# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:09:44 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2nc([nH]c2N1)SCc3ccccc3C#N
#
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
 5RV  5RV  2-[(2-azanyl-6-oxidanylidene-3,9-dihydropurin-8-yl)sulfanylmethyl]benzenecarbonitrile  ligand  31  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5RV
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
 5RV  C1   C  CSP   0   0.022  -3.2073  -1.2808  -1.3839
 5RV  C2   C  CR16  0  -0.256  -6.0462   0.3435   0.3451
 5RV  C3   C  CR16  0  -0.219  -5.3998   0.9170   1.4310
 5RV  C4   C  CR16  0  -0.230  -5.3196  -0.3839  -0.5824
 5RV  C5   C  CR16  0  -0.288  -4.0291   0.7655   1.5926
 5RV  C6   C  CR6   0   0.002  -3.9438  -0.5317  -0.4166
 5RV  C7   C  CR6   0   0.148  -3.2804   0.0373   0.6790
 5RV  C8   C  CR56  0  -0.094   2.4624  -0.3754   0.3614
 5RV  C9   C  CR56  0   0.618   2.7952   0.7138  -0.3931
 5RV  C10  C  CR6   0   0.408   3.5063  -1.2683   0.8086
 5RV  C11  C  CR6   0   0.671   5.0295   0.1379  -0.3114
 5RV  C12  C  CR5   0   0.292   0.6493   0.6382  -0.0737
 5RV  C13  C  CH2   0  -0.655  -1.8000  -0.1049   0.8493
 5RV  N14  N  NS    0  -0.240  -2.6203  -1.8916  -2.1650
 5RV  N15  N  NR16  0  -0.726   4.0689   1.0069  -0.7492
 5RV  N16  N  NR15  0  -0.682   1.6467   1.3673  -0.6737
 5RV  N17  N  N     0  -0.537   4.7764  -0.9182   0.4141
 5RV  N18  N  N     0  -0.439   1.0999  -0.4037   0.5527
 5RV  O20  O  O     0  -0.497   3.3065  -2.2690   1.4886
 5RV  S21  S  S2    0   0.078  -1.0124   1.1479  -0.2160
 5RV  H1   H  HCR6  0   0.278  -7.1136   0.4611   0.2188
 5RV  H2   H  HCR6  0   0.278  -5.9638   1.4861   2.1576
 5RV  H3   H  HCR6  0   0.286  -5.8111  -0.8372  -1.4321
 5RV  H4   H  HCR6  0   0.276  -3.5340   1.2156   2.4432
 5RV  H5   H  HCH2  0   0.321  -1.5046   0.0686   1.8826
 5RV  H6   H  HCH2  0   0.311  -1.4405  -1.0892   0.5513
 5RV  H7   H  HNR6  0   0.439   4.2962   1.8146  -1.3110
 5RV  H8   H  HNR5  0   0.437   1.5433   2.2143  -1.2133
 5RV  H10  H  HNH2  0   0.412   7.0246  -0.1594  -0.3076
 5RV  H11  H  HNH2  0   0.414   6.5432   1.2852  -1.1008
 5RV  N19  N  NH2   0  -0.827   6.2858   0.4040  -0.6911

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
 5RV  N19  C11  single    1.339  0.020  1.339
 5RV  C11  N17  double    1.306  0.020  1.306
 5RV  C11  N15  single    1.367  0.020  1.367
 5RV  N17  C10  single    1.375  0.020  1.375
 5RV  N15  C9   single    1.355  0.020  1.355
 5RV  C10  O20  double    1.226  0.020  1.226
 5RV  C10  C8   single    1.445  0.020  1.445
 5RV  C9   C8   aromatic  1.366  0.020  1.366
 5RV  C9   N16  aromatic  1.351  0.020  1.351
 5RV  C8   N18  aromatic  1.376  0.020  1.376
