# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:07:19 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-azanyl-8-[(4-chlorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(SCc3ccc(Cl)cc3)nc2C(=O)N1
#
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
 5RX  5RX  2-azanyl-8-[(4-chlorophenyl)methylsulfanyl]-1,9-dihydropurin-6-one  ligand  30  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5RX
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
 5RX  C1   C   CR16  0  -0.287  -3.3447  -0.2835   1.1986
 5RX  C2   C   CR16  0  -0.286  -3.3599  -0.2884  -1.1978
 5RX  C3   C   CR16  0  -0.196  -4.7110  -0.0476   1.2161
 5RX  C4   C   CR16  0  -0.196  -4.7261  -0.0522  -1.1992
 5RX  C5   C   CR6   0   0.102  -2.6563  -0.4112  -0.0037
 5RX  C6   C   CR56  0  -0.083   3.1237  -0.5448  -0.0264
 5RX  C7   C   CR6   0  -0.050  -5.3892   0.0659   0.0125
 5RX  C8   C   CR56  0   0.481   3.4702   0.7928  -0.0456
 5RX  C9   C   CR6   0   0.492   4.1596  -1.5192  -0.0106
 5RX  C10  C   CR6   0   0.688   5.6529   0.4443  -0.0399
 5RX  C11  C   CR5   0   0.290   1.2953   0.5154  -0.0395
 5RX  C12  C   CH2   0  -0.620  -1.1764  -0.6425  -0.0124
 5RX  N13  N   N     0  -0.503   4.6935   1.3373  -0.0510
 5RX  N14  N   NR15  0  -0.685   2.2869   1.4615  -0.0534
 5RX  N15  N   NR16  0  -0.722   5.4169  -0.8994  -0.0192
 5RX  N16  N   N     0  -0.443   1.7568  -0.6970  -0.0229
 5RX  O18  O   O     0  -0.477   4.0687  -2.7361   0.0080
 5RX  S19  S   S2    0   0.064  -0.3798   0.9984  -0.0422
 5RX  CL1  CL  CL    0  -0.126  -7.0975   0.3573   0.0229
 5RX  H1   H   HCR6  0   0.269  -2.8124  -0.3758   2.1372
 5RX  H2   H   HCR6  0   0.269  -2.8393  -0.3845  -2.1428
 5RX  H3   H   HCR6  0   0.283  -5.2372   0.0459   2.1563
 5RX  H4   H   HCR6  0   0.283  -5.2640   0.0391  -2.1329
 5RX  H5   H   HCH2  0   0.304  -0.8450  -1.1742   0.8780
 5RX  H6   H   HCH2  0   0.304  -0.8592  -1.2006  -0.8917
 5RX  H7   H   HNR5  0   0.426   2.1726   2.4642  -0.0671
 5RX  H8   H   HNR6  0   0.425   6.2115  -1.5260  -0.0174
 5RX  H10  H   HNH2  0   0.412   7.1231   1.8167   0.0530
 5RX  H11  H   HNH2  0   0.414   7.6782   0.2036   0.1485
 5RX  N17  N   NH2   0  -0.832   6.9344   0.8385  -0.0869

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
 5RX  C12  C5   single    1.498  0.020  1.498
 5RX  C12  S19  single    1.824  0.020  1.824
 5RX  C2   C5   aromatic  1.391  0.020  1.391
 5RX  C2   C4   aromatic  1.387  0.020  1.387
 5RX  C5   C1   aromatic  1.391  0.020  1.391
 5RX  C4   C7   aromatic  1.386  0.020  1.386
 5RX  C1   C3   aromatic  1.387  0.020  1.387
 5RX  C7   C3   aromatic  1.386  0.020  1.386
 5RX  C7   CL1  single    1.733  0.020  1.733
