# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 06:14:41 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-~{N}-[(2~{R},3~{R})-1,3-bis(oxidanyl)butan-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](CO)NC(=O)Cn1cnc2C(=O)NC(=Nc12)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
 GT3  GT3  2-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-~{N}-[(2~{R},3~{R})-1,3-bis(oxidanyl)butan-2-yl]ethanamide  ligand  37  21  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GT3
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
 GT3  O6   O  O     0  -0.475   -5.9609  -14.1805  -1.2027
 GT3  C6   C  CR6   0   0.502   -6.2019  -13.0578  -1.6145
 GT3  N1   N  NR16  0  -0.727   -6.6213  -12.8601  -2.9371
 GT3  C2   C  CR6   0   0.688   -6.9179  -11.6608  -3.5202
 GT3  N2   N  NH2   0  -0.834   -7.2671  -11.6838  -4.8132
 GT3  N3   N  N     0  -0.509   -6.8447  -10.5195  -2.8808
 GT3  C4   C  CR56  0   0.505   -6.4467  -10.6579  -1.6096
 GT3  C5   C  CR56  0  -0.092   -6.1238  -11.8145  -0.9244
 GT3  N7   N  N     0  -0.445   -5.7727  -11.5279   0.3705
 GT3  C8   C  CR15  0   0.095   -5.8818  -10.2382   0.4587
 GT3  N9   N  NR5   0  -0.482   -6.2701   -9.6516  -0.7168
 GT3  C2B  C  CH2   0  -0.458   -6.5856   -8.2721  -0.9374
 GT3  C2A  C  C     0   0.549   -8.0923   -8.0380  -0.8717
 GT3  O2A  O  O     0  -0.476   -8.8427   -8.8640  -0.3840
 GT3  N2'  N  NH1   0  -0.637   -8.4725   -6.8527  -1.3657
 GT3  C2'  C  CH1   0  -0.141   -9.8365   -6.3672  -1.3707
 GT3  C3'  C  CH1   0   0.045   -9.8956   -4.9362  -0.8385
 GT3  C3A  C  CH3   0  -0.691   -9.4371   -4.8441   0.6083
 GT3  O3'  O  OH1   0  -0.677   -9.1003   -4.1403  -1.6962
 GT3  C1'  C  CH2   0  -0.130  -10.4114   -6.5244  -2.7770
 GT3  O1'  O  OH1   0  -0.670  -11.7526   -6.0986  -2.7684
 GT3  H1   H  HNR6  0   0.425   -6.7014  -13.6979  -3.4994
 GT3  H2   H  HNH2  0   0.413   -7.6072  -10.8320  -5.2254
 GT3  H3   H  HNH2  0   0.416   -7.5144  -12.5423  -5.2745
 GT3  H4   H  HCR5  0   0.288   -5.6833   -9.6454   1.3395
 GT3  H5   H  HCH2  0   0.302   -6.1812   -7.9504  -1.8979
 GT3  H6   H  HCH2  0   0.319   -6.0964   -7.6730  -0.1675
 GT3  H7   H  HNH1  0   0.403   -7.7726   -6.2592  -1.7855
 GT3  H8   H  HCH1  0   0.263  -10.4145   -6.9951  -0.6902
 GT3  H9   H  HCH1  0   0.218  -10.9449   -4.6194  -0.8824
 GT3  H10  H  HCH3  0   0.237   -9.5319   -3.8191   0.9728
 GT3  H11  H  HCH3  0   0.230  -10.0530   -5.4741   1.2513
 GT3  H12  H  HCH3  0   0.228   -8.3964   -5.1479   0.7277
 GT3  H13  H  HOH1  0   0.455   -9.0901   -3.2406  -1.3555
 GT3  H14  H  HCH2  0   0.207  -10.3249   -7.5814  -3.0614
 GT3  H15  H  HCH2  0   0.201   -9.8047   -5.9518  -3.4885
 GT3  H16  H  HOH1  0   0.459  -12.0762   -6.1078  -3.6733

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
 GT3  N2   C2   single    1.340  0.020  1.340
 GT3  O1'  C1'  single    1.407  0.020  1.407
 GT3  C1'  C2'  single    1.527  0.020  1.527
 GT3  C2   N3   double    1.310  0.020  1.310
