# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:34:37 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: ~{S}-[4-(6-aminopurin-9-yl)butyl] ethanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)SCCCCn1cnc2c(N)ncnc12
#
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
 JYQ  JYQ  '~{S}-[4-(6-aminopurin-9-yl)butyl] ethanethioate'  ligand  33  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JYQ
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
 JYQ  C5   C  CR56  0  -0.003   3.7556   0.3868   0.2895
 JYQ  C8   C  CR15  0   0.108   2.4611   2.0500   0.2928
 JYQ  C2   C  CR16  0   0.038   3.4433  -2.0035  -0.8055
 JYQ  N3   N  N     0  -0.456   2.4247  -1.1850  -0.9976
 JYQ  N7   N  N     0  -0.455   3.6286   1.6773   0.7332
 JYQ  C4   C  CR56  0   0.479   2.6320   0.0009  -0.4271
 JYQ  C6   C  CR6   0   0.449   4.7692  -0.5795   0.4235
 JYQ  CAA  C  CH3   0  -0.750  -7.1256  -0.6533   0.2182
 JYQ  CAF  C  CH2   0  -0.437  -1.9581   0.6203  -0.6942
 JYQ  CAG  C  CH2   0  -0.431  -0.5785   0.5954  -0.0476
 JYQ  CAH  C  CH2   0  -0.556  -3.0215   0.1088   0.2674
 JYQ  CAN  C  C     0   0.259  -5.7041  -0.5084   0.6818
 JYQ  N1   N  N     0  -0.474   4.5748  -1.7755  -0.1416
 JYQ  N9   N  NR5   0  -0.497   1.8106   1.0870  -0.4215
 JYQ  OAC  O  O     0  -0.392  -5.3141  -0.8258   1.7772
 JYQ  SAM  S  S2    0  -0.002  -4.6348   0.1399  -0.5642
 JYQ  H1   H  HCR5  0   0.292   2.0166   3.0219   0.4509
 JYQ  H2   H  HCR6  0   0.250   3.3510  -2.9924  -1.2423
 JYQ  H3   H  HNH2  0   0.401   6.5509  -1.0992   1.2497
 JYQ  H4   H  HNH2  0   0.409   6.0307   0.5016   1.6065
 JYQ  H5   H  HCH3  0   0.262  -7.3751   0.0289  -0.5924
 JYQ  H6   H  HCH3  0   0.285  -7.2719  -1.6725  -0.1451
 JYQ  H7   H  HCH3  0   0.276  -7.8078  -0.4915   1.0509
 JYQ  H8   H  HCH2  0   0.244  -2.2009   1.6398  -1.0064
 JYQ  H9   H  HCH2  0   0.244  -1.9490   0.0045  -1.5976
 JYQ  H10  H  HCH2  0   0.240  -0.5875   1.1808   0.8758
 JYQ  H11  H  HCH2  0   0.244  -0.3141  -0.4297   0.2252
 JYQ  H12  H  HCH2  0   0.280  -2.8029  -0.9129   0.5786
 JYQ  H13  H  HCH2  0   0.280  -3.0741   0.7377   1.1564
 JYQ  H14  H  HCH2  0   0.266   0.4865   0.6156  -1.9311
 JYQ  H15  H  HCH2  0   0.273   0.2701   2.2055  -1.2170
 JYQ  N6   N  NH2   0  -0.817   5.9135  -0.3417   1.0723
 JYQ  CAI  C  CH2   0  -0.306   0.4786   1.1605  -0.9868

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
 JYQ  OAC  CAN  double    1.205  0.020  1.205
 JYQ  CAN  SAM  single    1.765  0.020  1.765
 JYQ  CAN  CAA  single    1.502  0.020  1.502
 JYQ  SAM  CAH  single    1.815  0.020  1.815
 JYQ  N6   C6   single    1.337  0.020  1.337
 JYQ  CAH  CAF  single    1.522  0.020  1.522
 JYQ  C6   N1   aromatic  1.337  0.020  1.337
 JYQ  C6   C5   aromatic  1.407  0.020  1.407
 JYQ  CAF  CAG  single    1.524  0.020  1.524