 5RV  N16  C12  aromatic  1.373  0.020  1.373
 5RV  N18  C12  aromatic  1.297  0.020  1.297
 5RV  C12  S21  single    1.744  0.020  1.744
 5RV  S21  C13  single    1.823  0.020  1.823
 5RV  N14  C1   triple    1.152  0.020  1.152
 5RV  C13  C7   single    1.497  0.020  1.497
 5RV  C1   C6   single    1.428  0.020  1.428
 5RV  C7   C6   aromatic  1.401  0.020  1.401
 5RV  C7   C5   aromatic  1.388  0.020  1.388
 5RV  C6   C4   aromatic  1.394  0.020  1.394
 5RV  C5   C3   aromatic  1.389  0.020  1.389
 5RV  C4   C2   aromatic  1.385  0.020  1.385
 5RV  C3   C2   aromatic  1.388  0.020  1.388
 5RV  C2   H1   single    0.930  0.020  1.080
 5RV  C3   H2   single    0.930  0.020  1.080
 5RV  C4   H3   single    0.930  0.020  1.080
 5RV  C5   H4   single    0.930  0.020  1.080
 5RV  C13  H5   single    0.970  0.020  1.090
 5RV  C13  H6   single    0.970  0.020  1.090
 5RV  N15  H7   single    0.860  0.020  1.020
 5RV  N16  H8   single    0.860  0.020  1.020
 5RV  N19  H10  single    0.860  0.020  1.020
 5RV  N19  H11  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
 5RV  N14  C1   C6   180.00  3.000
 5RV  H1   C2   C4   119.80  3.000
 5RV  H1   C2   C3   120.41  3.000
 5RV  C4   C2   C3   119.78  3.000
 5RV  H2   C3   C5   119.60  3.000
 5RV  H2   C3   C2   120.01  3.000
 5RV  C5   C3   C2   120.38  3.000
 5RV  H3   C4   C6   119.85  3.000
 5RV  H3   C4   C2   120.54  3.000
 5RV  C6   C4   C2   119.61  3.000
 5RV  H4   C5   C7   119.27  3.000
 5RV  H4   C5   C3   119.84  3.000
 5RV  C7   C5   C3   120.88  3.000
 5RV  C7   C6   C4   121.14  3.000
 5RV  C4   C6   C1   118.96  3.000
 5RV  C7   C6   C1   119.90  3.000
 5RV  C13  C7   C6   121.23  3.000
 5RV  C6   C7   C5   118.19  3.000
 5RV  C13  C7   C5   120.56  3.000
 5RV  N18  C8   C10  131.28  3.000
 5RV  N18  C8   C9   109.53  3.000
 5RV  C10  C8   C9   119.19  3.000
 5RV  N16  C9   N15  129.80  3.000
 5RV  N16  C9   C8   107.06  3.000
 5RV  N15  C9   C8   123.14  3.000
 5RV  O20  C10  N17  121.16  3.000
 5RV  O20  C10  C8   123.94  3.000
 5RV  N17  C10  C8   114.91  3.000
 5RV  N19  C11  N17  120.00  3.000
 5RV  N17  C11  N15  123.76  3.000
 5RV  N19  C11  N15  116.23  3.000
 5RV  S21  C12  N18  127.26  3.000
 5RV  S21  C12  N16  120.08  3.000
 5RV  N18  C12  N16  112.66  3.000
 5RV  H6   C13  H5   108.31  3.000
 5RV  H6   C13  S21  108.57  3.000
 5RV  H5   C13  S21  109.14  3.000
 5RV  H6   C13  C7   112.40  3.000
 5RV  H5   C13  C7   111.18  3.000
 5RV  S21  C13  C7   107.18  3.000
 5RV  H7   N15  C11  121.90  3.000
 5RV  H7   N15  C9   122.07  3.000
 5RV  C11  N15  C9   116.03  3.000
 5RV  H8   N16  C12  127.19  3.000
 5RV  H8   N16  C9   127.15  3.000
 5RV  C12  N16  C9   105.66  3.000
