# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:02:01 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-[(2-azanyl-6-oxidanylidene-1,9-dihydropurin-8-yl)sulfanylmethyl]-3-fluoranyl-benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]c(SCc3ccc(cc3F)C#N)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
 5RY  5RY  4-[(2-azanyl-6-oxidanylidene-1,9-dihydropurin-8-yl)sulfanylmethyl]-3-fluoranyl-benzenecarbonitrile  ligand  31  22  .  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_5RY
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
 5RY  C1   C  CSP   0   0.065   6.8617   0.2419   0.1947
 5RY  C2   C  CR16  0  -0.235   4.7823  -0.0123   1.4467
 5RY  C3   C  CR16  0  -0.253   3.4137  -0.2160   1.4602
 5RY  C4   C  CR16  0  -0.388   4.7566  -0.1092  -0.9753
 5RY  C5   C  CR6   0   0.011   5.4489   0.0383   0.2247
 5RY  C6   C  CR6   0  -0.093   2.6934  -0.3725   0.2800
 5RY  C7   C  CR56  0  -0.085  -3.0701  -0.5064   0.1090
 5RY  C8   C  CR6   0   0.568   3.3949  -0.3068  -0.9172
 5RY  C9   C  CR56  0   0.483  -3.4160   0.8184  -0.0812
 5RY  C10  C  CR6   0   0.493  -4.1064  -1.4743   0.2165
 5RY  C11  C  CR6   0   0.701  -5.5991   0.4685  -0.0810
 5RY  C12  C  CR5   0   0.292  -1.2426   0.5491   0.0094
 5RY  C13  C  CH2   0  -0.616   1.2130  -0.5844   0.3017
 5RY  N14  N  NS    0  -0.242   8.0015   0.4056   0.1731
 5RY  N15  N  N     0  -0.507  -4.6374   1.3561  -0.1807
 5RY  N16  N  NR15  0  -0.686  -2.2324   1.4843  -0.1441
 5RY  N17  N  NR16  0  -0.725  -5.3632  -0.8635   0.1046
 5RY  N18  N  N     0  -0.442  -1.7033  -0.6534   0.1621
 5RY  O20  O  O     0  -0.477  -4.0166  -2.6802   0.3816
 5RY  F21  F  F     0  -0.294   2.7197  -0.4444  -2.0619
 5RY  S22  S  S2    0   0.073   0.4320   1.0336  -0.0080
 5RY  H1   H  HCR6  0   0.290   5.3270   0.1058   2.3726
 5RY  H2   H  HCR6  0   0.288   2.8900  -0.2599   2.4062
 5RY  H3   H  HCR6  0   0.307   5.2675  -0.0692  -1.9282
 5RY  H4   H  HCH2  0   0.314   0.8839  -1.2898  -0.4590
 5RY  H5   H  HCH2  0   0.314   0.8929  -0.9511   1.2754
 5RY  H6   H  HNR5  0   0.426  -2.1173   2.4799  -0.2648
 5RY  H7   H  HNR6  0   0.423  -6.1564  -1.4886   0.1698
 5RY  H9   H  HNH2  0   0.417  -7.6455   0.2240  -0.0494
 5RY  H10  H  HNH2  0   0.416  -7.0797   1.8345  -0.2773
 5RY  N19  N  NH2   0  -0.836  -6.8742   0.8569  -0.1675

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
 5RY  N19  C11  single    1.336  0.020  1.336
 5RY  N15  C11  double    1.313  0.020  1.313
 5RY  N15  C9   single    1.338  0.020  1.338
 5RY  C11  N17  single    1.365  0.020  1.365
 5RY  C9   N16  aromatic  1.359  0.020  1.359
 5RY  C9   C7   aromatic  1.382  0.020  1.382
 5RY  N16  C12  aromatic  1.370  0.020  1.370
 5RY  N17  C10  single    1.402  0.020  1.402
 5RY  N14  C1   triple    1.152  0.020  1.152