 JYQ  N1   C2   aromatic  1.332  0.020  1.332
 JYQ  N7   C5   aromatic  1.370  0.020  1.370
 JYQ  N7   C8   aromatic  1.302  0.020  1.302
 JYQ  C5   C4   aromatic  1.387  0.020  1.387
 JYQ  C2   N3   aromatic  1.321  0.020  1.321
 JYQ  C8   N9   aromatic  1.364  0.020  1.364
 JYQ  C4   N3   aromatic  1.332  0.020  1.332
 JYQ  C4   N9   aromatic  1.362  0.020  1.362
 JYQ  N9   CAI  single    1.449  0.020  1.449
 JYQ  CAG  CAI  single    1.523  0.020  1.523
 JYQ  C8   H1   single    0.930  0.020  1.080
 JYQ  C2   H2   single    0.930  0.020  1.080
 JYQ  N6   H3   single    0.860  0.020  1.020
 JYQ  N6   H4   single    0.860  0.020  1.020
 JYQ  CAA  H5   single    0.970  0.020  1.090
 JYQ  CAA  H6   single    0.970  0.020  1.090
 JYQ  CAA  H7   single    0.970  0.020  1.090
 JYQ  CAF  H8   single    0.970  0.020  1.090
 JYQ  CAF  H9   single    0.970  0.020  1.090
 JYQ  CAG  H10  single    0.970  0.020  1.090
 JYQ  CAG  H11  single    0.970  0.020  1.090
 JYQ  CAH  H12  single    0.970  0.020  1.090
 JYQ  CAH  H13  single    0.970  0.020  1.090
 JYQ  CAI  H14  single    0.970  0.020  1.090
 JYQ  CAI  H15  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
 JYQ  C6   C5   C4   116.21  3.000
 JYQ  C4   C5   N7   110.74  3.000
 JYQ  C6   C5   N7   133.05  3.000
 JYQ  H1   C8   N9   121.03  3.000
 JYQ  H1   C8   N7   125.23  3.000
 JYQ  N9   C8   N7   113.74  3.000
 JYQ  H2   C2   N1   115.41  3.000
 JYQ  H2   C2   N3   116.15  3.000
 JYQ  N1   C2   N3   128.44  3.000
 JYQ  C4   N3   C2   111.68  3.000
 JYQ  C8   N7   C5   104.07  3.000
 JYQ  N9   C4   N3   128.17  3.000
 JYQ  N9   C4   C5   105.34  3.000
 JYQ  N3   C4   C5   126.50  3.000
 JYQ  N1   C6   N6   119.26  3.000
 JYQ  N1   C6   C5   118.00  3.000
 JYQ  N6   C6   C5   122.73  3.000
 JYQ  H7   CAA  H6   108.02  3.000
 JYQ  H7   CAA  H5   109.43  3.000
 JYQ  H6   CAA  H5   107.86  3.000
 JYQ  H7   CAA  CAN  110.04  3.000
 JYQ  H6   CAA  CAN  108.64  3.000
 JYQ  H5   CAA  CAN  112.73  3.000
 JYQ  H9   CAF  H8   106.91  3.000
 JYQ  H9   CAF  CAH  109.79  3.000
 JYQ  H8   CAF  CAH  109.79  3.000
 JYQ  H9   CAF  CAG  109.51  3.000
 JYQ  H8   CAF  CAG  109.72  3.000
 JYQ  CAH  CAF  CAG  111.04  3.000
 JYQ  H11  CAG  H10  107.06  3.000
 JYQ  H11  CAG  CAI  109.51  3.000
 JYQ  H10  CAG  CAI  109.14  3.000
 JYQ  H11  CAG  CAF  109.89  3.000
 JYQ  H10  CAG  CAF  110.01  3.000
 JYQ  CAI  CAG  CAF  111.14  3.000
 JYQ  H13  CAH  H12  108.51  3.000
 JYQ  H13  CAH  SAM  108.71  3.000
 JYQ  H12  CAH  SAM  108.97  3.000
 JYQ  H13  CAH  CAF  110.80  3.000
 JYQ  H12  CAH  CAF  110.80  3.000
 JYQ  SAM  CAH  CAF  109.01  3.000
 JYQ  SAM  CAN  OAC  122.83  3.000
 JYQ  SAM  CAN  CAA  113.00  3.000
 JYQ  OAC  CAN  CAA  124.15  3.000
 JYQ  C6   N1   C2   119.18  3.000
 JYQ  CAI  N9   C4   126.40  3.000