 5RV  C11  N17  C10  122.97  3.000
 5RV  C12  N18  C8   105.09  3.000
 5RV  C13  S21  C12   99.39  3.000
 5RV  H11  N19  H10  117.30  3.000
 5RV  H11  N19  C11  122.00  3.000
 5RV  H10  N19  C11  118.04  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
 5RV  CONST_01  C7   C6   C4   C2      0.00   0.0  0
 5RV  CONST_02  C7   C5   C3   C2      0.00   0.0  0
 5RV  CONST_03  C6   C7   C5   C3      0.00   0.0  0
 5RV  CONST_04  C6   C4   C2   C3      0.00   0.0  0
 5RV  CONST_05  C5   C7   C6   C4      0.00   0.0  0
 5RV  CONST_06  C5   C3   C2   C4      0.00   0.0  0
 5RV  CONST_07  C12  N16  C9   C8      0.00   0.0  0
 5RV  CONST_08  N16  C12  N18  C8      0.00   0.0  0
 5RV  CONST_09  C12  N18  C8   C9      0.00   0.0  0
 5RV  CONST_10  N18  C12  N16  C9      0.00   0.0  0
 5RV  CONST_11  N18  C8   C9   N16     0.00   0.0  0
 5RV  CONST_12  N17  C11  N15  C9      0.00   0.0  0
 5RV  CONST_13  N15  C11  N17  C10     0.00   0.0  0
 5RV  CONST_14  C5   C7   C6   C1    180.00   0.0  0
 5RV  CONST_15  C2   C4   C6   C1    180.00   0.0  0
 5RV  CONST_16  C13  C7   C5   C3    180.00   0.0  0
 5RV  CONST_17  C13  C7   C6   C4    180.00   0.0  0
 5RV  CONST_18  S21  C12  N18  C8    180.00   0.0  0
 5RV  CONST_19  S21  C12  N16  C9    180.00   0.0  0
 5RV  CONST_20  N19  C11  N15  C9    180.00   0.0  0
 5RV  CONST_21  N19  C11  N17  C10   180.00   0.0  0
 5RV  CONST_22  H4   C5   C3   C2    180.00   0.0  0
 5RV  CONST_23  H3   C4   C2   C3    180.00   0.0  0
 5RV  CONST_24  H2   C3   C2   C4    180.00   0.0  0
 5RV  CONST_25  H1   C2   C3   C5    180.00   0.0  0
 5RV  CONST_26  H8   N16  C9   C8    180.00   0.0  0
 5RV  CONST_27  H7   N15  C11  N17   180.00   0.0  0
 5RV  CONST_28  H10  N19  C11  N15   180.00   0.0  0
 5RV  CONST_29  H11  N19  C11  N15     0.00   0.0  0
 5RV  Var_01    S21  C13  C7   C5    -97.47  30.0  2
 5RV  Var_02    N16  C12  S21  C13  -176.21  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
 5RV  plan-1  C1   0.020
 5RV  plan-1  C2   0.020
 5RV  plan-1  C3   0.020
 5RV  plan-1  C4   0.020
 5RV  plan-1  C5   0.020
 5RV  plan-1  C6   0.020
 5RV  plan-1  C7   0.020
 5RV  plan-1  C13  0.020
 5RV  plan-1  N14  0.020
 5RV  plan-1  H1   0.020
 5RV  plan-1  H2   0.020
 5RV  plan-1  H3   0.020
 5RV  plan-1  H4   0.020
 5RV  plan-2  C8   0.020
 5RV  plan-2  C9   0.020
 5RV  plan-2  C10  0.020
 5RV  plan-2  C11  0.020
 5RV  plan-2  C12  0.020
 5RV  plan-2  N15  0.020
 5RV  plan-2  N16  0.020
 5RV  plan-2  N17  0.020
 5RV  plan-2  N18  0.020
 5RV  plan-2  O20  0.020
 5RV  plan-2  S21  0.020
 5RV  plan-2  H7   0.020
 5RV  plan-2  H8   0.020
 5RV  plan-2  H10  0.020
 5RV  plan-2  H11  0.020
 5RV  plan-2  N19  0.020

