# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 00:04:04 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-chloranyl-6-(phenylmethylsulfanyl)-7~{H}-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1nc(SCc2ccccc2)c3[nH]cnc3n1
#
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
 05Z  05Z  "6-benzylthio-2-chloropurine"  ligand  27  18  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_05Z
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
 05Z  C10  C   CR6   0   0.091  -30.6624   0.0640  27.0348
 05Z  C11  C   CR16  0  -0.280  -29.6420   0.3616  26.1361
 05Z  C12  C   CR16  0  -0.237  -29.8924   1.1547  25.0250
 05Z  C13  C   CR16  0  -0.260  -31.1661   1.6633  24.8060
 05Z  C14  C   CR16  0  -0.238  -32.1878   1.3744  25.7014
 05Z  C15  C   CR16  0  -0.279  -31.9359   0.5810  26.8117
 05Z  C2   C   CR6   0   0.265  -29.5197  -2.8117  31.8053
 05Z  C4   C   CR56  0   0.318  -29.0242  -1.1722  33.1911
 05Z  C5   C   CR56  0   0.285  -29.2460  -0.2441  32.1666
 05Z  C6   C   CR6   0   0.079  -29.6241  -0.7203  30.9153
 05Z  C8   C   CR15  0   0.127  -28.6701   0.7329  34.0195
 05Z  C9   C   CH2   0  -0.624  -30.3871  -0.7798  28.2437
 05Z  N1   N   N     0  -0.408  -29.7565  -2.0299  30.7622
 05Z  N3   N   N     0  -0.394  -29.1603  -2.4889  33.0165
 05Z  N7   N   NR15  0  -0.651  -29.0086   0.9727  32.7360
 05Z  N9   N   N     0  -0.443  -28.6656  -0.5377  34.3367
 05Z  S1   S   S2    0   0.106  -29.9134   0.3625  29.5862
 05Z  H1   H   HCR6  0   0.257  -28.6475  -0.0352  26.3031
 05Z  H2   H   HCR6  0   0.258  -29.0931   1.3746  24.3291
 05Z  H3   H   HCR6  0   0.258  -31.3628   2.2816  23.9397
 05Z  H4   H   HCR6  0   0.258  -33.1828   1.7663  25.5344
 05Z  H5   H   HCR6  0   0.257  -32.7351   0.3559  27.5082
 05Z  H7   H   HCH2  0   0.307  -31.2680  -1.3382  28.5561
 05Z  H8   H   HCH2  0   0.307  -29.5689  -1.4777  28.0734
 05Z  H6   H   HCR5  0   0.304  -28.4311   1.5410  34.6943
 05Z  H9   H   HNR5  0   0.439  -29.0739   1.8838  32.3056
 05Z  CL1  CL  CL    0  -0.099  -29.7209  -4.5058  31.4980

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
 05Z  C13  C12  aromatic  1.389  0.020  1.389
 05Z  C13  C14  aromatic  1.389  0.020  1.389
 05Z  C12  C11  aromatic  1.388  0.020  1.388
 05Z  C14  C15  aromatic  1.388  0.020  1.388
 05Z  C11  C10  aromatic  1.392  0.020  1.392
 05Z  C15  C10  aromatic  1.393  0.020  1.393
 05Z  C10  C9   single    1.500  0.020  1.500
 05Z  C9   S1   single    1.825  0.020  1.825
 05Z  S1   C6   single    1.739  0.020  1.739
 05Z  N1   C6   aromatic  1.325  0.020  1.325
 05Z  N1   C2   aromatic  1.325  0.020  1.325
 05Z  C6   C5   aromatic  1.391  0.020  1.391
 05Z  CL1  C2   single    1.733  0.020  1.733
 05Z  C2   N3   aromatic  1.304  0.020  1.304
 05Z  C5   N7   aromatic  1.364  0.020  1.364
 05Z  C5   C4   aromatic  1.400  0.020  1.400
 05Z  N3   C4   aromatic  1.335  0.020  1.335
 05Z  N7   C8   aromatic  1.349  0.020  1.349
