00   0.0  0
 BC0  CONST_20  C12  C13  C14  C15     0.00   0.0  0
 BC0  CONST_21  C14  C15  C16  C11     0.00   0.0  0
 BC0  CONST_22  C14  C13  C12  C11     0.00   0.0  0
 BC0  CONST_23  S1   C6   N3   C9    180.00   0.0  0
 BC0  CONST_24  N4   C8   C7   C4      0.00   0.0  0
 BC0  CONST_25  N4   C8   C7   C6    180.00   0.0  0
 BC0  CONST_26  S2   C9   N3   C6    180.00   0.0  0
 BC0  CONST_27  S2   C9   N2   C8    180.00   0.0  0
 BC0  CONST_28  C15  C16  C11  C10   180.00   0.0  0
 BC0  CONST_29  C13  C12  C11  C10   180.00   0.0  0
 BC0  CONST_30  CL   C14  C13  C12   180.00   0.0  0
 BC0  CONST_31  CL   C14  C15  C16   180.00   0.0  0
 BC0  CONST_32  N4   C8   N2   C9    180.00   0.0  0
 BC0  CONST_33  H4   C15  C14  C13   180.00   0.0  0
 BC0  CONST_34  H3   C13  C14  C15   180.00   0.0  0
 BC0  CONST_35  H13  C16  C11  C12   180.00   0.0  0
 BC0  CONST_36  H12  C12  C13  C14   180.00   0.0  0
 BC0  CONST_37  C17  N4   C8   C7    180.00   0.0  0
 BC0  CONST_38  N2   C8   N4   C17     0.00   0.0  0
 BC0  Var_01    S1   C5   C20  N1    159.85  30.0  1
 BC0  Var_02    C4   C3   C2   N1     -2.06  30.0  1
 BC0  Var_03    C2   N1   C20  C5     34.21  30.0  1
 BC0  Var_04    C2   C3   C4   C5     10.86  30.0  1
 BC0  Var_05    C3   C2   N1   C20   -22.73  30.0  1
 BC0  Var_06    N2   C9   S2   C10  -179.55  30.0  1
 BC0  Var_07    S2   C10  C11  C12   -86.53  30.0  2
 BC0  Var_08    H9   C1   N1   C20   178.37  30.0  3
 BC0  Var_09    C18  C17  N4   C8    160.01  30.0  3
 BC0  Var_10    N4   C17  C18  C19   121.32  30.0  3
 BC0  Var_11    H15  C19  C18  C17    -1.01   0.0  2

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
 BC0  plan-1  C10  0.020
 BC0  plan-1  C13  0.020
 BC0  plan-1  C15  0.020
 BC0  plan-1  C11  0.020
 BC0  plan-1  C12  0.020
 BC0  plan-1  C14  0.020
 BC0  plan-1  C16  0.020
 BC0  plan-1  CL   0.020
 BC0  plan-1  H4   0.020
 BC0  plan-1  H12  0.020
 BC0  plan-1  H13  0.020
 BC0  plan-1  H3   0.020
 BC0  plan-2  N3   0.020
 BC0  plan-2  C4   0.020
 BC0  plan-2  C5   0.020
 BC0  plan-2  C6   0.020
 BC0  plan-2  C7   0.020
 BC0  plan-2  C8   0.020
 BC0  plan-2  C20  0.020
 BC0  plan-2  C3   0.020
 BC0  plan-2  C9   0.020
 BC0  plan-2  N2   0.020
 BC0  plan-2  N4   0.020
 BC0  plan-2  S1   0.020
 BC0  plan-2  S2   0.020
 BC0  plan-3  C8   0.020
 BC0  plan-3  C17  0.020
 BC0  plan-3  N4   0.020
 BC0  plan-3  H19  0.020
 BC0  plan-4  N1   0.020
 BC0  plan-4  C20  0.020
 BC0  plan-4  C1   0.020
 BC0  plan-4  C2   0.020
 BC0  plan-5  C17  0.020
 BC0  plan-5  C18  0.020
 BC0  plan-5  C19  0.020
 BC0  plan-5  H14  0.020
 BC0  plan-5  H15  0.020
 BC0  plan-5  H16  0.020