 JYQ  CAI  N9   C8   127.37  3.000
 JYQ  C4   N9   C8   106.12  3.000
 JYQ  CAN  SAM  CAH  102.05  3.000
 JYQ  H4   N6   H3   117.66  3.000
 JYQ  H4   N6   C6   120.47  3.000
 JYQ  H3   N6   C6   119.61  3.000
 JYQ  H15  CAI  H14  107.31  3.000
 JYQ  H15  CAI  N9   107.87  3.000
 JYQ  H14  CAI  N9   107.81  3.000
 JYQ  H15  CAI  CAG  110.68  3.000
 JYQ  H14  CAI  CAG  110.72  3.000
 JYQ  N9   CAI  CAG  112.25  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
 JYQ  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 JYQ  CONST_02  N9   C8   N7   C5      0.00   0.0  0
 JYQ  CONST_03  C2   N3   C4   C5      0.00   0.0  0
 JYQ  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 JYQ  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 JYQ  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 JYQ  CONST_07  N3   C4   N9   C8    180.00   0.0  0
 JYQ  CONST_08  N9   C4   N3   C2    180.00   0.0  0
 JYQ  CONST_09  C6   N1   C2   N3      0.00   0.0  0
 JYQ  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 JYQ  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 JYQ  CONST_12  N1   C6   C5   N7    180.00   0.0  0
 JYQ  CONST_13  N9   C4   C5   N7      0.00   0.0  0
 JYQ  CONST_14  C4   N9   C8   N7      0.00   0.0  0
 JYQ  CONST_15  N1   C6   C5   C4      0.00   0.0  0
 JYQ  CONST_16  N1   C2   N3   C4      0.00   0.0  0
 JYQ  CONST_17  N9   C4   C5   C6    180.00   0.0  0
 JYQ  CONST_18  CAI  N9   C4   C5    180.00   0.0  0
 JYQ  CONST_19  N6   C6   N1   C2    180.00   0.0  0
 JYQ  CONST_20  CAI  N9   C4   N3      0.00   0.0  0
 JYQ  CONST_21  N7   C5   C6   N6      0.00   0.0  0
 JYQ  CONST_22  C4   C5   C6   N6    180.00   0.0  0
 JYQ  CONST_23  CAI  N9   C8   N7    180.00   0.0  0
 JYQ  CONST_24  H1   C8   N7   C5    180.00   0.0  0
 JYQ  CONST_25  H2   C2   N3   C4    180.00   0.0  0
 JYQ  CONST_26  H3   N6   C6   C5    180.00   0.0  0
 JYQ  CONST_27  H4   N6   C6   C5      0.00   0.0  0
 JYQ  Var_01    CAG  CAI  N9   C8    -93.13  30.0  2
 JYQ  Var_02    N9   CAI  CAG  CAF  -177.13  30.0  3
 JYQ  Var_03    SAM  CAH  CAF  CAG  -179.21  30.0  1
 JYQ  Var_04    OAC  CAN  SAM  CAH     1.21  30.0  1
 JYQ  Var_05    CAI  CAG  CAF  CAH  -177.64  30.0  3
 JYQ  Var_06    H5   CAA  CAN  OAC   156.33  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
 JYQ  plan-1  C5   0.020
 JYQ  plan-1  C8   0.020
 JYQ  plan-1  C2   0.020
 JYQ  plan-1  N3   0.020
 JYQ  plan-1  N7   0.020
 JYQ  plan-1  C4   0.020
 JYQ  plan-1  C6   0.020
 JYQ  plan-1  N1   0.020
 JYQ  plan-1  N9   0.020
 JYQ  plan-1  H1   0.020
 JYQ  plan-1  H2   0.020
 JYQ  plan-1  N6   0.020
 JYQ  plan-1  CAI  0.020
 JYQ  plan-2  C6   0.020
 JYQ  plan-2  H3   0.020
 JYQ  plan-2  H4   0.020
 JYQ  plan-2  N6   0.020
 JYQ  plan-3  CAA  0.020
 JYQ  plan-3  CAN  0.020
 JYQ  plan-3  OAC  0.020
 JYQ  plan-3  SAM  0.020