 GT3  C2   N1   single    1.366  0.020  1.366
 GT3  N3   C4   single    1.339  0.020  1.339
 GT3  N1   C6   single    1.402  0.020  1.402
 GT3  N2'  C2'  single    1.448  0.020  1.448
 GT3  N2'  C2A  single    1.339  0.020  1.339
 GT3  C2'  C3'  single    1.528  0.020  1.528
 GT3  C4   N9   aromatic  1.357  0.020  1.357
 GT3  C4   C5   aromatic  1.383  0.020  1.383
 GT3  C2B  C2A  single    1.526  0.020  1.526
 GT3  C2B  N9   single    1.432  0.020  1.432
 GT3  C2A  O2A  double    1.218  0.020  1.218
 GT3  C6   C5   single    1.424  0.020  1.424
 GT3  C6   O6   double    1.220  0.020  1.220
 GT3  N9   C8   aromatic  1.370  0.020  1.370
 GT3  C5   N7   aromatic  1.372  0.020  1.372
 GT3  C3'  O3'  single    1.415  0.020  1.415
 GT3  C3'  C3A  single    1.521  0.020  1.521
 GT3  C8   N7   aromatic  1.297  0.020  1.297
 GT3  N1   H1   single    0.860  0.020  1.020
 GT3  N2   H2   single    0.890  0.020  1.040
 GT3  N2   H3   single    0.890  0.020  1.040
 GT3  C8   H4   single    0.930  0.020  1.080
 GT3  C2B  H5   single    0.970  0.020  1.090
 GT3  C2B  H6   single    0.970  0.020  1.090
 GT3  N2'  H7   single    0.860  0.020  1.020
 GT3  C2'  H8   single    0.970  0.020  1.090
 GT3  C3'  H9   single    0.970  0.020  1.090
 GT3  C3A  H10  single    0.970  0.020  1.090
 GT3  C3A  H11  single    0.970  0.020  1.090
 GT3  C3A  H12  single    0.970  0.020  1.090
 GT3  O3'  H13  single    0.850  0.020  0.980
 GT3  C1'  H14  single    0.970  0.020  1.090
 GT3  C1'  H15  single    0.970  0.020  1.090
 GT3  O1'  H16  single    0.850  0.020  0.980

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
 GT3  C5   C6   N1   110.52  3.000
 GT3  C5   C6   O6   128.98  3.000
 GT3  N1   C6   O6   120.50  3.000
 GT3  H1   N1   C2   118.19  3.000
 GT3  H1   N1   C6   115.54  3.000
 GT3  C2   N1   C6   126.27  3.000
 GT3  N3   C2   N2   120.03  3.000
 GT3  N3   C2   N1   122.98  3.000
 GT3  N2   C2   N1   116.97  3.000
 GT3  H3   N2   H2   116.86  3.000
 GT3  H3   N2   C2   121.45  3.000
 GT3  H2   N2   C2   117.99  3.000
 GT3  C4   N3   C2   112.94  3.000
 GT3  N9   C4   C5   105.31  3.000
 GT3  C5   C4   N3   128.78  3.000
 GT3  N9   C4   N3   125.92  3.000
 GT3  N7   C5   C4   110.65  3.000
 GT3  N7   C5   C6   130.83  3.000
 GT3  C4   C5   C6   118.52  3.000
 GT3  C8   N7   C5   104.50  3.000
 GT3  H4   C8   N9   121.12  3.000
 GT3  H4   C8   N7   125.85  3.000
 GT3  N9   C8   N7   113.02  3.000
 GT3  C2B  N9   C8   127.37  3.000
 GT3  C8   N9   C4   106.50  3.000
 GT3  C2B  N9   C4   125.76  3.000
 GT3  H6   C2B  H5   107.04  3.000
 GT3  H6   C2B  C2A  109.14  3.000
 GT3  H5   C2B  C2A  111.02  3.000
 GT3  H6   C2B  N9   108.74  3.000
 GT3  H5   C2B  N9   109.76  3.000
 GT3  C2A  C2B  N9   111.02  3.000
 GT3  N2'  C2A  O2A  124.97  3.000
 GT3  O2A  C2A  C2B  121.43  3.000
 GT3  N2'  C2A  C2B  113.59  3.000
 GT3  H7   N2'  C2'  117.05  3.000
 GT3  H7   N2'  C2A  118.50  3.000
 GT3  C2'  N2'  C2A  124.43  3.000