 5RX  O18  C9   double    1.220  0.020  1.220
 5RX  S19  C11  single    1.743  0.020  1.743
 5RX  N16  C11  aromatic  1.297  0.020  1.297
 5RX  N16  C6   aromatic  1.375  0.020  1.375
 5RX  C11  N14  aromatic  1.371  0.020  1.371
 5RX  C9   C6   single    1.422  0.020  1.422
 5RX  C9   N15  single    1.402  0.020  1.402
 5RX  C6   C8   aromatic  1.382  0.020  1.382
 5RX  N14  C8   aromatic  1.359  0.020  1.359
 5RX  N15  C10  single    1.364  0.020  1.364
 5RX  C8   N13  single    1.339  0.020  1.339
 5RX  C10  N13  double    1.311  0.020  1.311
 5RX  C10  N17  single    1.342  0.020  1.342
 5RX  C1   H1   single    0.930  0.020  1.080
 5RX  C2   H2   single    0.930  0.020  1.080
 5RX  C3   H3   single    0.930  0.020  1.080
 5RX  C4   H4   single    0.930  0.020  1.080
 5RX  C12  H5   single    0.970  0.020  1.090
 5RX  C12  H6   single    0.970  0.020  1.090
 5RX  N14  H7   single    0.860  0.020  1.020
 5RX  N15  H8   single    0.860  0.020  1.020
 5RX  N17  H10  single    0.890  0.020  1.040
 5RX  N17  H11  single    0.890  0.020  1.040

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
 5RX  H1   C1   C5   119.86  3.000
 5RX  H1   C1   C3   119.20  3.000
 5RX  C5   C1   C3   120.93  3.000
 5RX  H2   C2   C5   119.86  3.000
 5RX  H2   C2   C4   119.20  3.000
 5RX  C5   C2   C4   120.94  3.000
 5RX  H3   C3   C7   120.64  3.000
 5RX  H3   C3   C1   120.34  3.000
 5RX  C7   C3   C1   119.02  3.000
 5RX  H4   C4   C7   120.63  3.000
 5RX  H4   C4   C2   120.36  3.000
 5RX  C7   C4   C2   119.01  3.000
 5RX  C12  C5   C2   120.54  3.000
 5RX  C2   C5   C1   118.91  3.000
 5RX  C12  C5   C1   120.53  3.000
 5RX  N16  C6   C9   130.39  3.000
 5RX  C9   C6   C8   118.73  3.000
 5RX  N16  C6   C8   110.88  3.000
 5RX  CL1  C7   C4   119.41  3.000
 5RX  CL1  C7   C3   119.40  3.000
 5RX  C4   C7   C3   121.19  3.000
 5RX  N14  C8   N13  126.53  3.000
 5RX  N13  C8   C6   128.51  3.000
 5RX  N14  C8   C6   104.95  3.000
 5RX  O18  C9   N15  120.51  3.000
 5RX  N15  C9   C6   110.51  3.000
 5RX  O18  C9   C6   128.98  3.000
 5RX  N17  C10  N15  117.08  3.000
 5RX  N17  C10  N13  119.91  3.000
 5RX  N15  C10  N13  122.99  3.000
 5RX  S19  C11  N16  126.92  3.000
 5RX  N16  C11  N14  112.82  3.000
 5RX  S19  C11  N14  120.26  3.000
 5RX  H6   C12  H5   108.75  3.000
 5RX  H6   C12  S19  108.71  3.000
 5RX  H5   C12  S19  108.65  3.000
 5RX  H6   C12  C5   111.82  3.000
 5RX  H5   C12  C5   111.80  3.000
 5RX  S19  C12  C5   107.01  3.000
 5RX  C10  N13  C8   113.06  3.000
 5RX  H7   N14  C11  127.16  3.000
 5RX  H7   N14  C8   125.97  3.000
 5RX  C11  N14  C8   106.87  3.000
 5RX  H8   N15  C10  118.30  3.000
 5RX  H8   N15  C9   115.50  3.000
