# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed Jul  8 16:52:44 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)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
 Y9Z  Y9Z  5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  54  34  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y9Z
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
 Y9Z  N    N  NR16   0  -0.726   5.0902   2.0701  -2.1839
 Y9Z  C    C  CR6    0   0.498   3.7234   2.1501  -2.4789
 Y9Z  O    O  O      0  -0.476   3.3225   2.8976  -3.3559
 Y9Z  P    P  P      0   1.359  -2.0581  -1.2190   1.1445
 Y9Z  P1   P  P      0   1.376  -4.3954  -2.9720   0.7985
 Y9Z  C1   C  CR6    0   0.681   5.6624   1.2745  -1.2335
 Y9Z  N1   N  NH2    0  -0.832   7.0013   1.3038  -1.1405
 Y9Z  O1   O  OH1    0  -0.667   4.2100  -1.6735   2.9009
 Y9Z  C2   C  CR56   0   0.503   3.6497   0.5245  -0.6931
 Y9Z  N2   N  N      0  -0.516   4.9704   0.4802  -0.4567
 Y9Z  O2   O  OH1    0  -0.657   2.6163   0.0110   4.3837
 Y9Z  C3   C  CR56   0  -0.090   2.9759   1.2757  -1.6385
 Y9Z  N3   N  N      0  -0.447   1.6321   1.0165  -1.5943
 Y9Z  O3   O  O2     0  -0.617  -1.0399  -1.4862   2.4171
 Y9Z  C4   C  CR15   0   0.045   1.4919   0.1370  -0.6474
 Y9Z  N4   N  NR5    0  -0.547   2.6874  -0.1858  -0.0448
 Y9Z  O4   O  O2     0  -0.731  -3.0071  -2.5101   1.5278
 Y9Z  C5   C  CR15   0   0.175   2.9112  -1.1953   0.9935
 Y9Z  N5   N  NH1    0  -0.649  -5.0908   0.0203  -0.7439
 Y9Z  O5   O  O2     0  -0.616  -5.4293  -1.9198   1.5124
 Y9Z  C6   C  CR15   0  -0.040   3.6033  -0.6081   2.2205
 Y9Z  O6   O  O      0  -0.536  -4.6605   2.2339  -0.7452
 Y9Z  C7   C  CR15   0  -0.049   2.4008  -0.0722   3.0018
 Y9Z  O7   O  OP    -1  -0.773  -4.6819  -4.3522   1.2924
 Y9Z  C8   C  CR15   0   0.015   1.3242  -1.1127   2.6965
 Y9Z  O8   O  O      0  -0.791  -4.3405  -2.6908  -0.6797
 Y9Z  C9   C  CH2    0  -0.162  -0.0580  -0.5032   2.6589
 Y9Z  O9   O  O      0  -0.762  -1.3266  -1.4865  -0.1336
 Y9Z  C10  C  CH2    0  -0.221  -6.4774  -1.2919   0.7912
 Y9Z  O10  O  OP    -1  -0.771  -2.7865   0.0665   1.3679
 Y9Z  C11  C  CH2    0  -0.263  -6.0972   0.0884   0.2901
 Y9Z  O11  O  O      0  -0.487   1.6825  -1.6770   1.4345
 Y9Z  C12  C  C      0   0.523  -4.3682   1.0910  -1.0893
 Y9Z  C13  C  CH3    0  -0.768  -3.1876   0.8150  -1.9870
 Y9Z  H1   H  HNR6   0   0.424   5.6932   2.6607  -2.7424
 Y9Z  H2   H  HNH2   0   0.413   7.5291   2.0554  -1.5507
 Y9Z  H3   H  HNH2   0   0.411   7.4181   0.8554  -0.3423
 Y9Z  H4   H  HOH1   0   0.451   4.1970  -1.4632   3.8427
 Y9Z  H5   H  HOH1   0   0.468   3.0654   0.8405   4.5759
 Y9Z  H6   H  HCR5   0   0.325   0.5571  -0.3308  -0.3647
 Y9Z  H7   H  HCR5   0   0.284   3.4911  -2.0099   0.5509
 Y9Z  H8   H  HNH1   0   0.411  -4.7056  -0.9066  -0.9261
 Y9Z  H9   H  HCR5   0   0.263   4.3252   0.1761   1.9712
 Y9Z  H10  H  HCR5   0   0.246   2.1121   0.9019   2.5857
 Y9Z  H12  H  HCR5   0   0.246   1.3531  -1.9088   3.4500