 5RY  C7   C10  single    1.422  0.020  1.422
 5RY  C7   N18  aromatic  1.376  0.020  1.376
 5RY  C10  O20  double    1.220  0.020  1.220
 5RY  C1   C5   single    1.428  0.020  1.428
 5RY  C12  N18  aromatic  1.297  0.020  1.297
 5RY  C12  S22  single    1.743  0.020  1.743
 5RY  C5   C2   aromatic  1.393  0.020  1.393
 5RY  C5   C4   aromatic  1.393  0.020  1.393
 5RY  S22  C13  single    1.823  0.020  1.823
 5RY  C2   C3   aromatic  1.384  0.020  1.384
 5RY  C4   C8   aromatic  1.377  0.020  1.377
 5RY  C3   C6   aromatic  1.391  0.020  1.391
 5RY  C8   C6   aromatic  1.389  0.020  1.389
 5RY  C8   F21  single    1.336  0.020  1.336
 5RY  C6   C13  single    1.496  0.020  1.496
 5RY  C2   H1   single    0.930  0.020  1.080
 5RY  C3   H2   single    0.930  0.020  1.080
 5RY  C4   H3   single    0.930  0.020  1.080
 5RY  C13  H4   single    0.970  0.020  1.090
 5RY  C13  H5   single    0.970  0.020  1.090
 5RY  N16  H6   single    0.860  0.020  1.020
 5RY  N17  H7   single    0.860  0.020  1.020
 5RY  N19  H9   single    0.860  0.020  1.020
 5RY  N19  H10  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
 5RY  N14  C1   C5   180.00  3.000
 5RY  H1   C2   C5   120.43  3.000
 5RY  H1   C2   C3   120.41  3.000
 5RY  C5   C2   C3   119.16  3.000
 5RY  H2   C3   C6   119.10  3.000
 5RY  H2   C3   C2   119.55  3.000
 5RY  C6   C3   C2   121.35  3.000
 5RY  H3   C4   C8   120.62  3.000
 5RY  H3   C4   C5   121.34  3.000
 5RY  C8   C4   C5   118.04  3.000
 5RY  C4   C5   C2   120.93  3.000
 5RY  C4   C5   C1   119.26  3.000
 5RY  C2   C5   C1   119.81  3.000
 5RY  C13  C6   C8   121.27  3.000
 5RY  C13  C6   C3   121.06  3.000
 5RY  C8   C6   C3   117.67  3.000
 5RY  N18  C7   C10  130.42  3.000
 5RY  N18  C7   C9   110.88  3.000
 5RY  C10  C7   C9   118.71  3.000
 5RY  F21  C8   C6   118.58  3.000
 5RY  F21  C8   C4   118.57  3.000
 5RY  C6   C8   C4   122.85  3.000
 5RY  N16  C9   N15  126.47  3.000
 5RY  N16  C9   C7   104.95  3.000
 5RY  N15  C9   C7   128.58  3.000
 5RY  O20  C10  N17  120.48  3.000
 5RY  O20  C10  C7   128.98  3.000
 5RY  N17  C10  C7   110.53  3.000
 5RY  N19  C11  N17  117.22  3.000
 5RY  N17  C11  N15  122.92  3.000
 5RY  N19  C11  N15  119.86  3.000
 5RY  S22  C12  N18  126.88  3.000
 5RY  S22  C12  N16  120.20  3.000
 5RY  N18  C12  N16  112.92  3.000
 5RY  H5   C13  H4   108.54  3.000
 5RY  H5   C13  S22  108.96  3.000
 5RY  H4   C13  S22  109.09  3.000
 5RY  H5   C13  C6   110.59  3.000
 5RY  H4   C13  C6   112.39  3.000
 5RY  S22  C13  C6   107.21  3.000
 5RY  C11  N15  C9   113.04  3.000
 5RY  H6   N16  C12  127.17  3.000
 5RY  H6   N16  C9   126.00  3.000
 5RY  C12  N16  C9   106.82  3.000
 5RY  H7   N17  C11  118.41  3.000
 5RY  H7   N17  C10  115.37  3.000
 5RY  C11  N17  C10  126.22  3.000