 05Z  C4   N9   aromatic  1.358  0.020  1.358
 05Z  C8   N9   aromatic  1.310  0.020  1.310
 05Z  C11  H1   single    0.930  0.020  1.080
 05Z  C12  H2   single    0.930  0.020  1.080
 05Z  C13  H3   single    0.930  0.020  1.080
 05Z  C14  H4   single    0.930  0.020  1.080
 05Z  C15  H5   single    0.930  0.020  1.080
 05Z  C9   H7   single    0.970  0.020  1.090
 05Z  C9   H8   single    0.970  0.020  1.090
 05Z  C8   H6   single    0.930  0.020  1.080
 05Z  N7   H9   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
 05Z  C9   C10  C15  120.39  3.000
 05Z  C9   C10  C11  120.41  3.000
 05Z  C15  C10  C11  119.19  3.000
 05Z  H1   C11  C12  119.88  3.000
 05Z  H1   C11  C10  119.67  3.000
 05Z  C12  C11  C10  120.45  3.000
 05Z  H2   C12  C13  120.10  3.000
 05Z  H2   C12  C11  119.84  3.000
 05Z  C13  C12  C11  120.06  3.000
 05Z  H3   C13  C14  120.08  3.000
 05Z  H3   C13  C12  120.14  3.000
 05Z  C14  C13  C12  119.79  3.000
 05Z  H4   C14  C15  119.82  3.000
 05Z  H4   C14  C13  120.10  3.000
 05Z  C15  C14  C13  120.08  3.000
 05Z  H5   C15  C14  119.94  3.000
 05Z  H5   C15  C10  119.62  3.000
 05Z  C14  C15  C10  120.43  3.000
 05Z  CL1  C2   N3   116.01  3.000
 05Z  N3   C2   N1   129.38  3.000
 05Z  CL1  C2   N1   114.61  3.000
 05Z  N9   C4   N3   126.73  3.000
 05Z  N9   C4   C5   110.45  3.000
 05Z  N3   C4   C5   122.81  3.000
 05Z  N7   C5   C6   136.72  3.000
 05Z  N7   C5   C4   104.97  3.000
 05Z  C6   C5   C4   118.31  3.000
 05Z  S1   C6   N1   120.70  3.000
 05Z  N1   C6   C5   118.00  3.000
 05Z  S1   C6   C5   121.31  3.000
 05Z  H6   C8   N9   125.04  3.000
 05Z  H6   C8   N7   121.15  3.000
 05Z  N9   C8   N7   113.81  3.000
 05Z  H8   C9   H7   108.91  3.000
 05Z  H8   C9   S1   108.74  3.000
 05Z  H7   C9   S1   108.66  3.000
 05Z  H8   C9   C10  111.87  3.000
 05Z  H7   C9   C10  111.80  3.000
 05Z  S1   C9   C10  106.76  3.000
 05Z  C6   N1   C2   118.32  3.000
 05Z  C4   N3   C2   113.18  3.000
 05Z  H9   N7   C8   125.61  3.000
 05Z  H9   N7   C5   127.99  3.000
 05Z  C8   N7   C5   106.40  3.000
 05Z  C8   N9   C4   104.37  3.000
 05Z  C9   S1   C6   102.46  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
 05Z  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 05Z  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 05Z  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 05Z  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 05Z  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 05Z  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 05Z  CONST_07  C5   C6   N1   C2      0.00   0.0  0
 05Z  CONST_08  C5   C4   N3   C2      0.00   0.0  0
 05Z  CONST_09  N9   C4   N3   C2    180.00   0.0  0
 05Z  CONST_10  N1   C6   C5   C4      0.00   0.0  0
 05Z  CONST_11  C8   N7   C5   C4      0.00   0.0  0
 05Z  CONST_12  N1   C2   N3   C4      0.00   0.0  0
 05Z  CONST_13  N7   C8   N9   C4      0.00   0.0  0