 Y9Z  H13  H  HCH2   0   0.207  -0.0787   0.3048   1.9173
 Y9Z  H14  H  HCH2   0   0.233  -0.2424  -0.0344   3.6322
 Y9Z  H15  H  HCH2   0   0.217  -6.8254  -1.9121  -0.0410
 Y9Z  H16  H  HCH2   0   0.239  -7.3179  -1.1824   1.4792
 Y9Z  H18  H  HCH2   0   0.226  -5.7389   0.6909   1.1295
 Y9Z  H19  H  HCH2   0   0.222  -7.0090   0.5677  -0.0802
 Y9Z  H20  H  HCH3   0   0.243  -2.9400  -0.2409  -2.0563
 Y9Z  H21  H  HCH3   0   0.244  -3.3880   1.2019  -2.9872
 Y9Z  H22  H  HCH3   0   0.248  -2.3124   1.3327  -1.5978

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
 Y9Z  O    C    double    1.220  0.020  1.220
 Y9Z  C    N    single    1.401  0.020  1.401
 Y9Z  C    C3   single    1.425  0.020  1.425
 Y9Z  N    C1   single    1.365  0.020  1.365
 Y9Z  C3   N3   aromatic  1.369  0.020  1.369
 Y9Z  C3   C2   aromatic  1.383  0.020  1.383
 Y9Z  N3   C4   aromatic  1.300  0.020  1.300
 Y9Z  C1   N1   single    1.342  0.020  1.342
 Y9Z  C1   N2   double    1.309  0.020  1.309
 Y9Z  C4   N4   aromatic  1.377  0.020  1.377
 Y9Z  C2   N2   single    1.342  0.020  1.342
 Y9Z  C2   N4   aromatic  1.360  0.020  1.360
 Y9Z  O1   C6   single    1.402  0.020  1.402
 Y9Z  O9   P    deloc     1.497  0.020  1.497
 Y9Z  N4   C5   single    1.465  0.020  1.465
 Y9Z  C6   C5   single    1.526  0.020  1.526
 Y9Z  C6   C7   single    1.531  0.020  1.531
 Y9Z  C5   O11  single    1.391  0.020  1.391
 Y9Z  P    O3   single    1.652  0.020  1.652
 Y9Z  P    O10  deloc     1.494  0.020  1.494
 Y9Z  P    O4   single    1.648  0.020  1.648
 Y9Z  O3   C9   single    1.410  0.020  1.410
 Y9Z  O8   P1   deloc     1.506  0.020  1.506
 Y9Z  C7   O2   single    1.401  0.020  1.401
 Y9Z  C7   C8   single    1.528  0.020  1.528
 Y9Z  O11  C8   single    1.428  0.020  1.428
 Y9Z  O4   P1   single    1.635  0.020  1.635
 Y9Z  P1   O7   deloc     1.494  0.020  1.494
 Y9Z  P1   O5   single    1.639  0.020  1.639
 Y9Z  C8   C9   single    1.511  0.020  1.511
 Y9Z  C11  C10  single    1.517  0.020  1.517
 Y9Z  C11  N5   single    1.445  0.020  1.445
 Y9Z  O5   C10  single    1.419  0.020  1.419
 Y9Z  N5   C12  single    1.337  0.020  1.337
 Y9Z  O6   C12  double    1.229  0.020  1.229
 Y9Z  C12  C13  single    1.509  0.020  1.509
 Y9Z  N    H1   single    0.860  0.020  1.020
 Y9Z  N1   H2   single    0.890  0.020  1.040
 Y9Z  N1   H3   single    0.890  0.020  1.040
 Y9Z  O1   H4   single    0.850  0.020  0.980
 Y9Z  O2   H5   single    0.850  0.020  0.980
 Y9Z  C4   H6   single    0.930  0.020  1.080
 Y9Z  C5   H7   single    0.970  0.020  1.090
 Y9Z  N5   H8   single    0.890  0.020  1.040
 Y9Z  C6   H9   single    0.970  0.020  1.090
 Y9Z  C7   H10  single    0.970  0.020  1.090
 Y9Z  C8   H12  single    0.970  0.020  1.090
 Y9Z  C9   H13  single    0.970  0.020  1.090
 Y9Z  C9   H14  single    0.970  0.020  1.090
 Y9Z  C10  H15  single    0.970  0.020  1.090
 Y9Z  C10  H16  single    0.970  0.020  1.090
 Y9Z  C11  H18  single    0.970  0.020  1.090