 GT3  H8   C2'  C1'  108.39  3.000
 GT3  H8   C2'  C3'  107.53  3.000
 GT3  C1'  C2'  C3'  113.73  3.000
 GT3  H8   C2'  N2'  107.69  3.000
 GT3  C3'  C2'  N2'  110.44  3.000
 GT3  C1'  C2'  N2'  108.86  3.000
 GT3  H9   C3'  O3'  110.55  3.000
 GT3  H9   C3'  C3A  108.00  3.000
 GT3  O3'  C3'  C3A  111.92  3.000
 GT3  H9   C3'  C2'  107.07  3.000
 GT3  C3A  C3'  C2'  112.11  3.000
 GT3  O3'  C3'  C2'  107.10  3.000
 GT3  H12  C3A  H11  108.26  3.000
 GT3  H12  C3A  H10  107.92  3.000
 GT3  H11  C3A  H10  107.24  3.000
 GT3  H12  C3A  C3'  112.02  3.000
 GT3  H11  C3A  C3'  110.84  3.000
 GT3  H10  C3A  C3'  110.38  3.000
 GT3  H13  O3'  C3'  108.50  3.000
 GT3  H15  C1'  H14  106.92  3.000
 GT3  H15  C1'  O1'  111.92  3.000
 GT3  H14  C1'  O1'  111.59  3.000
 GT3  H15  C1'  C2'  109.60  3.000
 GT3  H14  C1'  C2'  107.93  3.000
 GT3  O1'  C1'  C2'  108.78  3.000
 GT3  H16  O1'  C1'  108.19  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
 GT3  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 GT3  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 GT3  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 GT3  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 GT3  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 GT3  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 GT3  CONST_07  C4   N3   C2   N1      0.00   0.0  0
 GT3  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 GT3  CONST_09  C2B  N9   C4   N3      0.00   0.0  0
 GT3  CONST_10  C2B  N9   C4   C5    180.00   0.0  0
 GT3  CONST_11  C2B  N9   C8   N7    180.00   0.0  0
 GT3  CONST_12  C2   N1   C6   O6    180.00   0.0  0
 GT3  CONST_13  N2   C2   N1   C6    180.00   0.0  0
 GT3  CONST_14  C4   N3   C2   N2    180.00   0.0  0
 GT3  CONST_15  H4   C8   N9   C4    180.00   0.0  0
 GT3  CONST_16  H1   N1   C2   N3    180.00   0.0  0
 GT3  CONST_17  H2   N2   C2   N1    180.00   0.0  0
 GT3  CONST_18  H3   N2   C2   N1      0.00   0.0  0
 GT3  CONST_19  C2'  N2'  C2A  C2B   180.00   0.0  0
 GT3  CONST_20  C2'  N2'  C2A  O2A     0.00   0.0  0
 GT3  CONST_21  H7   N2'  C2A  C2B     0.00   0.0  0
 GT3  Var_01    C2A  C2B  N9   C4     75.01  30.0  2
 GT3  Var_02    N2'  C2A  C2B  N9   -165.53  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GT3  chir_01  C2'  C1'  N2'  C3'  negativ
 GT3  chir_02  C3'  O3'  C2'  C3A  negativ

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
 GT3  plan-1  O6   0.020
 GT3  plan-1  C6   0.020
 GT3  plan-1  N1   0.020
 GT3  plan-1  C2   0.020
 GT3  plan-1  N2   0.020
 GT3  plan-1  N3   0.020
 GT3  plan-1  C4   0.020
 GT3  plan-1  C5   0.020
 GT3  plan-1  N7   0.020
 GT3  plan-1  C8   0.020
 GT3  plan-1  N9   0.020
 GT3  plan-1  C2B  0.020
 GT3  plan-1  H1   0.020
 GT3  plan-1  H2   0.020
 GT3  plan-1  H3   0.020
 GT3  plan-1  H4   0.020
 GT3  plan-2  C2B  0.020
 GT3  plan-2  C2A  0.020
 GT3  plan-2  O2A  0.020
 GT3  plan-2  N2'  0.020
 GT3  plan-2  C2'  0.020
 GT3  plan-2  H7   0.020