 5RX  C10  N15  C9   126.20  3.000
 5RX  C11  N16  C6   104.48  3.000
 5RX  C12  S19  C11   99.81  3.000
 5RX  H11  N17  H10  116.27  3.000
 5RX  H11  N17  C10  120.84  3.000
 5RX  H10  N17  C10  117.39  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
 5RX  CONST_01  C4   C2   C5   C1     0.00   0.0  0
 5RX  CONST_02  C4   C7   C3   C1     0.00   0.0  0
 5RX  CONST_03  C3   C1   C5   C2     0.00   0.0  0
 5RX  CONST_04  C3   C7   C4   C2     0.00   0.0  0
 5RX  CONST_05  C7   C4   C2   C5     0.00   0.0  0
 5RX  CONST_06  C7   C3   C1   C5     0.00   0.0  0
 5RX  CONST_07  N14  C11  N16  C6     0.00   0.0  0
 5RX  CONST_08  C11  N14  C8   C6     0.00   0.0  0
 5RX  CONST_09  C11  N16  C6   C8     0.00   0.0  0
 5RX  CONST_10  N16  C11  N14  C8     0.00   0.0  0
 5RX  CONST_11  N16  C6   C8   N14    0.00   0.0  0
 5RX  CONST_12  C10  N15  C9   C6     0.00   0.0  0
 5RX  CONST_13  N15  C10  N13  C8     0.00   0.0  0
 5RX  CONST_14  N13  C10  N15  C9     0.00   0.0  0
 5RX  CONST_15  CL1  C7   C3   C1   180.00   0.0  0
 5RX  CONST_16  CL1  C7   C4   C2   180.00   0.0  0
 5RX  CONST_17  C12  C5   C1   C3   180.00   0.0  0
 5RX  CONST_18  C12  C5   C2   C4   180.00   0.0  0
 5RX  CONST_19  S19  C11  N16  C6   180.00   0.0  0
 5RX  CONST_20  S19  C11  N14  C8   180.00   0.0  0
 5RX  CONST_21  N17  C10  N13  C8   180.00   0.0  0
 5RX  CONST_22  N17  C10  N15  C9   180.00   0.0  0
 5RX  CONST_23  O18  C9   N15  C10  180.00   0.0  0
 5RX  CONST_24  H2   C2   C5   C1   180.00   0.0  0
 5RX  CONST_25  H1   C1   C5   C2   180.00   0.0  0
 5RX  CONST_26  H4   C4   C7   C3   180.00   0.0  0
 5RX  CONST_27  H3   C3   C7   C4   180.00   0.0  0
 5RX  CONST_28  H7   N14  C8   C6   180.00   0.0  0
 5RX  CONST_29  H8   N15  C9   C6   180.00   0.0  0
 5RX  CONST_30  H10  N17  C10  N13    0.00   0.0  0
 5RX  Var_01    S19  C12  C5   C1   -89.93  30.0  3
 5RX  Var_02    N16  C11  S19  C12    0.12  30.0  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
 5RX  plan-1  C1   0.020
 5RX  plan-1  C2   0.020
 5RX  plan-1  C3   0.020
 5RX  plan-1  C4   0.020
 5RX  plan-1  C5   0.020
 5RX  plan-1  C7   0.020
 5RX  plan-1  C12  0.020
 5RX  plan-1  CL1  0.020
 5RX  plan-1  H1   0.020
 5RX  plan-1  H2   0.020
 5RX  plan-1  H3   0.020
 5RX  plan-1  H4   0.020
 5RX  plan-2  C6   0.020
 5RX  plan-2  C8   0.020
 5RX  plan-2  C9   0.020
 5RX  plan-2  C10  0.020
 5RX  plan-2  C11  0.020
 5RX  plan-2  N13  0.020
 5RX  plan-2  N14  0.020
 5RX  plan-2  N15  0.020
 5RX  plan-2  N16  0.020
 5RX  plan-2  O18  0.020
 5RX  plan-2  S19  0.020
 5RX  plan-2  H7   0.020
 5RX  plan-2  H8   0.020
 5RX  plan-2  H10  0.020
 5RX  plan-2  H11  0.020
 5RX  plan-2  N17  0.020