 Y9Z  C11  H19  single    0.970  0.020  1.090
 Y9Z  C13  H20  single    0.970  0.020  1.090
 Y9Z  C13  H21  single    0.970  0.020  1.090
 Y9Z  C13  H22  single    0.970  0.020  1.090

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
 Y9Z  H1   N    C1   118.32  3.000
 Y9Z  H1   N    C    115.59  3.000
 Y9Z  C1   N    C    126.09  3.000
 Y9Z  C3   C    O    128.88  3.000
 Y9Z  C3   C    N    110.65  3.000
 Y9Z  O    C    N    120.47  3.000
 Y9Z  O10  P    O9   121.31  3.000
 Y9Z  O10  P    O4   111.01  3.000
 Y9Z  O9   P    O4   109.89  3.000
 Y9Z  O4   P    O3    92.81  3.000
 Y9Z  O10  P    O3   108.93  3.000
 Y9Z  O9   P    O3   109.13  3.000
 Y9Z  O8   P1   O7   120.28  3.000
 Y9Z  O7   P1   O5   109.16  3.000
 Y9Z  O8   P1   O5   109.31  3.000
 Y9Z  O5   P1   O4    99.21  3.000
 Y9Z  O7   P1   O4   106.05  3.000
 Y9Z  O8   P1   O4   110.75  3.000
 Y9Z  N2   C1   N1   119.96  3.000
 Y9Z  N2   C1   N    123.04  3.000
 Y9Z  N1   C1   N    116.98  3.000
 Y9Z  H3   N1   H2   116.05  3.000
 Y9Z  H3   N1   C1   117.29  3.000
 Y9Z  H2   N1   C1   120.76  3.000
 Y9Z  H4   O1   C6   107.58  3.000
 Y9Z  N4   C2   C3   105.35  3.000
 Y9Z  N4   C2   N2   126.50  3.000
 Y9Z  C3   C2   N2   128.15  3.000
 Y9Z  C2   N2   C1   113.30  3.000
 Y9Z  H5   O2   C7   108.65  3.000
 Y9Z  N3   C3   C2   110.69  3.000
 Y9Z  C2   C3   C    118.76  3.000
 Y9Z  N3   C3   C    130.55  3.000
 Y9Z  C4   N3   C3   104.92  3.000
 Y9Z  C9   O3   P    116.65  3.000
 Y9Z  H6   C4   N4   122.27  3.000
 Y9Z  H6   C4   N3   125.14  3.000
 Y9Z  N4   C4   N3   112.56  3.000
 Y9Z  C5   N4   C4   127.16  3.000
 Y9Z  C5   N4   C2   126.11  3.000
 Y9Z  C4   N4   C2   106.45  3.000
 Y9Z  P1   O4   P    127.36  3.000
 Y9Z  H7   C5   O11  109.80  3.000
 Y9Z  H7   C5   C6   111.81  3.000
 Y9Z  O11  C5   C6   106.19  3.000
 Y9Z  H7   C5   N4   107.90  3.000
 Y9Z  O11  C5   N4   109.16  3.000
 Y9Z  C6   C5   N4   111.95  3.000
 Y9Z  H8   N5   C12  118.51  3.000
 Y9Z  H8   N5   C11  115.71  3.000
 Y9Z  C12  N5   C11  121.57  3.000
 Y9Z  C10  O5   P1   121.92  3.000
 Y9Z  H9   C6   C7   112.55  3.000
 Y9Z  H9   C6   C5   113.06  3.000
 Y9Z  C7   C6   C5   100.88  3.000
 Y9Z  H9   C6   O1   111.69  3.000
 Y9Z  C7   C6   O1   110.99  3.000
 Y9Z  C5   C6   O1   107.10  3.000
 Y9Z  H10  C7   C8   110.07  3.000
 Y9Z  H10  C7   C6   108.88  3.000
 Y9Z  C8   C7   C6   102.31  3.000
 Y9Z  H10  C7   O2   111.20  3.000
 Y9Z  C8   C7   O2   110.24  3.000
 Y9Z  C6   C7   O2   113.79  3.000
 Y9Z  H12  C8   O11  108.29  3.000
 Y9Z  H12  C8   C9   109.51  3.000
 Y9Z  O11  C8   C9   111.52  3.000
 Y9Z  H12  C8   C7   109.79  3.000
 Y9Z  C9   C8   C7   112.01  3.000
 Y9Z  O11  C8   C7   105.60  3.000
 Y9Z  H14  C9   H13  106.39  3.000
 Y9Z  H14  C9   C8   107.71  3.000
 Y9Z  H13  C9   C8   109.34  3.000
 Y9Z  H14  C9   O3   109.47  3.000
 Y9Z  H13  C9   O3   112.61  3.000
 Y9Z  C8   C9   O3   111.10  3.000
 Y9Z  H16  C10  H15  106.93  3.000
 Y9Z  H16  C10  C11  108.05  3.000
