# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 13:54:49 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: ~{N},~{N},5,6-tetramethylthieno[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ncnc2sc(C)c(C)c12
#
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
 GV1  GV1  ~{N},~{N},5,6-tetramethylthieno[2,3-d]pyrimidin-4-amine  ligand  27  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GV1
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
 GV1  N1   N  N     0  -0.450  -1.9115   1.4068  -0.6772
 GV1  N3   N  NT    0  -0.469  -2.3334  -0.8261  -0.2405
 GV1  C4   C  CR56  0  -0.026   0.6553   1.2507  -0.0182
 GV1  C5   C  CR56  0   0.038  -0.0587   0.0494  -0.0735
 GV1  C6   C  CR6   0   0.465  -1.4456   0.2136  -0.3264
 GV1  C7   C  CR16  0   0.036  -1.0953   2.4542  -0.6476
 GV1  C8   C  CH3   0  -0.561  -2.4271  -1.5305   1.0299
 GV1  C10  C  CH3   0  -0.728   3.2716  -1.6356   0.4934
 GV1  C1   C  CH3   0  -0.747   0.4135  -2.5296  -0.1922
 GV1  C2   C  CR5   0   0.144   0.7957  -1.1061   0.0731
 GV1  C3   C  CR5   0  -0.233   2.0844  -0.7444   0.3178
 GV1  S1   S  S2    0   0.209   2.3184   0.9781   0.3461
 GV1  N2   N  N     0  -0.422   0.1671   2.4614  -0.2747
 GV1  C9   C  CH3   0  -0.527  -3.6269  -0.6584  -0.8723
 GV1  H1   H  HCR6  0   0.257  -1.5250   3.4064  -0.9388
 GV1  H2   H  HCH3  0   0.247  -3.2076  -1.0841   1.6558
 GV1  H3   H  HCH3  0   0.249  -2.6791  -2.5787   0.8697
 GV1  H4   H  HCH3  0   0.259  -1.4958  -1.4788   1.5874
 GV1  H5   H  HCH3  0   0.258   4.1752  -1.0688   0.7115
 GV1  H6   H  HCH3  0   0.261   3.1196  -2.3387   1.3129
 GV1  H7   H  HCH3  0   0.261   3.4625  -2.2174  -0.4096
 GV1  H8   H  HCH3  0   0.251   0.2018  -2.6729  -1.2537
 GV1  H9   H  HCH3  0   0.254   1.2261  -3.2037   0.0718
 GV1  H10  H  HCH3  0   0.259  -0.4641  -2.8597   0.3548
 GV1  H11  H  HCH3  0   0.223  -4.2955   0.0024  -0.3110
 GV1  H12  H  HCH3  0   0.249  -3.5158  -0.2626  -1.8788
 GV1  H13  H  HCH3  0   0.242  -4.0985  -1.6385  -0.9413

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
 GV1  C10  C3   single    1.495  0.020  1.495
 GV1  C3   S1   aromatic  1.739  0.020  1.739
 GV1  C3   C2   aromatic  1.361  0.020  1.361
 GV1  S1   C4   aromatic  1.724  0.020  1.724
 GV1  C2   C1   single    1.498  0.020  1.498
 GV1  C2   C5   aromatic  1.445  0.020  1.445
 GV1  C4   C5   aromatic  1.399  0.020  1.399
 GV1  C4   N2   aromatic  1.330  0.020  1.330
 GV1  C5   C6   aromatic  1.419  0.020  1.419
 GV1  N2   C7   aromatic  1.316  0.020  1.316
 GV1  C6   N3   single    1.370  0.020  1.370
 GV1  C6   N1   aromatic  1.328  0.020  1.328
 GV1  C7   N1   aromatic  1.328  0.020  1.328
 GV1  C9   N3   single    1.449  0.020  1.449
 GV1  N3   C8   single    1.456  0.020  1.456
 GV1  C7   H1   single    0.930  0.020  1.080
 GV1  C8   H2   single    0.970  0.020  1.090
 GV1  C8   H3   single    0.970  0.020  1.090
 GV1  C8   H4   single    0.970  0.020  1.090
 GV1  C10  H5   single    0.970  0.020  1.090
 GV1  C10  H6   single    0.970  0.020  1.090
 GV1  C10  H7   single    0.970  0.020  1.090
 GV1  C1   H8   single    0.970  0.020  1.090
 GV1  C1   H9   single    0.970  0.020  1.090
 GV1  C1   H10  single    0.970  0.020  1.090
 GV1  C9   H11  single    0.970  0.020  1.090
 GV1  C9   H12  single    0.970  0.020  1.090
 GV1  C9   H13  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
 GV1  C7   N1   C6   119.15  3.000
 GV1  C9   N3   C8   112.27  3.000
 GV1  C8   N3   C6   117.62  3.000
 GV1  C9   N3   C6   117.59  3.000
 GV1  N2   C4   S1   122.59  3.000