 5RY  C12  N18  C7   104.44  3.000
 5RY  C13  S22  C12   99.39  3.000
 5RY  H10  N19  H9   117.94  3.000
 5RY  H10  N19  C11  119.03  3.000
 5RY  H9   N19  C11  122.82  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
 5RY  CONST_01  C8   C4   C5   C2     0.00   0.0  0
 5RY  CONST_02  C8   C6   C3   C2     0.00   0.0  0
 5RY  CONST_03  C4   C5   C2   C3     0.00   0.0  0
 5RY  CONST_04  C4   C8   C6   C3     0.00   0.0  0
 5RY  CONST_05  C6   C3   C2   C5     0.00   0.0  0
 5RY  CONST_06  C6   C8   C4   C5     0.00   0.0  0
 5RY  CONST_07  C12  N16  C9   C7     0.00   0.0  0
 5RY  CONST_08  N16  C12  N18  C7     0.00   0.0  0
 5RY  CONST_09  N18  C12  N16  C9     0.00   0.0  0
 5RY  CONST_10  C12  N18  C7   C9     0.00   0.0  0
 5RY  CONST_11  N18  C7   C9   N16    0.00   0.0  0
 5RY  CONST_12  C11  N17  C10  C7     0.00   0.0  0
 5RY  CONST_13  N17  C11  N15  C9     0.00   0.0  0
 5RY  CONST_14  N15  C11  N17  C10    0.00   0.0  0
 5RY  CONST_15  C3   C2   C5   C1   180.00   0.0  0
 5RY  CONST_16  C8   C4   C5   C1   180.00   0.0  0
 5RY  CONST_17  C13  C6   C3   C2   180.00   0.0  0
 5RY  CONST_18  F21  C8   C6   C3   180.00   0.0  0
 5RY  CONST_19  C13  C6   C8   C4   180.00   0.0  0
 5RY  CONST_20  F21  C8   C4   C5   180.00   0.0  0
 5RY  CONST_21  S22  C12  N18  C7   180.00   0.0  0
 5RY  CONST_22  S22  C12  N16  C9   180.00   0.0  0
 5RY  CONST_23  N19  C11  N15  C9   180.00   0.0  0
 5RY  CONST_24  N19  C11  N17  C10  180.00   0.0  0
 5RY  CONST_25  O20  C10  N17  C11  180.00   0.0  0
 5RY  CONST_26  H3   C4   C5   C2   180.00   0.0  0
 5RY  CONST_27  H1   C2   C5   C4   180.00   0.0  0
 5RY  CONST_28  H2   C3   C2   C5   180.00   0.0  0
 5RY  CONST_29  H6   N16  C9   C7   180.00   0.0  0
 5RY  CONST_30  H7   N17  C10  C7   180.00   0.0  0
 5RY  CONST_31  H9   N19  C11  N15  180.00   0.0  0
 5RY  CONST_32  H10  N19  C11  N15    0.00   0.0  0
 5RY  Var_01    S22  C13  C6   C3    97.96  30.0  2
 5RY  Var_02    N16  C12  S22  C13  177.77  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
 5RY  plan-1  C1   0.020
 5RY  plan-1  C2   0.020
 5RY  plan-1  C3   0.020
 5RY  plan-1  C4   0.020
 5RY  plan-1  C5   0.020
 5RY  plan-1  C6   0.020
 5RY  plan-1  C8   0.020
 5RY  plan-1  C13  0.020
 5RY  plan-1  N14  0.020
 5RY  plan-1  F21  0.020
 5RY  plan-1  H1   0.020
 5RY  plan-1  H2   0.020
 5RY  plan-1  H3   0.020
 5RY  plan-2  C7   0.020
 5RY  plan-2  C9   0.020
 5RY  plan-2  C10  0.020
 5RY  plan-2  C11  0.020
 5RY  plan-2  C12  0.020
 5RY  plan-2  N15  0.020
 5RY  plan-2  N16  0.020
 5RY  plan-2  N17  0.020
 5RY  plan-2  N18  0.020
 5RY  plan-2  O20  0.020
 5RY  plan-2  S22  0.020
 5RY  plan-2  H6   0.020
 5RY  plan-2  H7   0.020
 5RY  plan-2  H9   0.020
 5RY  plan-2  H10  0.020
 5RY  plan-2  N19  0.020