 Y9Z  H15  C10  C11  110.13  3.000
 Y9Z  H16  C10  O5   107.03  3.000
 Y9Z  H15  C10  O5   111.75  3.000
 Y9Z  C11  C10  O5   112.67  3.000
 Y9Z  H19  C11  H18  106.94  3.000
 Y9Z  H19  C11  C10  107.54  3.000
 Y9Z  H18  C11  C10  109.26  3.000
 Y9Z  H19  C11  N5   111.03  3.000
 Y9Z  H18  C11  N5   110.32  3.000
 Y9Z  C10  C11  N5   111.60  3.000
 Y9Z  C8   O11  C5   111.40  3.000
 Y9Z  C13  C12  O6   121.53  3.000
 Y9Z  C13  C12  N5   115.48  3.000
 Y9Z  O6   C12  N5   122.95  3.000
 Y9Z  H22  C13  H21  107.86  3.000
 Y9Z  H22  C13  H20  107.56  3.000
 Y9Z  H21  C13  H20  109.15  3.000
 Y9Z  H22  C13  C12  109.23  3.000
 Y9Z  H21  C13  C12  109.69  3.000
 Y9Z  H20  C13  C12  113.20  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
 Y9Z  CONST_01  C4   N3   C3   C2      0.00   0.0  0
 Y9Z  CONST_02  N3   C4   N4   C2      0.00   0.0  0
 Y9Z  CONST_03  N4   C4   N3   C3      0.00   0.0  0
 Y9Z  CONST_04  C4   N4   C2   C3      0.00   0.0  0
 Y9Z  CONST_05  N4   C2   C3   N3      0.00   0.0  0
 Y9Z  CONST_06  C5   N4   C2   N2      0.00   0.0  0
 Y9Z  CONST_07  C5   N4   C2   C3    180.00   0.0  0
 Y9Z  CONST_08  C5   N4   C4   N3    180.00   0.0  0
 Y9Z  CONST_09  C2   N2   C1   N       0.00   0.0  0
 Y9Z  CONST_10  N2   C1   N    C       0.00   0.0  0
 Y9Z  CONST_11  C3   C    N    C1      0.00   0.0  0
 Y9Z  CONST_12  N1   C1   N    C     180.00   0.0  0
 Y9Z  CONST_13  C1   N    C    O     180.00   0.0  0
 Y9Z  CONST_14  C2   N2   C1   N1    180.00   0.0  0
 Y9Z  CONST_15  H6   C4   N4   C2    180.00   0.0  0
 Y9Z  CONST_16  H1   N    C1   N2    180.00   0.0  0
 Y9Z  CONST_18  H3   N1   C1   N     180.00   0.0  0
 Y9Z  CONST_19  C11  N5   C12  O6      0.00   0.0  0
 Y9Z  CONST_20  C13  C12  N5   C11   180.00   0.0  0
 Y9Z  CONST_21  H8   N5   C12  O6    180.00   0.0  0
 Y9Z  Var_01    C8   C9   O3   P    -125.73  30.0  3
 Y9Z  Var_02    O8   P1   O4   P      34.76  30.0  3
 Y9Z  Var_03    O9   P    O4   P1    -72.66  30.0  1
 Y9Z  Var_04    C11  C10  O5   P1    -95.75  30.0  3
 Y9Z  Var_05    O5   C10  C11  N5     68.56  30.0  3
 Y9Z  Var_06    C12  N5   C11  C10  -162.80  30.0  3
 Y9Z  Var_07    H20  C13  C12  N5    -13.17  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
 Y9Z  chir_03  C5  N4   C6  O11  negativ
 Y9Z  chir_04  C6  O1   C7  C5   positiv
 Y9Z  chir_05  C7  O2   C8  C6   positiv
 Y9Z  chir_06  C8  O11  C7  C9   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
 Y9Z  plan-1  N    0.020
 Y9Z  plan-1  C    0.020
 Y9Z  plan-1  O    0.020
 Y9Z  plan-1  C1   0.020
 Y9Z  plan-1  N1   0.020
 Y9Z  plan-1  C2   0.020
 Y9Z  plan-1  N2   0.020
 Y9Z  plan-1  C3   0.020
 Y9Z  plan-1  N3   0.020
 Y9Z  plan-1  C4   0.020
 Y9Z  plan-1  N4   0.020
 Y9Z  plan-1  C5   0.020
 Y9Z  plan-1  H1   0.020
 Y9Z  plan-1  H2   0.020
 Y9Z  plan-1  H3   0.020
 Y9Z  plan-1  H6   0.020
 Y9Z  plan-2  N5   0.020
 Y9Z  plan-2  O6   0.020
 Y9Z  plan-2  C11  0.020
 Y9Z  plan-2  C12  0.020
 Y9Z  plan-2  C13  0.020
 Y9Z  plan-2  H8   0.020