 05Z  CONST_14  N9   C8   N7   C5      0.00   0.0  0
 05Z  CONST_15  C8   N9   C4   C5      0.00   0.0  0
 05Z  CONST_16  N3   C2   N1   C6      0.00   0.0  0
 05Z  CONST_17  C8   N7   C5   C6    180.00   0.0  0
 05Z  CONST_18  N3   C4   C5   C6      0.00   0.0  0
 05Z  CONST_19  N9   C4   C5   C6    180.00   0.0  0
 05Z  CONST_20  N3   C4   N9   C8    180.00   0.0  0
 05Z  CONST_21  N7   C5   C6   N1    180.00   0.0  0
 05Z  CONST_22  N7   C5   C4   N3    180.00   0.0  0
 05Z  CONST_23  N9   C4   C5   N7      0.00   0.0  0
 05Z  CONST_24  C9   C10  C11  C12   180.00   0.0  0
 05Z  CONST_25  C9   C10  C15  C14   180.00   0.0  0
 05Z  CONST_26  S1   C6   N1   C2    180.00   0.0  0
 05Z  CONST_27  S1   C6   C5   C4    180.00   0.0  0
 05Z  CONST_28  CL1  C2   N3   C4    180.00   0.0  0
 05Z  CONST_29  CL1  C2   N1   C6    180.00   0.0  0
 05Z  CONST_30  S1   C6   C5   N7      0.00   0.0  0
 05Z  CONST_31  H2   C12  C11  C10   180.00   0.0  0
 05Z  CONST_32  H4   C14  C15  C10   180.00   0.0  0
 05Z  CONST_33  H3   C13  C12  C11   180.00   0.0  0
 05Z  CONST_34  H5   C15  C10  C11   180.00   0.0  0
 05Z  CONST_35  H4   C14  C13  C12   180.00   0.0  0
 05Z  CONST_36  H1   C11  C12  C13   180.00   0.0  0
 05Z  CONST_37  H5   C15  C14  C13   180.00   0.0  0
 05Z  CONST_38  H2   C12  C13  C14   180.00   0.0  0
 05Z  CONST_39  H3   C13  C14  C15   180.00   0.0  0
 05Z  CONST_40  H1   C11  C10  C15   180.00   0.0  0
 05Z  CONST_41  H9   N7   C5   C4    180.00   0.0  0
 05Z  CONST_42  H6   C8   N9   C4    180.00   0.0  0
 05Z  CONST_43  H6   C8   N7   C5    180.00   0.0  0
 05Z  CONST_44  H9   N7   C5   C6      0.00   0.0  0
 05Z  CONST_45  H9   N7   C8   N9    180.00   0.0  0
 05Z  Var_01    C6   S1   C9   C10   179.97  30.0  3
 05Z  Var_02    S1   C9   C10  C11    90.34  30.0  2
 05Z  Var_03    S1   C9   C10  C15   -88.40  30.0  2
 05Z  Var_04    C9   S1   C6   C5   -179.27  30.0  2
 05Z  Var_05    N1   C6   S1   C9      0.84  30.0  2
 05Z  Var_06    H7   C9   C10  C11  -150.96  30.0  2
 05Z  Var_07    H8   C9   C10  C11   -28.50  30.0  2
 05Z  Var_08    H7   C9   C10  C15    30.30  30.0  2
 05Z  Var_09    H8   C9   C10  C15   152.76  30.0  2
 05Z  Var_10    H7   C9   S1   C6     59.24  30.0  1
 05Z  Var_11    H8   C9   S1   C6    -59.17  30.0  1

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
 05Z  plan-1  C10  0.020
 05Z  plan-1  C11  0.020
 05Z  plan-1  C12  0.020
 05Z  plan-1  C13  0.020
 05Z  plan-1  C14  0.020
 05Z  plan-1  C15  0.020
 05Z  plan-1  C9   0.020
 05Z  plan-1  H1   0.020
 05Z  plan-1  H2   0.020
 05Z  plan-1  H3   0.020
 05Z  plan-1  H4   0.020
 05Z  plan-1  H5   0.020
 05Z  plan-2  C2   0.020
 05Z  plan-2  C4   0.020
 05Z  plan-2  C5   0.020
 05Z  plan-2  C6   0.020
 05Z  plan-2  C8   0.020
 05Z  plan-2  N1   0.020
 05Z  plan-2  N3   0.020
 05Z  plan-2  N7   0.020
 05Z  plan-2  N9   0.020
 05Z  plan-2  S1   0.020
 05Z  plan-2  H6   0.020
 05Z  plan-2  H9   0.020
 05Z  plan-2  CL1  0.020