 GV1  N2   C4   C5   125.93  3.000
 GV1  S1   C4   C5   111.41  3.000
 GV1  C2   C5   C6   133.52  3.000
 GV1  C6   C5   C4   113.99  3.000
 GV1  C2   C5   C4   112.40  3.000
 GV1  C5   C6   N3   122.29  3.000
 GV1  N3   C6   N1   118.11  3.000
 GV1  C5   C6   N1   119.59  3.000
 GV1  H1   C7   N2   116.82  3.000
 GV1  H1   C7   N1   116.29  3.000
 GV1  N2   C7   N1   126.87  3.000
 GV1  H4   C8   H3   108.63  3.000
 GV1  H4   C8   H2   107.35  3.000
 GV1  H3   C8   H2   108.13  3.000
 GV1  H4   C8   N3   111.69  3.000
 GV1  H3   C8   N3   110.61  3.000
 GV1  H2   C8   N3   110.32  3.000
 GV1  H7   C10  H6   107.61  3.000
 GV1  H7   C10  H5   107.35  3.000
 GV1  H6   C10  H5   107.50  3.000
 GV1  H7   C10  C3   111.08  3.000
 GV1  H6   C10  C3   111.22  3.000
 GV1  H5   C10  C3   111.86  3.000
 GV1  H10  C1   H9   107.04  3.000
 GV1  H10  C1   H8   107.06  3.000
 GV1  H9   C1   H8   107.42  3.000
 GV1  H10  C1   C2   113.96  3.000
 GV1  H9   C1   C2   110.81  3.000
 GV1  H8   C1   C2   110.27  3.000
 GV1  C3   C2   C1   121.75  3.000
 GV1  C1   C2   C5   126.26  3.000
 GV1  C3   C2   C5   111.46  3.000
 GV1  S1   C3   C2   113.19  3.000
 GV1  C2   C3   C10  127.94  3.000
 GV1  S1   C3   C10  118.81  3.000
 GV1  C3   S1   C4    91.34  3.000
 GV1  C7   N2   C4   113.67  3.000
 GV1  H13  C9   H12  108.23  3.000
 GV1  H13  C9   H11  108.12  3.000
 GV1  H12  C9   H11  108.50  3.000
 GV1  H13  C9   N3   108.05  3.000
 GV1  H12  C9   N3   110.76  3.000
 GV1  H11  C9   N3   113.05  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
 GV1  CONST_01  C2   C5   C6  N1   180.00   0.0  0
 GV1  CONST_02  C4   C5   C6  N1     0.00   0.0  0
 GV1  CONST_03  C4   N2   C7  N1     0.00   0.0  0
 GV1  CONST_04  C2   C3   S1  C4     0.00   0.0  0
 GV1  CONST_05  C3   C2   C5  C4     0.00   0.0  0
 GV1  CONST_06  S1   C3   C2  C5     0.00   0.0  0
 GV1  CONST_07  C3   S1   C4  C5     0.00   0.0  0
 GV1  CONST_08  C7   N2   C4  C5     0.00   0.0  0
 GV1  CONST_09  C7   N1   C6  C5     0.00   0.0  0
 GV1  CONST_10  C3   C2   C5  C6   180.00   0.0  0
 GV1  CONST_11  S1   C4   C5  C6   180.00   0.0  0
 GV1  CONST_12  N2   C4   C5  C6     0.00   0.0  0
 GV1  CONST_13  N2   C7   N1  C6     0.00   0.0  0
 GV1  CONST_14  S1   C4   N2  C7   180.00   0.0  0
 GV1  CONST_15  S1   C4   C5  C2     0.00   0.0  0
 GV1  CONST_16  N2   C4   C5  C2   180.00   0.0  0
 GV1  CONST_17  N2   C4   S1  C3   180.00   0.0  0
 GV1  CONST_18  C2   C5   C6  N3     0.00   0.0  0
 GV1  CONST_19  C4   C5   C6  N3   180.00   0.0  0
 GV1  CONST_20  C7   N1   C6  N3   180.00   0.0  0
 GV1  CONST_21  C10  C3   S1  C4   180.00   0.0  0
 GV1  CONST_22  C1   C2   C5  C4   180.00   0.0  0
 GV1  CONST_23  C10  C3   C2  C5   180.00   0.0  0
 GV1  CONST_24  C1   C2   C5  C6     0.00   0.0  0
 GV1  CONST_25  S1   C3   C2  C1   180.00   0.0  0
 GV1  CONST_26  H1   C7   N2  C4   180.00   0.0  0
 GV1  Var_01    H8   C1   C2  C5    65.54  30.0  2
 GV1  Var_02    H5   C10  C3  C2  -178.11  30.0  2
 GV1  Var_03    H11  C9   N3  C6   -74.96  30.0  3
 GV1  Var_04    H2   C8   N3  C6    91.87  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
 GV1  plan-1  N1   0.020
 GV1  plan-1  N3   0.020
 GV1  plan-1  C4   0.020
 GV1  plan-1  C5   0.020
 GV1  plan-1  C6   0.020
 GV1  plan-1  C7   0.020
 GV1  plan-1  C10  0.020
 GV1  plan-1  C1   0.020
 GV1  plan-1  C2   0.020
 GV1  plan-1  C3   0.020
 GV1  plan-1  S1   0.020
 GV1  plan-1  N2   0.020
 GV1  plan-1  H1   0.020
 GV1  plan-2  N3   0.020
 GV1  plan-2  C6   0.020
 GV1  plan-2  C8   0.020
 GV1  plan-2  C9   0.020

